label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
|---|---|---|---|
1 | public static String httpGet(URL url) throws Exception { URLConnection connection = url.openConnection(); BufferedReader reader = new BufferedReader(new InputStreamReader(connection.getInputStream())); StringBuffer content = new StringBuffer(); String line = null; while ((line = reader.readLine()) != null) { content.append(line); } return content.toString(); } | public static GoogleResponse getElevation(String lat, String lon) throws IOException { String url = "http://maps.google.com/maps/api/elevation/xml?locations="; url = url + String.valueOf(lat); url = url + ","; url = url + String.valueOf(lon); url = url + "&sensor=false"; BufferedReader in = new BufferedReader(new InputStreamReader(new URL(url).openStream())); String line; GoogleResponse googleResponse = new GoogleResponse(); googleResponse.lat = Double.valueOf(lat); googleResponse.lon = Double.valueOf(lon); while ((line = in.readLine()) != null) { line = line.trim(); if (line.startsWith("<status>")) { line = line.replace("<status>", ""); line = line.replace("</status>", ""); googleResponse.status = line; if (!line.toLowerCase().equals("ok")) return googleResponse; } else if (line.startsWith("<elevation>")) { line = line.replace("<elevation>", ""); line = line.replace("</elevation>", ""); googleResponse.elevation = Double.valueOf(line); return googleResponse; } } return googleResponse; } | 13,200 |
0 | public InetSocketAddress getServerAddress() throws IOException { URL url = new URL(ADDRESS_SERVER_URL); HttpURLConnection con = (HttpURLConnection) url.openConnection(); con.setRequestMethod("GET"); con.setDoOutput(true); con.setReadTimeout(2000); con.connect(); BufferedReader rd = new BufferedReader(new InputStreamReader(con.getInputStream())); String line = rd.readLine(); if (line == null) throw new IOException("Cannot read address from address server"); String addr[] = line.split(" ", 2); return new InetSocketAddress(addr[0], Integer.valueOf(addr[1])); } | public void testAddingEntries() throws Exception { DiskCache c = new DiskCache(); { c.setRoot(rootFolder.getAbsolutePath()); c.setHtmlExtension("htm"); c.setPropertiesExtension("txt"); assertEquals("htm", c.getHtmlExtension()); assertEquals("txt", c.getPropertiesExtension()); assertEquals(rootFolder.getAbsolutePath(), c.getRoot()); } String key1 = "cat1/key1"; String key2 = "cat1/key2"; try { try { { c.removeCacheEntry(key1, null); CacheItem i = c.getOrCreateCacheEntry(key1); assertNull(i.getEncoding()); assertEquals(-1L, i.getLastModified()); assertEquals(-1, i.getTranslationCount()); assertFalse(i.isCached()); assertNull(i.getHeaders()); i.setLastModified(300005L); i.setTranslationCount(10); i.setEncoding("ISO-8859-7"); i.setHeader(new ResponseHeaderImpl("Test2", new String[] { "Value3", "Value4" })); i.setHeader(new ResponseHeaderImpl("Test1", new String[] { "Value1", "Value2" })); byte[] greekTextBytes = new byte[] { -57, -20, -27, -15, -34, -13, -23, -31, 32, -48, -17, -21, -23, -12, -23, -22, -34, 32, -59, -10, -25, -20, -27, -15, -33, -28, -31, 32, -60, -23, -31, -19, -35, -20, -27, -12, -31, -23, 32, -22, -31, -24, -25, -20, -27, -15, -23, -19, -36, 32, -60, -39, -47, -59, -63, -51, 32, -13, -12, -17, 32, -28, -33, -22, -12, -11, -17, 32, -13, -11, -29, -22, -17, -23, -19, -7, -19, -23, -2, -19, 32, -12, -25, -14, 32, -56, -27, -13, -13, -31, -21, -17, -19, -33, -22, -25, -14 }; String greekText = new String(greekTextBytes, "ISO-8859-7"); { InputStream input = new ByteArrayInputStream(greekTextBytes); try { i.setContentAsStream(input); } finally { input.close(); } } assertEquals("ISO-8859-7", i.getEncoding()); assertEquals(300005L, i.getLastModified()); assertEquals(10, i.getTranslationCount()); assertFalse(i.isCached()); i.updateAfterAllContentUpdated(null, null); { assertEquals(3, i.getHeaders().size()); int ii = 0; for (ResponseHeader h : i.getHeaders()) { ii++; if (ii == 1) { assertEquals("Content-Length", h.getName()); assertEquals("[97]", Arrays.toString(h.getValues())); } else if (ii == 2) { assertEquals("Test1", h.getName()); assertEquals("[Value1, Value2]", Arrays.toString(h.getValues())); } else if (ii == 3) { assertEquals("Test2", h.getName()); assertEquals("[Value3, Value4]", Arrays.toString(h.getValues())); } } } c.storeInCache(key1, i); assertEquals("ISO-8859-7", i.getEncoding()); assertEquals(300005L, i.getLastModified()); assertEquals(10, i.getTranslationCount()); assertTrue(i.isCached()); { InputStream input = i.getContentAsStream(); StringWriter w = new StringWriter(); IOUtils.copy(input, w, "ISO-8859-7"); IOUtils.closeQuietly(input); IOUtils.closeQuietly(w); assertEquals(greekText, w.toString()); } } { c.removeCacheEntry(key2, null); CacheItem i = c.getOrCreateCacheEntry(key2); assertNull(i.getEncoding()); assertEquals(-1L, i.getLastModified()); assertEquals(-1, i.getTranslationCount()); assertFalse(i.isCached()); assertNull(i.getHeaders()); i.setLastModified(350000L); i.setTranslationCount(11); i.setEncoding("ISO-8859-1"); i.setHeader(new ResponseHeaderImpl("Test3", new String[] { "Value3", "Value4" })); i.setHeader(new ResponseHeaderImpl("Test4", new String[] { "Value1" })); String englishText = "Hello this is another example"; { InputStream input = new ByteArrayInputStream(englishText.getBytes("ISO-8859-1")); try { i.setContentAsStream(input); } finally { input.close(); } } assertEquals("ISO-8859-1", i.getEncoding()); assertEquals(350000L, i.getLastModified()); assertEquals(11, i.getTranslationCount()); assertFalse(i.isCached()); i.updateAfterAllContentUpdated(null, null); { assertEquals(3, i.getHeaders().size()); int ii = 0; for (ResponseHeader h : i.getHeaders()) { ii++; if (ii == 1) { assertEquals("Content-Length", h.getName()); assertEquals("[29]", Arrays.toString(h.getValues())); } else if (ii == 2) { assertEquals("Test3", h.getName()); assertEquals("[Value3, Value4]", Arrays.toString(h.getValues())); } else if (ii == 3) { assertEquals("Test4", h.getName()); assertEquals("[Value1]", Arrays.toString(h.getValues())); } } } c.storeInCache(key2, i); assertEquals("ISO-8859-1", i.getEncoding()); assertEquals(350000L, i.getLastModified()); assertEquals(11, i.getTranslationCount()); assertTrue(i.isCached()); { InputStream input = i.getContentAsStream(); StringWriter w = new StringWriter(); IOUtils.copy(input, w, "ISO-8859-1"); IOUtils.closeQuietly(input); IOUtils.closeQuietly(w); assertEquals(englishText, w.toString()); } } { CacheItem i = c.getOrCreateCacheEntry(key1); assertEquals("ISO-8859-7", i.getEncoding()); assertEquals(300005L, i.getLastModified()); assertEquals(10, i.getTranslationCount()); assertTrue(i.isCached()); { assertEquals(3, i.getHeaders().size()); int ii = 0; for (ResponseHeader h : i.getHeaders()) { ii++; if (ii == 1) { assertEquals("Content-Length", h.getName()); assertEquals("[97]", Arrays.toString(h.getValues())); } else if (ii == 2) { assertEquals("Test1", h.getName()); assertEquals("[Value1, Value2]", Arrays.toString(h.getValues())); } else if (ii == 3) { assertEquals("Test2", h.getName()); assertEquals("[Value3, Value4]", Arrays.toString(h.getValues())); } } } byte[] greekTextBytes = new byte[] { -57, -20, -27, -15, -34, -13, -23, -31, 32, -48, -17, -21, -23, -12, -23, -22, -34, 32, -59, -10, -25, -20, -27, -15, -33, -28, -31, 32, -60, -23, -31, -19, -35, -20, -27, -12, -31, -23, 32, -22, -31, -24, -25, -20, -27, -15, -23, -19, -36, 32, -60, -39, -47, -59, -63, -51, 32, -13, -12, -17, 32, -28, -33, -22, -12, -11, -17, 32, -13, -11, -29, -22, -17, -23, -19, -7, -19, -23, -2, -19, 32, -12, -25, -14, 32, -56, -27, -13, -13, -31, -21, -17, -19, -33, -22, -25, -14 }; String greekText = new String(greekTextBytes, "ISO-8859-7"); { InputStream input = i.getContentAsStream(); StringWriter w = new StringWriter(); IOUtils.copy(input, w, "ISO-8859-7"); IOUtils.closeQuietly(input); IOUtils.closeQuietly(w); assertEquals(greekText, w.toString()); } } { c.removeCacheEntry(key1, null); CacheItem i = c.getOrCreateCacheEntry(key1); assertNull(i.getEncoding()); assertEquals(-1L, i.getLastModified()); assertEquals(-1, i.getTranslationCount()); assertFalse(i.isCached()); assertNull(i.getHeaders()); } } finally { c.removeCacheEntry(key1, null); } } finally { c.removeCacheEntry(key2, null); } } | 13,201 |
1 | public void writeConfigurationFile() throws IOException, ComponentException { SystemConfig config = parent.getParentSystem().getConfiguration(); File original = config.getLocation(); File backup = new File(original.getParentFile(), original.getName() + "." + System.currentTimeMillis()); FileInputStream in = new FileInputStream(original); FileOutputStream out = new FileOutputStream(backup); byte[] buffer = new byte[2048]; try { int bytesread = 0; while ((bytesread = in.read(buffer)) > 0) { out.write(buffer, 0, bytesread); } } catch (IOException e) { logger.warn("Failed to copy backup of configuration file"); throw e; } finally { in.close(); out.close(); } FileWriter replace = new FileWriter(original); replace.write(config.toFileFormat()); replace.close(); logger.info("Re-wrote configuration file " + original.getPath()); } | public Reader transform(Reader reader, Map<String, Object> parameterMap) { try { File file = File.createTempFile("srx2", ".srx"); file.deleteOnExit(); Writer writer = getWriter(getFileOutputStream(file.getAbsolutePath())); transform(reader, writer, parameterMap); writer.close(); Reader resultReader = getReader(getFileInputStream(file.getAbsolutePath())); return resultReader; } catch (IOException e) { throw new IORuntimeException(e); } } | 13,202 |
1 | private void createJarArchive(File archiveFile, List<File> filesToBeJared, File base) throws Exception { FileOutputStream stream = new FileOutputStream(archiveFile); JarOutputStream out = new JarOutputStream(stream); for (File tobeJared : filesToBeJared) { if (tobeJared == null || !tobeJared.exists() || tobeJared.isDirectory()) continue; String entryName = tobeJared.getAbsolutePath().substring(base.getAbsolutePath().length() + 1).replace("\\", "/"); JarEntry jarEntry = new JarEntry(entryName); jarEntry.setTime(tobeJared.lastModified()); out.putNextEntry(jarEntry); FileInputStream in = new FileInputStream(tobeJared); IOUtils.copy(in, out); IOUtils.closeQuietly(in); out.closeEntry(); } out.close(); stream.close(); System.out.println("Generated file: " + archiveFile); } | public static void compressFile(File orig) throws IOException { File file = new File(INPUT + orig.toString()); File target = new File(OUTPUT + orig.toString().replaceAll(".xml", ".xml.gz")); System.out.println(" Compressing \"" + file.getName() + "\" into \"" + target + "\""); long l = file.length(); FileInputStream fileinputstream = new FileInputStream(file); GZIPOutputStream gzipoutputstream = new GZIPOutputStream(new FileOutputStream(target)); byte abyte0[] = new byte[1024]; int i; while ((i = fileinputstream.read(abyte0)) != -1) gzipoutputstream.write(abyte0, 0, i); fileinputstream.close(); gzipoutputstream.close(); long l1 = target.length(); System.out.println(" Initial size: " + l + "; Compressed size: " + l1 + "."); System.out.println(" Done."); System.out.println(); } | 13,203 |
0 | public synchronized void readModels(Project p, URL url) throws IOException { _proj = p; Argo.log.info("======================================="); Argo.log.info("== READING MODEL " + url); try { XMIReader reader = new XMIReader(); InputSource source = new InputSource(url.openStream()); source.setSystemId(url.toString()); _curModel = reader.parse(source); if (reader.getErrors()) { throw new IOException("XMI file " + url.toString() + " could not be parsed."); } _UUIDRefs = new HashMap(reader.getXMIUUIDToObjectMap()); } catch (SAXException saxEx) { Exception ex = saxEx.getException(); if (ex == null) { saxEx.printStackTrace(); } else { ex.printStackTrace(); } } catch (Exception ex) { ex.printStackTrace(); } Argo.log.info("======================================="); try { _proj.addModel((ru.novosoft.uml.foundation.core.MNamespace) _curModel); } catch (PropertyVetoException ex) { System.err.println("An error occurred adding the model to the project!"); ex.printStackTrace(); } Collection ownedElements = _curModel.getOwnedElements(); Iterator oeIterator = ownedElements.iterator(); while (oeIterator.hasNext()) { MModelElement me = (MModelElement) oeIterator.next(); if (me instanceof MClass) { _proj.defineType((MClass) me); } else if (me instanceof MDataType) { _proj.defineType((MDataType) me); } } } | public static void copyWithClose(InputStream is, OutputStream os) throws IOException { try { IOUtils.copy(is, os); } catch (IOException ioe) { try { if (os != null) os.close(); } catch (Exception e) { } try { if (is != null) is.close(); } catch (Exception e) { } } } | 13,204 |
0 | private void checkChartsyRegistration(String username, String password) { HttpPost post = new HttpPost(NbBundle.getMessage(RegisterPanel.class, "RegisterPanel.chartsyRegisterURL")); String message = ""; try { List<NameValuePair> nvps = new ArrayList<NameValuePair>(); nvps.add(new BasicNameValuePair("username", username)); nvps.add(new BasicNameValuePair("password", password)); post.setEntity(new UrlEncodedFormEntity(nvps)); HttpResponse response = ProxyManager.httpClient.execute(post); HttpEntity entity = response.getEntity(); if (entity != null) { String[] lines = EntityUtils.toString(entity).split("\n"); if (lines[0].equals("OK")) { RegisterAction.preferences.putBoolean("registred", true); RegisterAction.preferences.put("name", lines[1]); RegisterAction.preferences.put("email", lines[2]); RegisterAction.preferences.put("date", String.valueOf(Calendar.getInstance().getTimeInMillis())); RegisterAction.preferences.put("username", username); RegisterAction.preferences.put("password", new String(passwordTxt.getPassword())); if (lines[1] != null && !lines[1].isEmpty()) { message = NbBundle.getMessage(RegisterPanel.class, "RegisterPanel.registerDone.withUsername.message", lines[1]); } else { message = NbBundle.getMessage(RegisterPanel.class, "RegisterPanel.registerDone.noUsername.message"); } } else { message = NbBundle.getMessage(RegisterPanel.class, "RegisterPanel.registerAuthError.message"); } EntityUtils.consume(entity); } } catch (Exception ex) { message = NbBundle.getMessage(RegisterPanel.class, "RegisterPanel.registerConnectionError.message"); } finally { post.abort(); } messageLbl.setText(message); messageLbl.setVisible(true); } | private static void copyFile(String srFile, String dtFile) { try { File f1 = new File(srFile); File f2 = new File(dtFile); InputStream in = new FileInputStream(f1); OutputStream out = new FileOutputStream(f2); byte[] buf = new byte[1024]; int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); in.close(); out.close(); } catch (FileNotFoundException ex) { System.out.println("Error copying " + srFile + " to " + dtFile); System.out.println(ex.getMessage() + " in the specified directory."); } catch (IOException e) { System.out.println(e.getMessage()); } } | 13,205 |
0 | private void testURL(String urlStr) throws MalformedURLException, IOException { HttpURLConnection conn = null; try { URL url = new URL(urlStr); conn = (HttpURLConnection) url.openConnection(); int code = conn.getResponseCode(); assertEquals(HttpURLConnection.HTTP_OK, code); } finally { if (conn != null) { conn.disconnect(); } } } | protected BufferedImage handleNLIBException() { if (params.uri.startsWith("http://digar.nlib.ee/otsing/") || params.uri.startsWith("http://digar.nlib.ee/show")) try { String url = "http://digar.nlib.ee/gmap/nd" + params.uri.substring(params.uri.indexOf(":") + 1, params.uri.lastIndexOf("&")) + "-tiles/z0x0y0.jpeg"; URLConnection connection = new URL(url).openConnection(); return processNewUri(connection); } catch (Exception e) { try { if (params.uri.startsWith("http://digar.nlib.ee/show")) params.uri = "http://digar.nlib.ee/otsing/?pid=" + params.uri.substring(params.uri.lastIndexOf("/") + 1) + "&show"; URLConnection connection = new URL(params.uri).openConnection(); String url = params.uri; if (url.endsWith("&show")) url = url.substring(0, url.length() - 5); int index = url.lastIndexOf("?"); url = "stream" + url.substring(index); BufferedReader reader = new BufferedReader(new InputStreamReader(connection.getInputStream())); String aux = null; while ((aux = reader.readLine()) != null) { index = aux.indexOf(url); if (index != -1) { url = "http://digar.nlib.ee/otsing/" + aux.substring(index); index = url.indexOf('>'); if (index == -1) index = url.indexOf("\""); url = url.substring(0, index); break; } } connection = new URL(url).openConnection(); return processNewUri(connection); } catch (Exception e2) { } } return null; } | 13,206 |
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 EncodedScript(PackageScript source, DpkgData data) throws IOException { _source = source; final ByteArrayOutputStream bytes = new ByteArrayOutputStream(); OutputStream output = null; try { output = MimeUtility.encode(bytes, BASE64); } catch (final MessagingException e) { throw new IOException("Failed to uuencode script. name=[" + _source.getFriendlyName() + "], reason=[" + e.getMessage() + "]."); } IOUtils.write(HEADER, bytes, Dpkg.CHAR_ENCODING); bytes.flush(); IOUtils.copy(_source.getSource(data), output); output.flush(); IOUtils.write(FOOTER, bytes, Dpkg.CHAR_ENCODING); bytes.flush(); output.close(); bytes.close(); _encoded = bytes.toString(Dpkg.CHAR_ENCODING); } | 13,207 |
1 | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | private void copyFile(File in, File out) { try { FileChannel sourceChannel = new FileInputStream(in).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); } catch (IOException ex) { ex.printStackTrace(); } } | 13,208 |
0 | public void elimina(Cliente cli) throws errorSQL, errorConexionBD { System.out.println("GestorCliente.elimina()"); int id = cli.getId(); String sql; Statement stmt = null; try { gd.begin(); sql = "DELETE FROM cliente WHERE cod_cliente =" + id; System.out.println("Ejecutando: " + sql); stmt = gd.getConexion().createStatement(); stmt.executeUpdate(sql); System.out.println("executeUpdate"); sql = "DELETE FROM persona WHERE id =" + id; System.out.println("Ejecutando: " + sql); stmt.executeUpdate(sql); gd.commit(); System.out.println("commit"); stmt.close(); } catch (SQLException e) { gd.rollback(); throw new errorSQL(e.toString()); } catch (errorConexionBD e) { System.err.println("Error en GestorCliente.elimina(): " + e); } catch (errorSQL e) { System.err.println("Error en GestorCliente.elimina(): " + e); } } | public static String sendGetRequest(String urlStr) { String result = null; try { URL url = new URL(urlStr); System.out.println(urlStr); URLConnection conn = url.openConnection(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); StringBuffer sb = new StringBuffer(); String line = ""; System.out.println("aa" + line); while ((line = rd.readLine()) != null) { System.out.println("aa" + line); sb.append(line); } rd.close(); result = sb.toString(); } catch (Exception e) { e.printStackTrace(); } return result; } | 13,209 |
1 | public static void main(String args[]) { InputStream input = System.in; OutputStream output = System.out; if (args.length > 0) { try { input = new FileInputStream(args[0]); } catch (FileNotFoundException e) { System.err.println("Unable to open file: " + args[0]); System.exit(-1); } catch (IOException e) { System.err.println("Unable to access file: " + args[0]); System.exit(-1); } } if (args.length > 1) { try { output = new FileOutputStream(args[1]); } catch (FileNotFoundException e) { System.err.println("Unable to open file: " + args[1]); System.exit(-1); } catch (IOException e) { System.err.println("Unable to access file: " + args[1]); System.exit(-1); } } byte buffer[] = new byte[512]; int len; try { while ((len = input.read(buffer)) > 0) output.write(buffer, 0, len); } catch (IOException e) { System.err.println("Error copying file"); } finally { input.close(); output.close(); } } | public static File extract(File source, String filename, File target) { if (source.exists() == false || filename == null || filename.trim().length() < 1 || target == null) return null; boolean isDirectory = (filename.lastIndexOf("/") == filename.length() - 1); try { Map contents = (Map) jarContents.get(source.getPath()); if (contents == null) { contents = new HashMap(); jarContents.put(source.getPath(), contents); ZipInputStream input = new ZipInputStream(new FileInputStream(source)); ZipEntry zipEntry = null; while ((zipEntry = input.getNextEntry()) != null) { if (zipEntry.isDirectory()) continue; contents.put(zipEntry.getName(), zipEntry); } input.close(); } if (isDirectory) { Iterator it = contents.keySet().iterator(); while (it.hasNext()) { String next = (String) it.next(); if (next.startsWith(filename)) { ZipEntry zipEntry = (ZipEntry) contents.get(next); int n = filename.length(); File newTarget = new File(target, zipEntry.getName().substring(n)); extract(source, next, newTarget); } } return target; } ZipEntry entry = (ZipEntry) contents.get(filename); ZipFile input = new ZipFile(source); InputStream in = input.getInputStream(entry); target.getParentFile().mkdirs(); int bytesRead; byte[] buffer = new byte[1024]; FileOutputStream output = new FileOutputStream(target); while ((bytesRead = in.read(buffer)) != -1) output.write(buffer, 0, bytesRead); output.close(); input.close(); return target; } catch (Exception ex) { ex.printStackTrace(); } return null; } | 13,210 |
1 | public static final void copy(String source, String destination) { FileInputStream fis = null; FileOutputStream fos = null; try { fis = new FileInputStream(source); fos = new FileOutputStream(destination); java.nio.channels.FileChannel channelSrc = fis.getChannel(); java.nio.channels.FileChannel channelDest = fos.getChannel(); channelSrc.transferTo(0, channelSrc.size(), channelDest); fis.close(); fos.close(); } catch (FileNotFoundException e2) { e2.printStackTrace(); } catch (IOException e2) { e2.printStackTrace(); } } | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | 13,211 |
1 | public static void copyFile(File in, File out) { int len; byte[] buffer = new byte[1024]; try { FileInputStream fin = new FileInputStream(in); FileOutputStream fout = new FileOutputStream(out); while ((len = fin.read(buffer)) >= 0) fout.write(buffer, 0, len); fin.close(); fout.close(); } catch (IOException ex) { } } | public static void extract(final File destDir, final Collection<ZipEntryInfo> entryInfos) throws IOException { if (destDir == null || CollectionUtils.isEmpty(entryInfos)) throw new IllegalArgumentException("One or parameter is null or empty!"); if (!destDir.exists()) destDir.mkdirs(); for (ZipEntryInfo entryInfo : entryInfos) { ZipEntry entry = entryInfo.getZipEntry(); InputStream in = entryInfo.getInputStream(); File entryDest = new File(destDir, entry.getName()); entryDest.getParentFile().mkdirs(); if (!entry.isDirectory()) { OutputStream out = new FileOutputStream(new File(destDir, entry.getName())); try { IOUtils.copy(in, out); out.flush(); } finally { IOUtils.closeQuietly(in); IOUtils.closeQuietly(out); } } } } | 13,212 |
1 | private final long test(final boolean applyFilter, final int executionCount) throws NoSuchAlgorithmException, NoSuchPaddingException, FileNotFoundException, IOException, RuleLoadingException { final boolean stripHtmlEnabled = true; final boolean injectSecretTokensEnabled = true; final boolean encryptQueryStringsEnabled = true; final boolean protectParamsAndFormsEnabled = true; final boolean applyExtraProtectionForDisabledFormFields = true; final boolean applyExtraProtectionForReadonlyFormFields = false; final boolean applyExtraProtectionForRequestParamValueCount = false; final ContentInjectionHelper helper = new ContentInjectionHelper(); final RuleFileLoader ruleFileLoaderModificationExcludes = new ClasspathZipRuleFileLoader(); ruleFileLoaderModificationExcludes.setPath(RuleParameter.MODIFICATION_EXCLUDES_DEFAULT.getValue()); final ContentModificationExcludeDefinitionContainer containerModExcludes = new ContentModificationExcludeDefinitionContainer(ruleFileLoaderModificationExcludes); containerModExcludes.parseDefinitions(); helper.setContentModificationExcludeDefinitions(containerModExcludes); final AttackHandler attackHandler = new AttackHandler(null, 123, 600000, 100000, 300000, 300000, null, "MOCK", false, false, 0, false, false, Pattern.compile("sjghggfakgfjagfgajgfjasgfs"), Pattern.compile("sjghggfakgfjagfgajgfjasgfs"), true, new AttackMailHandler()); final SessionCreationTracker sessionCreationTracker = new SessionCreationTracker(attackHandler, 0, 600000, 300000, 0, "", "", "", ""); final RequestWrapper request = new RequestWrapper(new RequestMock(), helper, sessionCreationTracker, "123.456.789.000", false, true, true); final RuleFileLoader ruleFileLoaderResponseModifications = new ClasspathZipRuleFileLoader(); ruleFileLoaderResponseModifications.setPath(RuleParameter.RESPONSE_MODIFICATIONS_DEFAULT.getValue()); final ResponseModificationDefinitionContainer container = new ResponseModificationDefinitionContainer(ruleFileLoaderResponseModifications); container.parseDefinitions(); final ResponseModificationDefinition[] responseModificationDefinitions = downCast(container.getAllEnabledRequestDefinitions()); final List<Pattern> tmpPatternsToExcludeCompleteTag = new ArrayList<Pattern>(responseModificationDefinitions.length); final List<Pattern> tmpPatternsToExcludeCompleteScript = new ArrayList<Pattern>(responseModificationDefinitions.length); final List<Pattern> tmpPatternsToExcludeLinksWithinScripts = new ArrayList<Pattern>(responseModificationDefinitions.length); final List<Pattern> tmpPatternsToExcludeLinksWithinTags = new ArrayList<Pattern>(responseModificationDefinitions.length); final List<Pattern> tmpPatternsToCaptureLinksWithinScripts = new ArrayList<Pattern>(responseModificationDefinitions.length); final List<Pattern> tmpPatternsToCaptureLinksWithinTags = new ArrayList<Pattern>(responseModificationDefinitions.length); final List<WordDictionary> tmpPrefiltersToExcludeCompleteTag = new ArrayList<WordDictionary>(responseModificationDefinitions.length); final List<WordDictionary> tmpPrefiltersToExcludeCompleteScript = new ArrayList<WordDictionary>(responseModificationDefinitions.length); final List<WordDictionary> tmpPrefiltersToExcludeLinksWithinScripts = new ArrayList<WordDictionary>(responseModificationDefinitions.length); final List<WordDictionary> tmpPrefiltersToExcludeLinksWithinTags = new ArrayList<WordDictionary>(responseModificationDefinitions.length); final List<WordDictionary> tmpPrefiltersToCaptureLinksWithinScripts = new ArrayList<WordDictionary>(responseModificationDefinitions.length); final List<WordDictionary> tmpPrefiltersToCaptureLinksWithinTags = new ArrayList<WordDictionary>(responseModificationDefinitions.length); final List<Integer[]> tmpGroupNumbersToCaptureLinksWithinScripts = new ArrayList<Integer[]>(responseModificationDefinitions.length); final List<Integer[]> tmpGroupNumbersToCaptureLinksWithinTags = new ArrayList<Integer[]>(responseModificationDefinitions.length); for (int i = 0; i < responseModificationDefinitions.length; i++) { final ResponseModificationDefinition responseModificationDefinition = responseModificationDefinitions[i]; if (responseModificationDefinition.isMatchesScripts()) { tmpPatternsToExcludeCompleteScript.add(responseModificationDefinition.getScriptExclusionPattern()); tmpPrefiltersToExcludeCompleteScript.add(responseModificationDefinition.getScriptExclusionPrefilter()); tmpPatternsToExcludeLinksWithinScripts.add(responseModificationDefinition.getUrlExclusionPattern()); tmpPrefiltersToExcludeLinksWithinScripts.add(responseModificationDefinition.getUrlExclusionPrefilter()); tmpPatternsToCaptureLinksWithinScripts.add(responseModificationDefinition.getUrlCapturingPattern()); tmpPrefiltersToCaptureLinksWithinScripts.add(responseModificationDefinition.getUrlCapturingPrefilter()); tmpGroupNumbersToCaptureLinksWithinScripts.add(ServerUtils.convertSimpleToObjectArray(responseModificationDefinition.getCapturingGroupNumbers())); } if (responseModificationDefinition.isMatchesTags()) { tmpPatternsToExcludeCompleteTag.add(responseModificationDefinition.getTagExclusionPattern()); tmpPrefiltersToExcludeCompleteTag.add(responseModificationDefinition.getTagExclusionPrefilter()); tmpPatternsToExcludeLinksWithinTags.add(responseModificationDefinition.getUrlExclusionPattern()); tmpPrefiltersToExcludeLinksWithinTags.add(responseModificationDefinition.getUrlExclusionPrefilter()); tmpPatternsToCaptureLinksWithinTags.add(responseModificationDefinition.getUrlCapturingPattern()); tmpPrefiltersToCaptureLinksWithinTags.add(responseModificationDefinition.getUrlCapturingPrefilter()); tmpGroupNumbersToCaptureLinksWithinTags.add(ServerUtils.convertSimpleToObjectArray(responseModificationDefinition.getCapturingGroupNumbers())); } } final Matcher[] matchersToExcludeCompleteTag = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToExcludeCompleteTag); final Matcher[] matchersToExcludeCompleteScript = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToExcludeCompleteScript); final Matcher[] matchersToExcludeLinksWithinScripts = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToExcludeLinksWithinScripts); final Matcher[] matchersToExcludeLinksWithinTags = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToExcludeLinksWithinTags); final Matcher[] matchersToCaptureLinksWithinScripts = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToCaptureLinksWithinScripts); final Matcher[] matchersToCaptureLinksWithinTags = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToCaptureLinksWithinTags); final WordDictionary[] prefiltersToExcludeCompleteTag = (WordDictionary[]) tmpPrefiltersToExcludeCompleteTag.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToExcludeCompleteScript = (WordDictionary[]) tmpPrefiltersToExcludeCompleteScript.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToExcludeLinksWithinScripts = (WordDictionary[]) tmpPrefiltersToExcludeLinksWithinScripts.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToExcludeLinksWithinTags = (WordDictionary[]) tmpPrefiltersToExcludeLinksWithinTags.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToCaptureLinksWithinScripts = (WordDictionary[]) tmpPrefiltersToCaptureLinksWithinScripts.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToCaptureLinksWithinTags = (WordDictionary[]) tmpPrefiltersToCaptureLinksWithinTags.toArray(new WordDictionary[0]); final int[][] groupNumbersToCaptureLinksWithinScripts = ServerUtils.convertArrayIntegerListTo2DimIntArray(tmpGroupNumbersToCaptureLinksWithinScripts); final int[][] groupNumbersToCaptureLinksWithinTags = ServerUtils.convertArrayIntegerListTo2DimIntArray(tmpGroupNumbersToCaptureLinksWithinTags); final Cipher cipher = CryptoUtils.getCipher(); final CryptoKeyAndSalt key = CryptoUtils.generateRandomCryptoKeyAndSalt(false); Cipher.getInstance("AES"); MessageDigest.getInstance("SHA-1"); final ResponseWrapper response = new ResponseWrapper(new ResponseMock(), request, attackHandler, helper, false, "___ENCRYPTED___", cipher, key, "___SEC-KEY___", "___SEC-VALUE___", "___PROT-KEY___", false, false, false, false, "123.456.789.000", new HashSet(), prefiltersToExcludeCompleteScript, matchersToExcludeCompleteScript, prefiltersToExcludeCompleteTag, matchersToExcludeCompleteTag, prefiltersToExcludeLinksWithinScripts, matchersToExcludeLinksWithinScripts, prefiltersToExcludeLinksWithinTags, matchersToExcludeLinksWithinTags, prefiltersToCaptureLinksWithinScripts, matchersToCaptureLinksWithinScripts, prefiltersToCaptureLinksWithinTags, matchersToCaptureLinksWithinTags, groupNumbersToCaptureLinksWithinScripts, groupNumbersToCaptureLinksWithinTags, true, false, true, true, true, true, true, true, true, true, true, false, false, true, "", "", (short) 3, true, false, false); final List durations = new ArrayList(); for (int i = 0; i < executionCount; i++) { final long start = System.currentTimeMillis(); Reader reader = null; Writer writer = null; try { reader = new BufferedReader(new FileReader(this.htmlFile)); writer = new FileWriter(this.outputFile); if (applyFilter) { writer = new ResponseFilterWriter(writer, true, "http://127.0.0.1/test/sample", "/test", "/test", "___SEC-KEY___", "___SEC-VALUE___", "___PROT-KEY___", cipher, key, helper, "___ENCRYPTED___", request, response, stripHtmlEnabled, injectSecretTokensEnabled, protectParamsAndFormsEnabled, encryptQueryStringsEnabled, applyExtraProtectionForDisabledFormFields, applyExtraProtectionForReadonlyFormFields, applyExtraProtectionForRequestParamValueCount, prefiltersToExcludeCompleteScript, matchersToExcludeCompleteScript, prefiltersToExcludeCompleteTag, matchersToExcludeCompleteTag, prefiltersToExcludeLinksWithinScripts, matchersToExcludeLinksWithinScripts, prefiltersToExcludeLinksWithinTags, matchersToExcludeLinksWithinTags, prefiltersToCaptureLinksWithinScripts, matchersToCaptureLinksWithinScripts, prefiltersToCaptureLinksWithinTags, matchersToCaptureLinksWithinTags, groupNumbersToCaptureLinksWithinScripts, groupNumbersToCaptureLinksWithinTags, true, true, false, true, true, true, true, true, true, true, true, false, false, true, "", "", (short) 3, true, false); writer = new BufferedWriter(writer); } char[] chars = new char[16 * 1024]; int read; while ((read = reader.read(chars)) != -1) { if (read > 0) { writer.write(chars, 0, read); } } durations.add(new Long(System.currentTimeMillis() - start)); } finally { if (reader != null) { try { reader.close(); } catch (IOException ignored) { } } if (writer != null) { try { writer.close(); } catch (IOException ignored) { } } } } long sum = 0; for (final Iterator iter = durations.iterator(); iter.hasNext(); ) { Long value = (Long) iter.next(); sum += value.longValue(); } return sum / durations.size(); } | private void writeToFile(Body b, File mime4jFile) throws FileNotFoundException, IOException { if (b instanceof TextBody) { String charset = CharsetUtil.toJavaCharset(b.getParent().getCharset()); if (charset == null) { charset = "ISO8859-1"; } OutputStream out = new FileOutputStream(mime4jFile); IOUtils.copy(((TextBody) b).getReader(), out, charset); } else { OutputStream out = new FileOutputStream(mime4jFile); IOUtils.copy(((BinaryBody) b).getInputStream(), out); } } | 13,213 |
0 | public synchronized List<AnidbSearchResult> getAnimeTitles() throws Exception { URL url = new URL("http", host, "/api/animetitles.dat.gz"); ResultCache cache = getCache(); @SuppressWarnings("unchecked") List<AnidbSearchResult> anime = (List) cache.getSearchResult(null, Locale.ROOT); if (anime != null) { return anime; } Pattern pattern = Pattern.compile("^(?!#)(\\d+)[|](\\d)[|]([\\w-]+)[|](.+)$"); Map<Integer, String> primaryTitleMap = new HashMap<Integer, String>(); Map<Integer, Map<String, String>> officialTitleMap = new HashMap<Integer, Map<String, String>>(); Map<Integer, Map<String, String>> synonymsTitleMap = new HashMap<Integer, Map<String, String>>(); Scanner scanner = new Scanner(new GZIPInputStream(url.openStream()), "UTF-8"); try { while (scanner.hasNextLine()) { Matcher matcher = pattern.matcher(scanner.nextLine()); if (matcher.matches()) { int aid = Integer.parseInt(matcher.group(1)); String type = matcher.group(2); String language = matcher.group(3); String title = matcher.group(4); if (type.equals("1")) { primaryTitleMap.put(aid, title); } else if (type.equals("2") || type.equals("4")) { Map<Integer, Map<String, String>> titleMap = (type.equals("4") ? officialTitleMap : synonymsTitleMap); Map<String, String> languageTitleMap = titleMap.get(aid); if (languageTitleMap == null) { languageTitleMap = new HashMap<String, String>(); titleMap.put(aid, languageTitleMap); } languageTitleMap.put(language, title); } } } } finally { scanner.close(); } anime = new ArrayList<AnidbSearchResult>(primaryTitleMap.size()); for (Entry<Integer, String> entry : primaryTitleMap.entrySet()) { Map<String, String> localizedTitles = new HashMap<String, String>(); if (synonymsTitleMap.containsKey(entry.getKey())) { localizedTitles.putAll(synonymsTitleMap.get(entry.getKey())); } if (officialTitleMap.containsKey(entry.getKey())) { localizedTitles.putAll(officialTitleMap.get(entry.getKey())); } anime.add(new AnidbSearchResult(entry.getKey(), entry.getValue(), localizedTitles)); } return cache.putSearchResult(null, Locale.ROOT, anime); } | public static synchronized String getPageContent(String pageUrl) { URL url = null; InputStreamReader inputStreamReader = null; BufferedReader bufferedReader = null; String line = null; StringBuilder page = null; if (pageUrl == null || pageUrl.trim().length() == 0) { return null; } else { try { url = new URL(pageUrl); inputStreamReader = new InputStreamReader(url.openStream()); bufferedReader = new BufferedReader(inputStreamReader); page = new StringBuilder(); while ((line = bufferedReader.readLine()) != null) { page.append(line); page.append("\n"); } } catch (IOException e) { logger.error("IOException", e); } catch (Exception e) { logger.error("Exception", e); } finally { try { if (bufferedReader != null) { bufferedReader.close(); } if (inputStreamReader != null) { inputStreamReader.close(); } } catch (IOException e) { logger.error("IOException", e); } catch (Exception e) { logger.error("Exception", e); } } } if (page == null) { return null; } else { return page.toString(); } } | 13,214 |
1 | public static void copyFile(File src, File dst) throws ResourceNotFoundException, ParseErrorException, Exception { if (src.getAbsolutePath().endsWith(".vm")) { copyVMFile(src, dst.getAbsolutePath().substring(0, dst.getAbsolutePath().lastIndexOf(".vm"))); } else { FileInputStream fIn; FileOutputStream fOut; FileChannel fIChan, fOChan; long fSize; MappedByteBuffer mBuf; fIn = new FileInputStream(src); fOut = new FileOutputStream(dst); fIChan = fIn.getChannel(); fOChan = fOut.getChannel(); fSize = fIChan.size(); mBuf = fIChan.map(FileChannel.MapMode.READ_ONLY, 0, fSize); fOChan.write(mBuf); fIChan.close(); fIn.close(); fOChan.close(); fOut.close(); } } | 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!"); } | 13,215 |
0 | public String uploadReport(Collection c) { try { String id = generateRandomId(); Iterator iter = c.iterator(); URL url = new URL(ZorobotSystem.props.getProperty("zoro.url") + "auplo2.jsp"); URLConnection connection = url.openConnection(); connection.setDoOutput(true); PrintWriter out = new PrintWriter(connection.getOutputStream()); out.print("id=" + id + "&"); StringBuffer sb = new StringBuffer(); int gg = 0; while (iter.hasNext()) { if (gg++ >= 500) break; Question tq = (Question) iter.next(); sb.append("a="); sb.append(URLEncoder.encode(tq.question, "UTF-8")); sb.append("*"); StringBuffer ss = new StringBuffer(); String[] ans; if (tq.ansDisplay != null) { ans = tq.ansDisplay; } else { ans = tq.answer; } for (int j = 0; j < ans.length; j++) { if (j > 0) ss.append("*"); ss.append(ans[j]); } sb.append(URLEncoder.encode(ss.toString(), "UTF-8")); if (iter.hasNext() && gg < 500) sb.append("&"); } out.println(sb.toString()); out.close(); BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream())); String inputLine; if ((inputLine = in.readLine()) != null) { if (!inputLine.equals("OK!") && inputLine.length() > 3) { System.out.println("Not OK: " + inputLine); return "xxxxxxxxxx"; } } in.close(); return id; } catch (Exception e) { e.printStackTrace(); } return null; } | private String createHash() { String hash = ""; try { final java.util.Calendar c = java.util.Calendar.getInstance(); String day = "" + c.get(java.util.Calendar.DATE); day = (day.length() == 1) ? '0' + day : day; String month = "" + (c.get(java.util.Calendar.MONTH) + 1); month = (month.length() == 1) ? '0' + month : month; final String hashString = getStringProperty("hashkey") + day + "." + month + "." + c.get(java.util.Calendar.YEAR); final MessageDigest md = MessageDigest.getInstance("MD5"); md.update(hashString.getBytes()); final byte digest[] = md.digest(); hash = ""; for (int i = 0; i < digest.length; i++) { final String s = Integer.toHexString(digest[i] & 0xFF); hash += ((s.length() == 1) ? "0" + s : s); } } catch (final NoSuchAlgorithmException e) { bot.getLogger().log(e); } return hash; } | 13,216 |
1 | public void testMemberSeek() throws IOException { GZIPMembersInputStream gzin = new GZIPMembersInputStream(new ByteArrayInputStream(allfour_gz)); gzin.setEofEachMember(true); gzin.compressedSeek(noise1k_gz.length + noise32k_gz.length); int count2 = IOUtils.copy(gzin, new NullOutputStream()); assertEquals("wrong 1-byte member count", 1, count2); assertEquals("wrong Member2 start", noise1k_gz.length + noise32k_gz.length, gzin.getCurrentMemberStart()); assertEquals("wrong Member2 end", noise1k_gz.length + noise32k_gz.length + a_gz.length, gzin.getCurrentMemberEnd()); gzin.nextMember(); int count3 = IOUtils.copy(gzin, new NullOutputStream()); assertEquals("wrong 5-byte member count", 5, count3); assertEquals("wrong Member3 start", noise1k_gz.length + noise32k_gz.length + a_gz.length, gzin.getCurrentMemberStart()); assertEquals("wrong Member3 end", noise1k_gz.length + noise32k_gz.length + a_gz.length + hello_gz.length, gzin.getCurrentMemberEnd()); gzin.nextMember(); int countEnd = IOUtils.copy(gzin, new NullOutputStream()); assertEquals("wrong eof count", 0, countEnd); } | public ActualTask(TEditor editor, TIGDataBase dataBase, String directoryPath) { File myDirectory = new File(directoryPath); int i; Vector images = new Vector(); images = dataBase.allImageSearch(); lengthOfTask = images.size() * 2; String directory = directoryPath + "Images" + myDirectory.separator; File newDirectoryFolder = new File(directory); newDirectoryFolder.mkdirs(); try { DocumentBuilderFactory domFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder domBuilder = domFactory.newDocumentBuilder(); doc = domBuilder.newDocument(); } catch (Exception exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } Element dbElement = doc.createElement("dataBase"); for (i = 0; ((i < images.size()) && !stop); i++) { current = i; String element = (String) images.elementAt(i); String pathSrc = "Images" + File.separator + element.substring(0, 1).toUpperCase() + File.separator + element; String name = pathSrc.substring(pathSrc.lastIndexOf(myDirectory.separator) + 1, pathSrc.length()); String pathDst = directory + name; try { FileChannel srcChannel = new FileInputStream(pathSrc).getChannel(); FileChannel dstChannel = new FileOutputStream(pathDst).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } Vector keyWords = new Vector(); keyWords = dataBase.asociatedConceptSearch((String) images.elementAt(i)); Element imageElement = doc.createElement("image"); Element imageNameElement = doc.createElement("name"); imageNameElement.appendChild(doc.createTextNode(name)); imageElement.appendChild(imageNameElement); for (int j = 0; j < keyWords.size(); j++) { Element keyWordElement = doc.createElement("keyWord"); keyWordElement.appendChild(doc.createTextNode((String) keyWords.elementAt(j))); imageElement.appendChild(keyWordElement); } dbElement.appendChild(imageElement); } try { doc.appendChild(dbElement); File dst = new File(directory.concat("Images")); BufferedWriter bufferWriter = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(dst), "UTF-8")); TransformerFactory transformerFactory = TransformerFactory.newInstance(); Transformer transformer = transformerFactory.newTransformer(); DOMSource source = new DOMSource(doc); StreamResult result = new StreamResult(bufferWriter); transformer.transform(source, result); bufferWriter.close(); } catch (Exception exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } current = lengthOfTask; } | 13,217 |
0 | private void storeFieldMap(Content c, Connection conn) throws SQLException { SQLDialect dialect = getDatabase().getSQLDialect(); if (TRANSACTIONS_ENABLED) { conn.setAutoCommit(false); } try { Object thisKey = c.getPrimaryKey(); deleteFieldContent(thisKey, conn); PreparedStatement ps = null; StructureItem nextItem; Map fieldMap = c.getFieldMap(); String type; Object value, siKey; for (Iterator i = c.getStructure().getStructureItems().iterator(); i.hasNext(); ) { nextItem = (StructureItem) i.next(); type = nextItem.getDataType().toUpperCase(); siKey = nextItem.getPrimaryKey(); value = fieldMap.get(nextItem.getName()); if (type.equals(StructureItem.DATE)) { ps = conn.prepareStatement(sqlConstants.get("INSERT_DATE_FIELD")); ps.setObject(1, thisKey); ps.setObject(2, siKey); dialect.setDate(ps, 3, (java.util.Date) value); ps.executeUpdate(); } else if (type.equals(StructureItem.INT) || type.equals(StructureItem.FLOAT) || type.equals(StructureItem.VARCHAR)) { ps = conn.prepareStatement(sqlConstants.get("INSERT_" + type + "_FIELD")); ps.setObject(1, thisKey); ps.setObject(2, siKey); if (value != null) { ps.setObject(3, value); } else { int sqlType = Types.INTEGER; if (type.equals(StructureItem.FLOAT)) { sqlType = Types.FLOAT; } else if (type.equals(StructureItem.VARCHAR)) { sqlType = Types.VARCHAR; } ps.setNull(3, sqlType); } ps.executeUpdate(); } else if (type.equals(StructureItem.TEXT)) { setTextField(c, siKey, (String) value, conn); } if (ps != null) { ps.close(); ps = null; } } if (TRANSACTIONS_ENABLED) { conn.commit(); } } catch (SQLException e) { if (TRANSACTIONS_ENABLED) { conn.rollback(); } throw e; } finally { if (TRANSACTIONS_ENABLED) { conn.setAutoCommit(true); } } } | public static byte[] downloadHttpFile(String url) throws IOException { HttpURLConnection conn = (HttpURLConnection) new URL(url).openConnection(); int responseCode = conn.getResponseCode(); if (responseCode != HttpURLConnection.HTTP_OK) throw new IOException("Invalid HTTP response: " + responseCode + " for url " + conn.getURL()); InputStream in = conn.getInputStream(); try { return Utilities.getInputBytes(in); } finally { in.close(); } } | 13,218 |
0 | public static void copy(String from_name, String to_name) throws IOException { File from_file = new File(from_name); File to_file = new File(to_name); if (!from_file.exists()) abort("FileCopy: no such source file: " + from_name); if (!from_file.isFile()) abort("FileCopy: can't copy directory: " + from_name); if (!from_file.canRead()) abort("FileCopy: source file is unreadable: " + from_name); if (to_file.isDirectory()) to_file = new File(to_file, from_file.getName()); if (to_file.exists()) { if (!to_file.canWrite()) abort("FileCopy: destination file is unwriteable: " + to_name); System.out.print("Overwrite existing file " + to_name + "? (Y/N): "); System.out.flush(); BufferedReader in = new BufferedReader(new InputStreamReader(System.in)); String response = in.readLine(); if (!response.equals("Y") && !response.equals("y")) abort("FileCopy: existing file was not overwritten."); } else { String parent = to_file.getParent(); if (parent == null) parent = System.getProperty("user.dir"); File dir = new File(parent); if (!dir.exists()) abort("FileCopy: destination directory doesn't exist: " + parent); if (dir.isFile()) abort("FileCopy: destination is not a directory: " + parent); if (!dir.canWrite()) abort("FileCopy: destination directory is unwriteable: " + parent); } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(from_file); to = new FileOutputStream(to_file); byte[] buffer = new byte[4096]; int bytes_read; while ((bytes_read = from.read(buffer)) != -1) to.write(buffer, 0, bytes_read); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } | public static void test(String args[]) { int trace; int bytes_read = 0; int last_contentLenght = 0; try { BufferedReader reader; URL url; url = new URL(args[0]); URLConnection istream = url.openConnection(); last_contentLenght = istream.getContentLength(); reader = new BufferedReader(new InputStreamReader(istream.getInputStream())); System.out.println(url.toString()); String line; trace = t2pNewTrace(); while ((line = reader.readLine()) != null) { bytes_read = bytes_read + line.length() + 1; t2pProcessLine(trace, line); } t2pHandleEventPairs(trace); t2pSort(trace, 0); t2pExportTrace(trace, new String("pngtest2.png"), 1000, 700, (float) 0, (float) 33); t2pExportTrace(trace, new String("pngtest3.png"), 1000, 700, (float) 2.3, (float) 2.44); System.out.println("Press any key to contiune read from stream !!!"); System.out.println(t2pGetProcessName(trace, 0)); System.in.read(); istream = url.openConnection(); if (last_contentLenght != istream.getContentLength()) { istream = url.openConnection(); istream.setRequestProperty("Range", "bytes=" + Integer.toString(bytes_read) + "-"); System.out.println(Integer.toString(istream.getContentLength())); reader = new BufferedReader(new InputStreamReader(istream.getInputStream())); while ((line = reader.readLine()) != null) { System.out.println(line); t2pProcessLine(trace, line); } } else System.out.println("File not changed !"); t2pDeleteTrace(trace); } catch (MalformedURLException e) { System.out.println("MalformedURLException !!!"); } catch (IOException e) { System.out.println("File not found " + args[0]); } ; } | 13,219 |
1 | public static byte[] ComputeForBinary(String ThisString) throws Exception { byte[] Result; MessageDigest MD5Hasher; MD5Hasher = MessageDigest.getInstance("MD5"); MD5Hasher.update(ThisString.getBytes("iso-8859-1")); Result = MD5Hasher.digest(); return Result; } | private static MyCookieData parseCookie(Cookie cookie) throws CookieException { String value = cookie.getValue(); System.out.println("original cookie: " + value); value = value.replace("%3A", ":"); value = value.replace("%40", "@"); System.out.println("cookie after replacement: " + value); String[] parts = value.split(":"); if (parts.length < 4) throw new CookieException("only " + parts.length + " parts in the cookie! " + value); String email = parts[0]; String nickname = parts[1]; boolean admin = Boolean.getBoolean(parts[2].toLowerCase()); String hsh = parts[3]; boolean valid_cookie = true; String cookie_secret = System.getProperty("COOKIE_SECRET"); if (cookie_secret == "") throw new CookieException("cookie secret is not set"); if (email.equals("")) { System.out.println("email is empty!"); nickname = ""; admin = false; } else { try { MessageDigest sha = MessageDigest.getInstance("SHA"); sha.update((email + nickname + admin + cookie_secret).getBytes()); StringBuilder builder = new StringBuilder(); for (byte b : sha.digest()) { byte tmphigh = (byte) (b >> 4); tmphigh = (byte) (tmphigh & 0xf); builder.append(hextab.charAt(tmphigh)); byte tmplow = (byte) (b & 0xf); builder.append(hextab.charAt(tmplow)); } System.out.println(); String vhsh = builder.toString(); if (!vhsh.equals(hsh)) { System.out.println("hash not same!"); System.out.println("hash passed in: " + hsh); System.out.println("hash generated: " + vhsh); valid_cookie = false; } else System.out.println("cookie match!"); } catch (NoSuchAlgorithmException ex) { } } return new MyCookieData(email, admin, nickname, valid_cookie); } | 13,220 |
1 | static void createCompleteXML(File file) { FileInputStream fis = null; FileOutputStream fos = null; try { fis = new FileInputStream(errorFile); fos = new FileOutputStream(file); byte[] data = new byte[Integer.parseInt(BlueXStatics.prop.getProperty("allocationUnit"))]; int offset; while ((offset = fis.read(data)) != -1) fos.write(data, 0, offset); } catch (Exception e) { e.printStackTrace(); } finally { try { fis.close(); } catch (Exception e) { } try { fos.close(); } catch (Exception e) { } } FileWriter fw = null; try { fw = new FileWriter(file, true); fw.append("</detail>"); fw.append("\n</exception>"); fw.append("\n</log>"); } catch (Exception e) { e.printStackTrace(); } finally { try { fw.close(); } catch (Exception e) { } } } | private void unzipResource(final String resourceName, final File targetDirectory) throws IOException { final URL resource = this.getClass().getResource(resourceName); assertNotNull("Expected '" + resourceName + "' not found.", resource); assertTrue(targetDirectory.isAbsolute()); FileUtils.deleteDirectory(targetDirectory); assertTrue(targetDirectory.mkdirs()); ZipInputStream in = null; boolean suppressExceptionOnClose = true; try { in = new ZipInputStream(resource.openStream()); ZipEntry e; while ((e = in.getNextEntry()) != null) { if (e.isDirectory()) { continue; } final File dest = new File(targetDirectory, e.getName()); assertTrue(dest.isAbsolute()); OutputStream out = null; try { out = FileUtils.openOutputStream(dest); IOUtils.copy(in, out); suppressExceptionOnClose = false; } finally { try { if (out != null) { out.close(); } suppressExceptionOnClose = true; } catch (final IOException ex) { if (!suppressExceptionOnClose) { throw ex; } } } in.closeEntry(); } suppressExceptionOnClose = false; } finally { try { if (in != null) { in.close(); } } catch (final IOException e) { if (!suppressExceptionOnClose) { throw e; } } } } | 13,221 |
0 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public void actionPerformed(ActionEvent e) { Object src = e.getSource(); if (src == submitButton) { SubmissionProfile profile = (SubmissionProfile) destinationCombo.getSelectedItem(); String uri = profile.endpoint; String authPoint = profile.authenticationPoint; String user = userIDField.getText(); String passwd = new String(passwordField.getPassword()); try { URL url = new URL(authPoint + "?username=" + user + "&password=" + passwd); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line = ""; String text = ""; while ((line = reader.readLine()) != null) { text = text + line; } reader.close(); submit(uri, user); JOptionPane.showMessageDialog(null, "Submission accepted", "Success", JOptionPane.INFORMATION_MESSAGE); this.setVisible(false); this.dispose(); } catch (Exception ex) { ex.printStackTrace(); if (ex instanceof java.io.IOException) { String msg = ex.getMessage(); if (msg.indexOf("HTTP response code: 401") != -1) JOptionPane.showMessageDialog(null, "Invalid Username/Password", "Invalid Username/Password", JOptionPane.ERROR_MESSAGE); else if (msg.indexOf("HTTP response code: 404") != -1) { try { submit(uri, user); JOptionPane.showMessageDialog(null, "Submission accepted", "Success", JOptionPane.INFORMATION_MESSAGE); } catch (Exception exc) { exc.printStackTrace(); } } } } } else if (src == cancelButton) { this.setVisible(false); this.dispose(); } } | 13,222 |
1 | public void run() { GZIPInputStream gzipInputStream = null; try { gzipInputStream = new GZIPInputStream(pipedInputStream); IOUtils.copy(gzipInputStream, outputStream); } catch (Throwable t) { ungzipThreadThrowableList.add(t); } finally { IOUtils.closeQuietly(gzipInputStream); IOUtils.closeQuietly(pipedInputStream); } } | private void update() { if (VERSION.contains("dev")) return; System.out.println(updateURL_s); try { URL updateURL = new URL(updateURL_s); InputStream uis = updateURL.openStream(); InputStreamReader uisr = new InputStreamReader(uis); BufferedReader ubr = new BufferedReader(uisr); String header = ubr.readLine(); if (header.equals("GENREMANUPDATEPAGE")) { String cver = ubr.readLine(); String cdl = ubr.readLine(); if (!cver.equals(VERSION)) { System.out.println("Update available!"); int i = JOptionPane.showConfirmDialog(this, Language.get("UPDATE_AVAILABLE_MSG").replaceAll("%o", VERSION).replaceAll("%c", cver), Language.get("UPDATE_AVAILABLE_TITLE"), JOptionPane.YES_NO_OPTION); if (i == 0) { URL url = new URL(cdl); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.connect(); if (connection.getResponseCode() / 100 != 2) { throw new Exception("Server error! Response code: " + connection.getResponseCode()); } int contentLength = connection.getContentLength(); if (contentLength < 1) { throw new Exception("Invalid content length!"); } int size = contentLength; File tempfile = File.createTempFile("genreman_update", ".zip"); tempfile.deleteOnExit(); RandomAccessFile file = new RandomAccessFile(tempfile, "rw"); InputStream stream = connection.getInputStream(); int downloaded = 0; ProgressWindow pwin = new ProgressWindow(this, "Downloading"); pwin.setVisible(true); pwin.setProgress(0); pwin.setText("Connecting..."); while (downloaded < size) { byte buffer[]; if (size - downloaded > 1024) { buffer = new byte[1024]; } else { buffer = new byte[size - downloaded]; } int read = stream.read(buffer); if (read == -1) break; file.write(buffer, 0, read); downloaded += read; pwin.setProgress(downloaded / size); } file.close(); System.out.println("Downloaded file to " + tempfile.getAbsolutePath()); pwin.setVisible(false); pwin.dispose(); pwin = null; ZipInputStream zin = new ZipInputStream(new FileInputStream(tempfile)); ZipEntry entry; while ((entry = zin.getNextEntry()) != null) { File outf = new File(entry.getName()); System.out.println(outf.getAbsoluteFile()); if (outf.exists()) outf.delete(); OutputStream out = new FileOutputStream(outf); byte[] buf = new byte[1024]; int len; while ((len = zin.read(buf)) > 0) { out.write(buf, 0, len); } out.close(); } JOptionPane.showMessageDialog(this, Language.get("UPDATE_SUCCESS_MSG"), Language.get("UPDATE_SUCCESS_TITLE"), JOptionPane.INFORMATION_MESSAGE); setVisible(false); if (System.getProperty("os.name").indexOf("Windows") != -1) { Runtime.getRuntime().exec("iTunesGenreArtManager.exe"); } else { Runtime.getRuntime().exec("java -jar \"iTunes Genre Art Manager.app/Contents/Resources/Java/iTunes_Genre_Art_Manager.jar\""); } System.exit(0); } else { } } ubr.close(); uisr.close(); uis.close(); } else { while (ubr.ready()) { System.out.println(ubr.readLine()); } ubr.close(); uisr.close(); uis.close(); throw new Exception("Update page had invalid header: " + header); } } catch (Exception ex) { JOptionPane.showMessageDialog(this, Language.get("UPDATE_ERROR_MSG"), Language.get("UPDATE_ERROR_TITLE"), JOptionPane.ERROR_MESSAGE); ex.printStackTrace(); } } | 13,223 |
0 | protected void downloadFile(String filename, java.io.File targetFile, File partFile, ProgressMonitor monitor) throws java.io.IOException { FileOutputStream out = null; InputStream is = null; try { filename = toCanonicalFilename(filename); URL url = new URL(root + filename.substring(1)); URLConnection urlc = url.openConnection(); int i = urlc.getContentLength(); monitor.setTaskSize(i); out = new FileOutputStream(partFile); is = urlc.getInputStream(); monitor.started(); copyStream(is, out, monitor); monitor.finished(); out.close(); is.close(); if (!partFile.renameTo(targetFile)) { throw new IllegalArgumentException("unable to rename " + partFile + " to " + targetFile); } } catch (IOException e) { if (out != null) out.close(); if (is != null) is.close(); if (partFile.exists() && !partFile.delete()) { throw new IllegalArgumentException("unable to delete " + partFile); } throw e; } } | @Override public void excluir(Disciplina t) throws Exception { PreparedStatement stmt = null; String sql = "DELETE from disciplina where id_disciplina = ?"; try { stmt = conexao.prepareStatement(sql); stmt.setInt(1, t.getIdDisciplina()); stmt.executeUpdate(); conexao.commit(); } catch (SQLException e) { conexao.rollback(); throw e; } finally { try { stmt.close(); conexao.close(); } catch (SQLException e) { throw e; } } } | 13,224 |
0 | public static void redirect(String strRequest, PrintWriter sortie) throws Exception { String level = "info."; if (ConnectorServlet.debug) level = "debug."; Log log = LogFactory.getLog(level + "fr.brgm.exows.gml2gsml.GFI"); URL url2Request = new URL(strRequest); URLConnection conn = url2Request.openConnection(); DataInputStream buffin = new DataInputStream(new BufferedInputStream(conn.getInputStream())); String strLine = null; while ((strLine = buffin.readLine()) != null) { sortie.println(strLine); } buffin.close(); } | public static TerminatedInputStream find(URL url, String entryName) throws IOException { if (url.getProtocol().equals("file")) { return find(new File(url.getFile()), entryName); } else { return find(url.openStream(), entryName); } } | 13,225 |
0 | public static final void main(String[] args) throws FileNotFoundException, IOException { ArrayList<String[]> result = new ArrayList<String[]>(); IStream is = new StreamImpl(); IOUtils.copy(new FileInputStream("H:\\7-项目预算表.xlsx"), is.getOutputStream()); int count = loadExcel(result, is, 0, 0, -1, 16, 1); System.out.println(count); for (String[] rs : result) { for (String r : rs) { System.out.print(r + "\t"); } System.out.println(); } } | public static void main(String[] args) { if (args.length != 2) { printUsage(); } String url = args[0]; String path = args[1]; BufferedReader pbsFileReader = null; try { pbsFileReader = new BufferedReader(new FileReader(path)); } catch (FileNotFoundException ex) { System.err.println("Pbs file " + path + " not found"); System.exit(1); } String line = ""; HttpURLConnection conn = null; BufferedWriter out = null; BufferedReader in = null; try { conn = (HttpURLConnection) new URL(url).openConnection(); conn.setDoOutput(true); out = new BufferedWriter(new OutputStreamWriter(conn.getOutputStream())); while (true) { line = pbsFileReader.readLine(); if (line == null) { break; } out.write(line); out.newLine(); System.err.println(line); } in = new BufferedReader(new InputStreamReader(conn.getInputStream())); line = ""; while (true) { line = in.readLine(); if (line == null) { break; } System.out.println(line); } out.close(); in.close(); } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } | 13,226 |
0 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public static void testMapSource(MapSource mapSource, EastNorthCoordinate coordinate) throws Exception { int zoom = mapSource.getMaxZoom(); MapSpace mapSpace = mapSource.getMapSpace(); int tilex = mapSpace.cLonToX(coordinate.lon, zoom) / mapSpace.getTileSize(); int tiley = mapSpace.cLatToY(coordinate.lat, zoom) / mapSpace.getTileSize(); URL url = new URL(mapSource.getTileUrl(zoom, tilex, tiley)); HttpURLConnection c = (HttpURLConnection) url.openConnection(); c.connect(); c.disconnect(); if (c.getResponseCode() != 200) throw new MapSourceTestFailed(mapSource, c.getResponseCode()); } | 13,227 |
1 | private static void copyFile(String src, String dst) throws InvocationTargetException { try { FileChannel srcChannel; srcChannel = new FileInputStream(src).getChannel(); FileChannel dstChannel = new FileOutputStream(dst).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (FileNotFoundException e) { throw new InvocationTargetException(e, Messages.ALFWizardCreationAction_errorSourceFilesNotFound); } catch (IOException e) { throw new InvocationTargetException(e, Messages.ALFWizardCreationAction_errorCopyingFiles); } } | public static void fileCopy(File src, File dst) throws FileNotFoundException, IOException { if (src.isDirectory() && (!dst.exists() || dst.isDirectory())) { if (!dst.exists()) { if (!dst.mkdirs()) throw new IOException("unable to mkdir " + dst); } File dst1 = new File(dst, src.getName()); if (!dst1.exists() && !dst1.mkdir()) throw new IOException("unable to mkdir " + dst1); dst = dst1; File[] files = src.listFiles(); for (File f : files) { if (f.isDirectory()) { dst1 = new File(dst, f.getName()); if (!dst1.exists() && !dst1.mkdir()) throw new IOException("unable to mkdir " + dst1); } else { dst1 = dst; } fileCopy(f, dst1); } return; } else if (dst.isDirectory()) { dst = new File(dst, src.getName()); } FileChannel ic = new FileInputStream(src).getChannel(); FileChannel oc = new FileOutputStream(dst).getChannel(); ic.transferTo(0, ic.size(), oc); ic.close(); oc.close(); } | 13,228 |
1 | private CharBuffer decodeToFile(ReplayInputStream inStream, String backingFilename, String encoding) throws IOException { CharBuffer charBuffer = null; BufferedReader reader = new BufferedReader(new InputStreamReader(inStream, encoding)); File backingFile = new File(backingFilename); this.decodedFile = File.createTempFile(backingFile.getName(), WRITE_ENCODING, backingFile.getParentFile()); FileOutputStream fos; fos = new FileOutputStream(this.decodedFile); IOUtils.copy(reader, fos, WRITE_ENCODING); fos.close(); charBuffer = getReadOnlyMemoryMappedBuffer(this.decodedFile).asCharBuffer(); return charBuffer; } | 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(); } } | 13,229 |
1 | private File Gzip(File f) throws IOException { if (f == null || !f.exists()) return null; File dest_dir = f.getParentFile(); String dest_filename = f.getName() + ".gz"; File zipfile = new File(dest_dir, dest_filename); GZIPOutputStream out = new GZIPOutputStream(new FileOutputStream(zipfile)); FileInputStream in = new FileInputStream(f); byte buf[] = new byte[1024]; int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); out.finish(); try { in.close(); } catch (Exception e) { } try { out.close(); } catch (Exception e) { } try { f.delete(); } catch (Exception e) { } return zipfile; } | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | 13,230 |
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 copyFile(String oldPathFile, String newPathFile) { try { int bytesum = 0; int byteread = 0; File oldfile = new File(oldPathFile); if (oldfile.exists()) { InputStream inStream = new FileInputStream(oldPathFile); FileOutputStream fs = new FileOutputStream(newPathFile); byte[] buffer = new byte[1444]; while ((byteread = inStream.read(buffer)) != -1) { bytesum += byteread; System.out.println(bytesum); fs.write(buffer, 0, byteread); } inStream.close(); } } catch (Exception e) { message = ("���Ƶ����ļ���������"); } } | 13,231 |
0 | protected Drawing loadDrawing(ProgressIndicator progress) throws IOException { Drawing drawing = createDrawing(); if (getParameter("datafile") != null) { URL url = new URL(getDocumentBase(), getParameter("datafile")); URLConnection uc = url.openConnection(); if (uc instanceof HttpURLConnection) { ((HttpURLConnection) uc).setUseCaches(false); } int contentLength = uc.getContentLength(); InputStream in = uc.getInputStream(); try { if (contentLength != -1) { in = new BoundedRangeInputStream(in); ((BoundedRangeInputStream) in).setMaximum(contentLength + 1); progress.setProgressModel((BoundedRangeModel) in); progress.setIndeterminate(false); } BufferedInputStream bin = new BufferedInputStream(in); bin.mark(512); IOException formatException = null; for (InputFormat format : drawing.getInputFormats()) { try { bin.reset(); } catch (IOException e) { uc = url.openConnection(); in = uc.getInputStream(); in = new BoundedRangeInputStream(in); ((BoundedRangeInputStream) in).setMaximum(contentLength + 1); progress.setProgressModel((BoundedRangeModel) in); bin = new BufferedInputStream(in); bin.mark(512); } try { bin.reset(); format.read(bin, drawing, true); formatException = null; break; } catch (IOException e) { formatException = e; } } if (formatException != null) { throw formatException; } } finally { in.close(); } } return drawing; } | public RFC1345List(URL url) { if (url == null) return; try { BufferedReader br = new BufferedReader(new InputStreamReader(new GZIPInputStream(url.openStream()))); final String linePattern = " XX??????? HHHH X"; String line; mnemos = new HashMap(); nextline: while ((line = br.readLine()) != null) { if (line.length() < 9) continue nextline; if (line.charAt(7) == ' ' || line.charAt(8) != ' ') { line = line.substring(0, 8) + " " + line.substring(8); } if (line.length() < linePattern.length()) continue nextline; for (int i = 0; i < linePattern.length(); i++) { char c = line.charAt(i); switch(linePattern.charAt(i)) { case ' ': if (c != ' ') continue nextline; break; case 'X': if (c == ' ') continue nextline; break; case '?': break; case 'H': if ((c >= '0' && c <= '9') || (c >= 'a' && c <= 'f')) ; else continue nextline; break; default: throw new RuntimeException("Pattern broken!"); } } char c = (char) Integer.parseInt(line.substring(16, 20), 16); String mnemo = line.substring(1, 16).trim(); if (mnemo.length() < 2) throw new RuntimeException(); mnemos.put(mnemo, new Character(c)); } br.close(); } catch (FileNotFoundException ex) { } catch (IOException ex) { ex.printStackTrace(); } } | 13,232 |
1 | public void postProcess() throws StopWriterVisitorException { dxfWriter.postProcess(); try { FileChannel fcinDxf = new FileInputStream(fTemp).getChannel(); FileChannel fcoutDxf = new FileOutputStream(m_Fich).getChannel(); DriverUtilities.copy(fcinDxf, fcoutDxf); fTemp.delete(); } catch (FileNotFoundException e) { throw new StopWriterVisitorException(getName(), e); } catch (IOException e) { throw new StopWriterVisitorException(getName(), e); } } | 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(); } } } | 13,233 |
1 | public static void main(String[] args) { if (args.length != 3) { System.out.println("Usage: HexStrToBin enc/dec <infileName> <outfilename>"); System.exit(1); } try { ByteArrayOutputStream os = new ByteArrayOutputStream(); InputStream in = new FileInputStream(args[1]); int len = 0; byte buf[] = new byte[1024]; while ((len = in.read(buf)) > 0) os.write(buf, 0, len); in.close(); os.close(); byte[] data = null; if (args[0].equals("dec")) data = decode(os.toString()); else { String strData = encode(os.toByteArray()); data = strData.getBytes(); } FileOutputStream fos = new FileOutputStream(args[2]); fos.write(data); fos.close(); } catch (Exception e) { e.printStackTrace(); } } | private boolean saveLOBDataToFileSystem() { if ("".equals(m_attachmentPathRoot)) { log.severe("no attachmentPath defined"); return false; } if (m_items == null || m_items.size() == 0) { setBinaryData(null); return true; } final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); try { final DocumentBuilder builder = factory.newDocumentBuilder(); final Document document = builder.newDocument(); final Element root = document.createElement("attachments"); document.appendChild(root); document.setXmlStandalone(true); for (int i = 0; i < m_items.size(); i++) { log.fine(m_items.get(i).toString()); File entryFile = m_items.get(i).getFile(); final String path = entryFile.getAbsolutePath(); log.fine(path + " - " + m_attachmentPathRoot); if (!path.startsWith(m_attachmentPathRoot)) { log.fine("move file: " + path); FileChannel in = null; FileChannel out = null; try { final File destFolder = new File(m_attachmentPathRoot + File.separator + getAttachmentPathSnippet()); if (!destFolder.exists()) { if (!destFolder.mkdirs()) { log.warning("unable to create folder: " + destFolder.getPath()); } } final File destFile = new File(m_attachmentPathRoot + File.separator + getAttachmentPathSnippet() + File.separator + entryFile.getName()); in = new FileInputStream(entryFile).getChannel(); out = new FileOutputStream(destFile).getChannel(); in.transferTo(0, in.size(), out); in.close(); out.close(); if (entryFile.exists()) { if (!entryFile.delete()) { entryFile.deleteOnExit(); } } entryFile = destFile; } catch (IOException e) { e.printStackTrace(); log.severe("unable to copy file " + entryFile.getAbsolutePath() + " to " + m_attachmentPathRoot + File.separator + getAttachmentPathSnippet() + File.separator + entryFile.getName()); } finally { if (in != null && in.isOpen()) { in.close(); } if (out != null && out.isOpen()) { out.close(); } } } final Element entry = document.createElement("entry"); entry.setAttribute("name", getEntryName(i)); String filePathToStore = entryFile.getAbsolutePath(); filePathToStore = filePathToStore.replaceFirst(m_attachmentPathRoot.replaceAll("\\\\", "\\\\\\\\"), ATTACHMENT_FOLDER_PLACEHOLDER); log.fine(filePathToStore); entry.setAttribute("file", filePathToStore); root.appendChild(entry); } final Source source = new DOMSource(document); final ByteArrayOutputStream bos = new ByteArrayOutputStream(); final Result result = new StreamResult(bos); final Transformer xformer = TransformerFactory.newInstance().newTransformer(); xformer.transform(source, result); final byte[] xmlData = bos.toByteArray(); log.fine(bos.toString()); setBinaryData(xmlData); return true; } catch (Exception e) { log.log(Level.SEVERE, "saveLOBData", e); } setBinaryData(null); return false; } | 13,234 |
0 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public boolean authorize(String username, String password, String filename) { open(filename); boolean isAuthorized = false; StringBuffer encPasswd = null; try { MessageDigest mdAlgorithm = MessageDigest.getInstance("MD5"); mdAlgorithm.update(password.getBytes()); byte[] digest = mdAlgorithm.digest(); encPasswd = new StringBuffer(); for (int i = 0; i < digest.length; i++) { password = Integer.toHexString(255 & digest[i]); if (password.length() < 2) { password = "0" + password; } encPasswd.append(password); } } catch (NoSuchAlgorithmException ex) { } String encPassword = encPasswd.toString(); String tempPassword = getPassword(username); System.out.println("epass" + encPassword); System.out.println("pass" + tempPassword); if (tempPassword.equals(encPassword)) { isAuthorized = true; } else { isAuthorized = false; } close(); return isAuthorized; } | 13,235 |
1 | public static void copyURLToFile(URL source, File destination) throws IOException { if (destination.getParentFile() != null && !destination.getParentFile().exists()) { destination.getParentFile().mkdirs(); } if (destination.exists() && !destination.canWrite()) { String message = "Unable to open file " + destination + " for writing."; throw new IOException(message); } InputStream input = source.openStream(); try { FileOutputStream output = new FileOutputStream(destination); try { IOUtils.copy(input, output); } finally { IOUtils.closeQuietly(output); } } finally { IOUtils.closeQuietly(input); } } | public byte[] getFile(final String file) throws IOException { if (this.files.contains(file)) { ZipInputStream input = new ZipInputStream(new ByteArrayInputStream(this.bytes)); ZipEntry entry = input.getNextEntry(); while (entry != null) { entry = input.getNextEntry(); if ((entry.getName().equals(file)) && (!entry.isDirectory())) { ByteArrayOutputStream output = new ByteArrayOutputStream(); IOUtils.copy(input, output); output.close(); input.close(); return output.toByteArray(); } } input.close(); } return null; } | 13,236 |
1 | public static void copyFile(final String inFile, final String outFile) { FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(inFile).getChannel(); out = new FileOutputStream(outFile).getChannel(); in.transferTo(0, in.size(), out); } catch (final Exception e) { } finally { if (in != null) { try { in.close(); } catch (final Exception e) { } } if (out != null) { try { out.close(); } catch (final Exception e) { } } } } | public static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileOutputStream fos = new FileOutputStream(out); FileChannel outChannel = fos.getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); fos.flush(); fos.close(); } } | 13,237 |
0 | private void writeStatsToDatabase(long transferJobAIPCount, long reprocessingJobAIPCount, long transferJobAIPVolume, long reprocessingJobAIPVolume, long overallBinaryAIPCount, Map<String, AIPStatistics> mimeTypeRegister) throws SQLException { int nextAIPStatsID; long nextMimetypeStatsID; Statement select = dbConnection.createStatement(); String aipStatsQuery = "select max(aip_statistics_id) from aip_statistics"; ResultSet result = select.executeQuery(aipStatsQuery); if (result.next()) { nextAIPStatsID = result.getInt(1) + 1; } else { throw new SQLException("Problem getting maximum AIP Statistics ID"); } String mimetypeStatsQuery = "select max(mimetype_aip_statistics_id) from mimetype_aip_statistics"; result = select.executeQuery(mimetypeStatsQuery); if (result.next()) { nextMimetypeStatsID = result.getLong(1) + 1; } else { throw new SQLException("Problem getting maximum MIME type AIP Statistics ID"); } String insertAIPStatsEntryQuery = "insert into aip_statistics " + "(aip_statistics_id, tj_aip_count, tj_aip_volume, rj_aip_count, rj_aip_volume, " + "collation_date, binary_aip_count) " + "values (?, ?, ?, ?, ?, ?, ?)"; PreparedStatement insert = dbConnection.prepareStatement(insertAIPStatsEntryQuery); insert.setInt(1, nextAIPStatsID); insert.setLong(2, transferJobAIPCount); insert.setLong(3, transferJobAIPVolume); insert.setLong(4, reprocessingJobAIPCount); insert.setLong(5, reprocessingJobAIPVolume); insert.setDate(6, new java.sql.Date(System.currentTimeMillis())); insert.setLong(7, overallBinaryAIPCount); int rowsAdded = insert.executeUpdate(); if (rowsAdded != 1) { dbConnection.rollback(); throw new SQLException("Could not insert row into AIP statistics table"); } String insertMimeTypeStatsQuery = "insert into mimetype_aip_statistics " + "(mimetype_aip_statistics_id, aip_statistics_id, mimetype_aip_count, mimetype_aip_volume, mimetype) " + "values (?, ?, ?, ?, ?)"; insert = dbConnection.prepareStatement(insertMimeTypeStatsQuery); insert.setInt(2, nextAIPStatsID); for (String mimeType : mimeTypeRegister.keySet()) { AIPStatistics mimeTypeStats = mimeTypeRegister.get(mimeType); insert.setLong(1, nextMimetypeStatsID); insert.setLong(3, mimeTypeStats.aipCount); insert.setLong(4, mimeTypeStats.aipVolume); insert.setString(5, mimeType); nextMimetypeStatsID++; rowsAdded = insert.executeUpdate(); if (rowsAdded != 1) { dbConnection.rollback(); throw new SQLException("Could not insert row into MIME Type AIP statistics table"); } } dbConnection.commit(); } | public static String hash(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("MD5"); byte[] md5hash = new byte[32]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } | 13,238 |
0 | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public static String createMD5(String str) { String sig = null; String strSalt = str + sSalt; try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(strSalt.getBytes(), 0, strSalt.length()); byte byteData[] = md5.digest(); StringBuffer sb = new StringBuffer(); for (int i = 0; i < byteData.length; i++) { sb.append(Integer.toString((byteData[i] & 0xff) + 0x100, 16).substring(1)); } sig = sb.toString(); } catch (NoSuchAlgorithmException e) { System.err.println("Can not use md5 algorithm"); } return sig; } | 13,239 |
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 SearchHandler(String criteria, int langId) { try { URL url = new URL("http://eiffel.itba.edu.ar/hci/service/Catalog.groovy?method=GetProductListByName&criteria=" + criteria + "&language_id=" + langId); URLConnection urlc = url.openConnection(); urlc.setDoOutput(false); urlc.setAllowUserInteraction(false); BufferedReader br = new BufferedReader(new InputStreamReader(urlc.getInputStream())); String str; StringBuffer sb = new StringBuffer(); while ((str = br.readLine()) != null) { sb.append(str); sb.append("\n"); } br.close(); String response = sb.toString(); if (response == null) { return; } DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); DocumentBuilder db = dbf.newDocumentBuilder(); InputSource is = new InputSource(); is.setCharacterStream(new StringReader(response)); Document dom = db.parse(is); NodeList nl = dom.getElementsByTagName("product"); for (int i = 0; i < nl.getLength(); i++) { Element nodes = (Element) nl.item(i); String id = nodes.getAttribute("id").toString(); NodeList name = nodes.getElementsByTagName("name"); NodeList rank2 = nodes.getElementsByTagName("sales_rank"); NodeList price = nodes.getElementsByTagName("price"); NodeList url2 = nodes.getElementsByTagName("image_url"); String nameS = getCharacterDataFromElement((Element) name.item(0)); String rank2S = getCharacterDataFromElement((Element) rank2.item(0)); String priceS = getCharacterDataFromElement((Element) price.item(0)); String url2S = getCharacterDataFromElement((Element) url2.item(0)); list.add(new ProductShort(id, nameS, rank2S, priceS, url2S)); } } catch (Exception e) { e.printStackTrace(); } } | 13,240 |
1 | public static byte[] expandPasswordToKeySSHCom(String password, int keyLen) { try { if (password == null) { password = ""; } MessageDigest md5 = MessageDigest.getInstance("MD5"); int digLen = md5.getDigestLength(); byte[] buf = new byte[((keyLen + digLen) / digLen) * digLen]; int cnt = 0; while (cnt < keyLen) { md5.update(password.getBytes()); if (cnt > 0) { md5.update(buf, 0, cnt); } md5.digest(buf, cnt, digLen); cnt += digLen; } byte[] key = new byte[keyLen]; System.arraycopy(buf, 0, key, 0, keyLen); return key; } catch (Exception e) { throw new Error("Error in SSH2KeyPairFile.expandPasswordToKeySSHCom: " + e); } } | public String SHA1(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md = MessageDigest.getInstance(SHA1); md.update(text.getBytes(CHAR_SET), 0, text.length()); byte[] mdbytes = md.digest(); return byteToHex(mdbytes); } | 13,241 |
0 | protected static String getURLandWriteToDisk(String url, Model retModel) throws MalformedURLException, IOException { String path = null; URL ontURL = new URL(url); InputStream ins = ontURL.openStream(); InputStreamReader bufRead; OutputStreamWriter bufWrite; int offset = 0, read = 0; initModelHash(); if (System.getProperty("user.dir") != null) { String delimiter; path = System.getProperty("user.dir"); if (path.contains("/")) { delimiter = "/"; } else { delimiter = "\\"; } char c = path.charAt(path.length() - 1); if (c == '/' || c == '\\') { path = path.substring(0, path.length() - 2); } path = path.substring(0, path.lastIndexOf(delimiter) + 1); path = path.concat("ontologies" + delimiter + "downloaded"); (new File(path)).mkdir(); path = path.concat(delimiter); path = createFullPath(url, path); bufWrite = new OutputStreamWriter(new FileOutputStream(path)); bufRead = new InputStreamReader(ins); read = bufRead.read(); while (read != -1) { bufWrite.write(read); offset += read; read = bufRead.read(); } bufRead.close(); bufWrite.close(); ins.close(); FileInputStream fs = new FileInputStream(path); retModel.read(fs, ""); } return path; } | void setURLString(String path, boolean forceLoad) { if (path != null) { if (this.url != null || inputStream != null) throw new IllegalArgumentException(Ding3dI18N.getString("MediaContainer5")); try { URL url = new URL(path); InputStream stream; stream = url.openStream(); stream.close(); } catch (Exception e) { throw new SoundException(javax.media.ding3d.Ding3dI18N.getString("MediaContainer0")); } } this.urlString = path; if (forceLoad) dispatchMessage(); } | 13,242 |
0 | public static final String getUniqueId() { String digest = ""; try { MessageDigest md = MessageDigest.getInstance("MD5"); String timeVal = "" + (System.currentTimeMillis() + 1); String localHost = ""; try { localHost = InetAddress.getLocalHost().toString(); } catch (UnknownHostException e) { throw new RuntimeException("Error trying to get localhost" + e.getMessage()); } String randVal = "" + new Random().nextInt(); String val = timeVal + localHost + randVal; md.reset(); md.update(val.getBytes()); digest = toHexString(md.digest()); } catch (NoSuchAlgorithmException e) { throw new RuntimeException("NoSuchAlgorithmException : " + e.getMessage()); } return digest; } | public int delete(BusinessObject o) throws DAOException { int delete = 0; Currency curr = (Currency) o; try { PreparedStatement pst = connection.prepareStatement(XMLGetQuery.getQuery("DELETE_CURRENCY")); pst.setInt(1, curr.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; } | 13,243 |
1 | public static String calcHA1(String algorithm, String username, String realm, String password, String nonce, String cnonce) throws FatalException, MD5DigestException { MD5Encoder encoder = new MD5Encoder(); MessageDigest md5 = null; try { md5 = MessageDigest.getInstance("MD5"); } catch (Exception e) { throw new FatalException(e); } if (username == null || realm == null) { throw new MD5DigestException(WebdavStatus.SC_BAD_REQUEST, "username or realm"); } if (password == null) { System.err.println("No password has been provided"); throw new IllegalStateException(); } if (algorithm != null && algorithm.equals("MD5-sess") && (nonce == null || cnonce == null)) { throw new MD5DigestException(WebdavStatus.SC_BAD_REQUEST, "nonce or cnonce"); } md5.update((username + ":" + realm + ":" + password).getBytes()); if (algorithm != null && algorithm.equals("MD5-sess")) { md5.update((":" + nonce + ":" + cnonce).getBytes()); } return encoder.encode(md5.digest()); } | 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); } } | 13,244 |
1 | public void testConvert() throws IOException, ConverterException { InputStreamReader reader = new InputStreamReader(new FileInputStream("test" + File.separator + "input" + File.separator + "A0851ohneex.dat"), CharsetUtil.forName("x-PICA")); FileWriter writer = new FileWriter("test" + File.separator + "output" + File.separator + "ddbInterToMarcxmlTest.out"); Converter c = context.getConverter("ddb-intern", "MARC21-xml", "x-PICA", "UTF-8"); ConversionParameters params = new ConversionParameters(); params.setSourceCharset("x-PICA"); params.setTargetCharset("UTF-8"); params.setAddCollectionHeader(true); params.setAddCollectionFooter(true); c.convert(reader, writer, params); } | 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(); } } | 13,245 |
0 | public void doInsertImage() { logger.debug(">>> Inserting image..."); logger.debug(" fullFileName : #0", uploadedFileName); String fileName = uploadedFileName.substring(uploadedFileName.lastIndexOf(File.separator) + 1); logger.debug(" fileName : #0", fileName); String newFileName = System.currentTimeMillis() + "_" + fileName; String filePath = ImageResource.getResourceDirectory() + File.separator + newFileName; logger.debug(" filePath : #0", filePath); try { File file = new File(filePath); file.createNewFile(); FileChannel srcChannel = null; FileChannel dstChannel = null; try { srcChannel = new FileInputStream(uploadedFile).getChannel(); dstChannel = new FileOutputStream(file).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); } finally { closeChannel(srcChannel); closeChannel(dstChannel); } StringBuilder imageTag = new StringBuilder(); imageTag.append("<img src=\""); imageTag.append(getRequest().getContextPath()); imageTag.append("/seam/resource"); imageTag.append(ImageResource.RESOURCE_PATH); imageTag.append("/"); imageTag.append(newFileName); imageTag.append("\"/>"); if (getQuestionDefinition().getDescription() == null) { getQuestionDefinition().setDescription(""); } getQuestionDefinition().setDescription(getQuestionDefinition().getDescription() + imageTag); } catch (IOException e) { logger.error("Error during saving image file", e); } uploadedFile = null; uploadedFileName = null; logger.debug("<<< Inserting image...Ok"); } | public static InputStream getInputStream(String name) throws java.io.IOException { URL url = getURL(name); if (url != null) { return url.openStream(); } throw new FileNotFoundException("UniverseData: Resource \"" + name + "\" not found."); } | 13,246 |
0 | @Override protected String doInBackground(Void... params) { try { HttpGet request = new HttpGet(UPDATE_URL); request.setHeader("Accept", "text/plain"); HttpResponse response = MyMovies.getHttpClient().execute(request); int statusCode = response.getStatusLine().getStatusCode(); if (statusCode != HttpStatus.SC_OK) { return "Error: Failed getting update notes"; } return EntityUtils.toString(response.getEntity()); } catch (Exception e) { return "Error: " + e.getMessage(); } } | @Override public void setOntology1Document(URL url1) throws IllegalArgumentException { if (url1 == null) throw new IllegalArgumentException("Input parameter URL for ontology 1 is null."); try { ont1 = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(url1.openStream()); } catch (IOException e) { throw new IllegalArgumentException("Cannot open stream for ontology 1 from given URL."); } catch (OWLOntologyCreationException e) { throw new IllegalArgumentException("Cannot load ontology 1 from given URL."); } } | 13,247 |
1 | public static String md5(String text) { String hashed = ""; try { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(text.getBytes(), 0, text.length()); hashed = new BigInteger(1, digest.digest()).toString(16); } catch (Exception e) { Log.e(ctGlobal.tag, "ctCommon.md5: " + e.toString()); } return hashed; } | public static void processString(String text) throws Exception { MessageDigest md5 = MessageDigest.getInstance(MD5_DIGEST); md5.reset(); md5.update(text.getBytes()); displayResult(null, md5.digest()); } | 13,248 |
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(); } } } | 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!"); } | 13,249 |
0 | public static String SHA1(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } | public void doCompress(File[] files, File out, List<String> excludedKeys) { Map<String, File> map = new HashMap<String, File>(); String parent = FilenameUtils.getBaseName(out.getName()); for (File f : files) { CompressionUtil.list(f, parent, map, excludedKeys); } if (!map.isEmpty()) { FileOutputStream fos = null; ArchiveOutputStream aos = null; InputStream is = null; try { fos = new FileOutputStream(out); aos = getArchiveOutputStream(fos); for (Map.Entry<String, File> entry : map.entrySet()) { File file = entry.getValue(); ArchiveEntry ae = getArchiveEntry(file, entry.getKey()); aos.putArchiveEntry(ae); if (file.isFile()) { IOUtils.copy(is = new FileInputStream(file), aos); IOUtils.closeQuietly(is); is = null; } aos.closeArchiveEntry(); } aos.finish(); } catch (IOException ex) { ex.printStackTrace(); } finally { IOUtils.closeQuietly(is); IOUtils.closeQuietly(aos); IOUtils.closeQuietly(fos); } } } | 13,250 |
0 | public static void copy(String fromFileName, String toFileName) throws IOException { File fromFile = new File(fromFileName); File toFile = new File(toFileName); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFileName); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFileName); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFileName); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!toFile.canWrite()) throw new IOException("FileCopy: " + "destination file is unwriteable: " + toFileName); System.out.print("Overwrite existing file " + toFile.getName() + "? (Y/N): "); System.out.flush(); BufferedReader in = new BufferedReader(new InputStreamReader(System.in)); String response = in.readLine(); if (!response.equals("Y") && !response.equals("y")) throw new IOException("FileCopy: " + "existing file was not overwritten."); } else { String parent = toFile.getParent(); if (parent == null) parent = System.getProperty("user.dir"); File dir = new File(parent); if (!dir.exists()) throw new IOException("FileCopy: " + "destination directory doesn't exist: " + parent); if (dir.isFile()) throw new IOException("FileCopy: " + "destination is not a directory: " + parent); if (!dir.canWrite()) throw new IOException("FileCopy: " + "destination directory is unwriteable: " + parent); } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } | private String getShaderIncludeSource(String path) throws Exception { URL url = this.getClass().getResource(path); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); boolean run = true; String str; String ret = new String(); while (run) { str = in.readLine(); if (str != null) ret += str + "\n"; else run = false; } in.close(); return ret; } | 13,251 |
0 | protected List<Datastream> getDatastreams(final DepositCollection pDeposit) throws IOException, SWORDException { List<Datastream> tDatastreams = super.getDatastreams(pDeposit); FileInputStream tInput = null; String tFileName = ((LocalDatastream) tDatastreams.get(0)).getPath(); String tTempFileName = this.getTempDir() + "uploaded-file.tmp"; IOUtils.copy(tInput = new FileInputStream(tFileName), new FileOutputStream(tTempFileName + ".thum")); tInput.close(); Datastream tThum = new LocalDatastream("THUMBRES_IMG", this.getContentType(), tTempFileName + ".thum"); tDatastreams.add(tThum); IOUtils.copy(tInput = new FileInputStream(tFileName), new FileOutputStream(tTempFileName + ".mid")); tInput.close(); Datastream tMid = new LocalDatastream("MEDRES_IMG", this.getContentType(), tTempFileName + ".mid"); tDatastreams.add(tMid); IOUtils.copy(tInput = new FileInputStream(tFileName), new FileOutputStream(tTempFileName + ".high")); tInput.close(); Datastream tLarge = new LocalDatastream("HIGHRES_IMG", this.getContentType(), tTempFileName + ".high"); tDatastreams.add(tLarge); IOUtils.copy(tInput = new FileInputStream(tFileName), new FileOutputStream(tTempFileName + ".vhigh")); tInput.close(); Datastream tVLarge = new LocalDatastream("VERYHIGHRES_IMG", this.getContentType(), tTempFileName + ".vhigh"); tDatastreams.add(tVLarge); return tDatastreams; } | public static void retriveRemote(ISource source, Node[] nodes, String outDirName, boolean isBinary) throws Exception { FTPClient client = new FTPClient(); client.connect(source.getSourceDetail().getHost()); client.login(source.getSourceDetail().getUser(), source.getSourceDetail().getPassword()); if (isBinary) client.setFileType(FTPClient.BINARY_FILE_TYPE); FileOutputStream out = null; for (Node node : nodes) { if (!node.isLeaf()) { Node[] childern = source.getChildern(node); File dir = new File(outDirName + File.separator + node.getAlias()); dir.mkdir(); retriveRemote(source, childern, outDirName + File.separator + node.getAlias(), isBinary); } else { out = new FileOutputStream(outDirName + File.separator + node.getAlias()); client.retrieveFile(node.getAbsolutePath(), out); out.flush(); out.close(); } } client.disconnect(); } | 13,252 |
0 | protected Set<String> moduleNamesFromReader(URL url) throws IOException { BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); Set<String> names = new HashSet<String>(); String line; while ((line = reader.readLine()) != null) { line = line.trim(); Matcher m = nonCommentPattern.matcher(line); if (m.find()) { names.add(m.group().trim()); } } return names; } | private NodeInfo loadNodeMeta(int id, int properties) { String query = mServer + "load.php" + ("?id=" + id) + ("&mask=" + properties); NodeInfo info = null; try { URL url = new URL(query); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setAllowUserInteraction(false); conn.setRequestMethod("GET"); setCredentials(conn); conn.connect(); if (conn.getResponseCode() == HttpURLConnection.HTTP_OK) { InputStream stream = conn.getInputStream(); MimeType contentType = new MimeType(conn.getContentType()); if (contentType.getBaseType().equals("text/xml")) { try { JAXBContext context = JAXBContext.newInstance(NetProcessorInfo.class); Unmarshaller unm = context.createUnmarshaller(); NetProcessorInfo root = (NetProcessorInfo) unm.unmarshal(stream); if ((root != null) && (root.getNodes().length == 1)) { info = root.getNodes()[0]; } } catch (Exception ex) { } } stream.close(); } } catch (Exception ex) { } return info; } | 13,253 |
1 | @Override public CasAssembly build() { try { prepareForBuild(); File casWorkingDirectory = casFile.getParentFile(); DefaultCasFileReadIndexToContigLookup read2contigMap = new DefaultCasFileReadIndexToContigLookup(); AbstractDefaultCasFileLookup readIdLookup = new DefaultReadCasFileLookup(casWorkingDirectory); CasParser.parseOnlyMetaData(casFile, MultipleWrapper.createMultipleWrapper(CasFileVisitor.class, read2contigMap, readIdLookup)); ReadWriteDirectoryFileServer consedOut = DirectoryFileServer.createReadWriteDirectoryFileServer(commandLine.getOptionValue("o")); long startTime = DateTimeUtils.currentTimeMillis(); int numberOfCasContigs = read2contigMap.getNumberOfContigs(); for (long i = 0; i < numberOfCasContigs; i++) { File outputDir = consedOut.createNewDir("" + i); Command aCommand = new Command(new File("fakeCommand")); aCommand.setOption("-casId", "" + i); aCommand.setOption("-cas", commandLine.getOptionValue("cas")); aCommand.setOption("-o", outputDir.getAbsolutePath()); aCommand.setOption("-tempDir", tempDir.getAbsolutePath()); aCommand.setOption("-prefix", "temp"); if (commandLine.hasOption("useIllumina")) { aCommand.addFlag("-useIllumina"); } if (commandLine.hasOption("useClosureTrimming")) { aCommand.addFlag("-useClosureTrimming"); } if (commandLine.hasOption("trim")) { aCommand.setOption("-trim", commandLine.getOptionValue("trim")); } if (commandLine.hasOption("trimMap")) { aCommand.setOption("-trimMap", commandLine.getOptionValue("trimMap")); } if (commandLine.hasOption("chromat_dir")) { aCommand.setOption("-chromat_dir", commandLine.getOptionValue("chromat_dir")); } submitSingleCasAssemblyConversion(aCommand); } waitForAllAssembliesToFinish(); int numContigs = 0; int numReads = 0; for (int i = 0; i < numberOfCasContigs; i++) { File countMap = consedOut.getFile(i + "/temp.counts"); Scanner scanner = new Scanner(countMap); if (!scanner.hasNextInt()) { throw new IllegalStateException("single assembly conversion # " + i + " did not complete"); } numContigs += scanner.nextInt(); numReads += scanner.nextInt(); scanner.close(); } System.out.println("num contigs =" + numContigs); System.out.println("num reads =" + numReads); consedOut.createNewDir("edit_dir"); consedOut.createNewDir("phd_dir"); String prefix = commandLine.hasOption("prefix") ? commandLine.getOptionValue("prefix") : DEFAULT_PREFIX; OutputStream masterAceOut = new FileOutputStream(consedOut.createNewFile("edit_dir/" + prefix + ".ace.1")); OutputStream masterPhdOut = new FileOutputStream(consedOut.createNewFile("phd_dir/" + prefix + ".phd.ball")); OutputStream masterConsensusOut = new FileOutputStream(consedOut.createNewFile(prefix + ".consensus.fasta")); OutputStream logOut = new FileOutputStream(consedOut.createNewFile(prefix + ".log")); try { masterAceOut.write(String.format("AS %d %d%n", numContigs, numReads).getBytes()); for (int i = 0; i < numberOfCasContigs; i++) { InputStream aceIn = consedOut.getFileAsStream(i + "/temp.ace"); IOUtils.copy(aceIn, masterAceOut); InputStream phdIn = consedOut.getFileAsStream(i + "/temp.phd"); IOUtils.copy(phdIn, masterPhdOut); InputStream consensusIn = consedOut.getFileAsStream(i + "/temp.consensus.fasta"); IOUtils.copy(consensusIn, masterConsensusOut); IOUtil.closeAndIgnoreErrors(aceIn, phdIn, consensusIn); File tempDir = consedOut.getFile(i + ""); IOUtil.recursiveDelete(tempDir); } consedOut.createNewSymLink("../phd_dir/" + prefix + ".phd.ball", "edit_dir/phd.ball"); if (commandLine.hasOption("chromat_dir")) { consedOut.createNewDir("chromat_dir"); File originalChromatDir = new File(commandLine.getOptionValue("chromat_dir")); for (File chromat : originalChromatDir.listFiles(new FilenameFilter() { @Override public boolean accept(File dir, String name) { return name.endsWith(".scf"); } })) { File newChromatFile = consedOut.createNewFile("chromat_dir/" + FilenameUtils.getBaseName(chromat.getName())); FileOutputStream newChromat = new FileOutputStream(newChromatFile); InputStream in = new FileInputStream(chromat); IOUtils.copy(in, newChromat); IOUtil.closeAndIgnoreErrors(in, newChromat); } } System.out.println("finished making casAssemblies"); for (File traceFile : readIdLookup.getFiles()) { final String name = traceFile.getName(); String extension = FilenameUtils.getExtension(name); if (name.contains("fastq")) { if (!consedOut.contains("solexa_dir")) { consedOut.createNewDir("solexa_dir"); } if (consedOut.contains("solexa_dir/" + name)) { IOUtil.delete(consedOut.getFile("solexa_dir/" + name)); } consedOut.createNewSymLink(traceFile.getAbsolutePath(), "solexa_dir/" + name); } else if ("sff".equals(extension)) { if (!consedOut.contains("sff_dir")) { consedOut.createNewDir("sff_dir"); } if (consedOut.contains("sff_dir/" + name)) { IOUtil.delete(consedOut.getFile("sff_dir/" + name)); } consedOut.createNewSymLink(traceFile.getAbsolutePath(), "sff_dir/" + name); } } long endTime = DateTimeUtils.currentTimeMillis(); logOut.write(String.format("took %s%n", new Period(endTime - startTime)).getBytes()); } finally { IOUtil.closeAndIgnoreErrors(masterAceOut, masterPhdOut, masterConsensusOut, logOut); } } catch (Exception e) { handleException(e); } finally { cleanup(); } return null; } | public static void copyFile(File src, File dst) throws IOException { FileInputStream fis = null; FileOutputStream fos = null; fis = new FileInputStream(src); fos = new FileOutputStream(dst); byte[] buffer = new byte[16384]; int read = 0; while ((read = fis.read(buffer)) != -1) { fos.write(buffer, 0, read); } fis.close(); fos.flush(); fos.close(); } | 13,254 |
0 | public static void decryptFile(String input, String output, String pwd) throws Exception { CipherInputStream in; OutputStream out; Cipher cipher; SecretKey key; byte[] byteBuffer; cipher = Cipher.getInstance("DES"); key = new SecretKeySpec(pwd.getBytes(), "DES"); cipher.init(Cipher.DECRYPT_MODE, key); in = new CipherInputStream(new FileInputStream(input), cipher); out = new FileOutputStream(output); byteBuffer = new byte[1024]; for (int n; (n = in.read(byteBuffer)) != -1; out.write(byteBuffer, 0, n)) ; in.close(); out.close(); } | public static String getMD5(String s) throws NoSuchAlgorithmException { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.reset(); md5.update(s.getBytes()); byte[] result = md5.digest(); StringBuilder hexString = new StringBuilder(); for (int i = 0; i < result.length; i++) { hexString.append(String.format("%02x", 0xFF & result[i])); } return hexString.toString(); } | 13,255 |
1 | private void displayDiffResults() throws IOException { File outFile = File.createTempFile("diff", ".htm"); outFile.deleteOnExit(); FileOutputStream outStream = new FileOutputStream(outFile); BufferedWriter out = new BufferedWriter(new OutputStreamWriter(outStream)); out.write("<html><head><title>LOC Differences</title>\n" + SCRIPT + "</head>\n" + "<body bgcolor='#ffffff'>\n" + "<div onMouseOver=\"window.defaultStatus='Metrics'\">\n"); if (addedTable.length() > 0) { out.write("<table border><tr><th>Files Added:</th>" + "<th>Add</th><th>Type</th></tr>"); out.write(addedTable.toString()); out.write("</table><br><br>"); } if (modifiedTable.length() > 0) { out.write("<table border><tr><th>Files Modified:</th>" + "<th>Base</th><th>Del</th><th>Mod</th><th>Add</th>" + "<th>Total</th><th>Type</th></tr>"); out.write(modifiedTable.toString()); out.write("</table><br><br>"); } if (deletedTable.length() > 0) { out.write("<table border><tr><th>Files Deleted:</th>" + "<th>Del</th><th>Type</th></tr>"); out.write(deletedTable.toString()); out.write("</table><br><br>"); } out.write("<table name=METRICS BORDER>\n"); if (modifiedTable.length() > 0 || deletedTable.length() > 0) { out.write("<tr><td>Base: </td><td>"); out.write(Long.toString(base)); out.write("</td></tr>\n<tr><td>Deleted: </td><td>"); out.write(Long.toString(deleted)); out.write("</td></tr>\n<tr><td>Modified: </td><td>"); out.write(Long.toString(modified)); out.write("</td></tr>\n<tr><td>Added: </td><td>"); out.write(Long.toString(added)); out.write("</td></tr>\n<tr><td>New & Changed: </td><td>"); out.write(Long.toString(added + modified)); out.write("</td></tr>\n"); } out.write("<tr><td>Total: </td><td>"); out.write(Long.toString(total)); out.write("</td></tr>\n</table></div>"); redlinesOut.close(); out.flush(); InputStream redlines = new FileInputStream(redlinesTempFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = redlines.read(buffer)) != -1) outStream.write(buffer, 0, bytesRead); outStream.write("</BODY></HTML>".getBytes()); outStream.close(); Browser.launch(outFile.toURL().toString()); } | private static final void cloneFile(File origin, File target) throws IOException { FileChannel srcChannel = null; FileChannel destChannel = null; try { srcChannel = new FileInputStream(origin).getChannel(); destChannel = new FileOutputStream(target).getChannel(); destChannel.transferFrom(srcChannel, 0, srcChannel.size()); } finally { if (srcChannel != null) srcChannel.close(); if (destChannel != null) destChannel.close(); } } | 13,256 |
0 | public static void copyFile(final String src, final String dest) { Runnable r1 = new Runnable() { public void run() { try { File inf = new File(dest); if (!inf.exists()) { inf.getParentFile().mkdirs(); } FileChannel in = new FileInputStream(src).getChannel(); FileChannel out = new FileOutputStream(dest).getChannel(); out.transferFrom(in, 0, in.size()); in.close(); out.close(); } catch (IOException e) { e.printStackTrace(); System.err.println("Error copying file \n" + src + "\n" + dest); } } }; Thread cFile = new Thread(r1, "copyFile"); cFile.start(); } | public synchronized void connectURL(String url) throws IllegalArgumentException, IOException, MalformedURLException { URL myurl = new URL(url); InputStream in = myurl.openStream(); BufferedReader page = new BufferedReader(new InputStreamReader(in)); String ior = null; ArrayList nodesAL = new ArrayList(); while ((ior = page.readLine()) != null) { if (ior.trim().equals("")) continue; nodesAL.add(ior); } in.close(); Object[] nodesOA = nodesAL.toArray(); Node[] nodes = new Node[nodesOA.length]; for (int i = 0; i < nodesOA.length; i++) nodes[i] = TcbnetOrb.getInstance().getNode((String) nodesOA[i]); this.connect(nodes); } | 13,257 |
1 | public static void doVersionCheck(View view) { view.showWaitCursor(); try { URL url = new URL(jEdit.getProperty("version-check.url")); InputStream in = url.openStream(); BufferedReader bin = new BufferedReader(new InputStreamReader(in)); String line; String version = null; String build = null; while ((line = bin.readLine()) != null) { if (line.startsWith(".version")) version = line.substring(8).trim(); else if (line.startsWith(".build")) build = line.substring(6).trim(); } bin.close(); if (version != null && build != null) { if (jEdit.getBuild().compareTo(build) < 0) newVersionAvailable(view, version, url); else { GUIUtilities.message(view, "version-check" + ".up-to-date", new String[0]); } } } catch (IOException e) { String[] args = { jEdit.getProperty("version-check.url"), e.toString() }; GUIUtilities.error(view, "read-error", args); } view.hideWaitCursor(); } | private void importExample(boolean server) throws IOException, XMLStreamException, FactoryConfigurationError { InputStream example = null; if (server) { monitor.setNote(Messages.getString("ImportExampleDialog.Cont")); monitor.setProgress(0); String page = engine.getConfiguration().getProperty("example.url"); URL url = new URL(page); BufferedReader rr = new BufferedReader(new InputStreamReader(url.openStream())); try { sleep(3000); } catch (InterruptedException e1) { Logger.getLogger(this.getClass()).debug("Internal error.", e1); } if (monitor.isCanceled()) { return; } try { while (rr.ready()) { if (monitor.isCanceled()) { return; } String l = rr.readLine(); if (example == null) { int i = l.indexOf("id=\"example\""); if (i > 0) { l = l.substring(i + 19); l = l.substring(0, l.indexOf('"')); url = new URL(l); example = url.openStream(); } } } } catch (IOException ex) { throw ex; } finally { if (rr != null) { try { rr.close(); } catch (Exception e) { Logger.getLogger(this.getClass()).debug("Internal error.", e); } } } } else { InputStream is = ApplicationHelper.class.getClassLoader().getResourceAsStream("gtd-free-example.xml"); if (is != null) { example = is; } } if (example != null) { if (monitor.isCanceled()) { try { example.close(); } catch (IOException e) { Logger.getLogger(this.getClass()).debug("Internal error.", e); } return; } monitor.setNote(Messages.getString("ImportExampleDialog.Read")); monitor.setProgress(1); model = new GTDModel(null); GTDDataXMLTools.importFile(model, example); try { example.close(); } catch (IOException e) { Logger.getLogger(this.getClass()).debug("Internal error.", e); } if (monitor.isCanceled()) { return; } monitor.setNote(Messages.getString("ImportExampleDialog.Imp.File")); monitor.setProgress(2); try { SwingUtilities.invokeAndWait(new Runnable() { @Override public void run() { if (monitor.isCanceled()) { return; } engine.getGTDModel().importData(model); } }); } catch (InterruptedException e1) { Logger.getLogger(this.getClass()).debug("Internal error.", e1); } catch (InvocationTargetException e1) { Logger.getLogger(this.getClass()).debug("Internal error.", e1); } } else { throw new IOException("Failed to obtain remote example file."); } } | 13,258 |
0 | public static void main(String args[]) { URL url = null; try { url = new URL(urlString); } catch (MalformedURLException e) { System.err.println(e.toString()); System.exit(1); } try { InputStream ins = url.openStream(); BufferedReader breader = new BufferedReader(new InputStreamReader(ins)); String info = breader.readLine(); while (info != null) { System.out.println(info); info = breader.readLine(); } } catch (IOException e) { System.err.println(e.toString()); System.exit(1); } } | public void process(Group group, List resourcesName, List excludeResources, ServletContext servletContext, Writer out, String location) throws IOException { LOG.debug("Merging content of group : " + group.getName()); for (Iterator iterator = group.getSubgroups().iterator(); iterator.hasNext(); ) { Group subGroup = (Group) iterator.next(); String subLocation = subGroup.getBestLocation(location); ResourcesProcessor subGroupProcessor = null; if (subGroup.isMinimize() == null) subGroupProcessor = this; else subGroupProcessor = subGroup.getJSProcessor(); subGroupProcessor.process(subGroup, subGroup.getJsNames(), excludeResources, servletContext, out, subLocation); } for (Iterator it = resourcesName.iterator(); it.hasNext(); ) { URL url = null; String path = (String) it.next(); if (!excludeResources.contains(path)) { url = URLUtils.getLocalURL(path, servletContext); if (url == null) { String webPath = URLUtils.concatUrlWithSlaches(group.getBestLocation(location), path); url = URLUtils.getWebUrlResource(webPath); } if (url == null) { throw new IOException("The resources '" + path + "' could not be found neither in the webapp folder nor in a jar"); } InputStream in = null; try { in = url.openStream(); IOUtils.copy(in, out, URLUtils.DEFAULT_ENCODING); out.write("\n\n"); } catch (Exception e) { LOG.error("Merge failed for file " + path, e); } finally { if (in != null) in.close(); } excludeResources.add(path); } } } | 13,259 |
0 | public ProgramSymbol createNewProgramSymbol(int programID, String module, String symbol, int address, int size) throws AdaptationException { ProgramSymbol programSymbol = null; Connection connection = null; Statement statement = null; ResultSet resultSet = null; try { String query = "INSERT INTO ProgramSymbols " + "(programID, module, symbol, address, size)" + " VALUES (" + programID + ", '" + module + "', '" + symbol + "', " + address + ", " + size + ")"; connection = DriverManager.getConnection(CONN_STR); statement = connection.createStatement(); statement.executeUpdate(query); query = "SELECT * FROM ProgramSymbols WHERE " + "programID = " + programID + " AND " + "module = '" + module + "' AND " + "symbol = '" + symbol + "'"; resultSet = statement.executeQuery(query); if (!resultSet.next()) { connection.rollback(); String msg = "Attempt to create program symbol failed."; log.error(msg); throw new AdaptationException(msg); } programSymbol = getProgramSymbol(resultSet); connection.commit(); } catch (SQLException ex) { try { connection.rollback(); } catch (Exception e) { } String msg = "SQLException in createNewProgramSymbol"; log.error(msg, ex); throw new AdaptationException(msg, ex); } finally { try { resultSet.close(); } catch (Exception ex) { } try { statement.close(); } catch (Exception ex) { } try { connection.close(); } catch (Exception ex) { } } return programSymbol; } | public static int getUrl(final String s) { try { final URL url = new URL(s); final BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); int count = 0; String data = null; while ((data = reader.readLine()) != null) { System.out.printf("Results(%3d) of data: %s\n", count, data); ++count; } return count; } catch (Exception ex) { throw new RuntimeException(ex); } } | 13,260 |
1 | @Override public void createCopy(File sourceFile, File destinnationFile) throws IOException { FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destinnationFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | 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); } } | 13,261 |
1 | public static void loadConfig(DeviceEntry defaultDevice, EmulatorContext emulatorContext) { Config.defaultDevice = defaultDevice; Config.emulatorContext = emulatorContext; File configFile = new File(getConfigPath(), "config2.xml"); try { if (configFile.exists()) { loadConfigFile("config2.xml"); } else { configFile = new File(getConfigPath(), "config.xml"); if (configFile.exists()) { loadConfigFile("config.xml"); for (Enumeration e = getDeviceEntries().elements(); e.hasMoreElements(); ) { DeviceEntry entry = (DeviceEntry) e.nextElement(); if (!entry.canRemove()) { continue; } removeDeviceEntry(entry); File src = new File(getConfigPath(), entry.getFileName()); File dst = File.createTempFile("dev", ".jar", getConfigPath()); IOUtils.copyFile(src, dst); entry.setFileName(dst.getName()); addDeviceEntry(entry); } } else { createDefaultConfigXml(); } saveConfig(); } } catch (IOException ex) { Logger.error(ex); createDefaultConfigXml(); } finally { if (configXml == null) { createDefaultConfigXml(); } } urlsMRU.read(configXml.getChildOrNew("files").getChildOrNew("recent")); initSystemProperties(); } | public void copyHashAllFilesToDirectory(String baseDirStr, Hashtable newNamesTable, String destDirStr) throws Exception { if (baseDirStr.endsWith(sep)) { baseDirStr = baseDirStr.substring(0, baseDirStr.length() - 1); } if (destDirStr.endsWith(sep)) { destDirStr = destDirStr.substring(0, destDirStr.length() - 1); } FileUtils.getInstance().createDirectory(baseDirStr); if (null == newNamesTable) { newNamesTable = new Hashtable(); } BufferedInputStream in = null; BufferedOutputStream out = null; byte dataBuff[] = new byte[bufferSize]; File baseDir = new File(baseDirStr); baseDir.mkdirs(); if ((baseDir.exists()) && (baseDir.isDirectory())) { if (!newNamesTable.isEmpty()) { Enumeration enumFiles = newNamesTable.keys(); while (enumFiles.hasMoreElements()) { String newName = (String) enumFiles.nextElement(); String oldPathName = (String) newNamesTable.get(newName); if ((newName != null) && (!"".equals(newName)) && (oldPathName != null) && (!"".equals(oldPathName))) { String newPathFileName = destDirStr + sep + newName; String oldPathFileName = baseDirStr + sep + oldPathName; if (oldPathName.startsWith(sep)) { oldPathFileName = baseDirStr + oldPathName; } File f = new File(oldPathFileName); if ((f.exists()) && (f.isFile())) { in = new BufferedInputStream(new FileInputStream(oldPathFileName), bufferSize); out = new BufferedOutputStream(new FileOutputStream(newPathFileName), bufferSize); int readLen; while ((readLen = in.read(dataBuff)) > 0) { out.write(dataBuff, 0, readLen); } out.flush(); in.close(); out.close(); } else { } } } } else { } } else { throw new Exception("Base (baseDirStr) dir not exist !"); } } | 13,262 |
1 | protected static String getFileContentAsString(URL url, String encoding) throws IOException { InputStream input = null; StringWriter sw = new StringWriter(); try { System.out.println("Free mem :" + Runtime.getRuntime().freeMemory()); input = url.openStream(); IOUtils.copy(input, sw, encoding); System.out.println("Free mem :" + Runtime.getRuntime().freeMemory()); } finally { if (input != null) { input.close(); System.gc(); input = null; System.out.println("Free mem :" + Runtime.getRuntime().freeMemory()); } } return sw.toString(); } | protected void checkWeavingJar() throws IOException { OutputStream out = null; try { final File weaving = new File(getWeavingPath()); if (!weaving.exists()) { new File(getWeavingFolder()).mkdir(); weaving.createNewFile(); final Path src = new Path("weaving/openfrwk-weaving.jar"); final InputStream in = FileLocator.openStream(getBundle(), src, false); out = new FileOutputStream(getWeavingPath(), true); IOUtils.copy(in, out); Logger.log(Logger.INFO, "Put weaving jar at location " + weaving); } else { Logger.getLog().info("File openfrwk-weaving.jar already exists at " + weaving); } } catch (final SecurityException e) { Logger.log(Logger.ERROR, "[SECURITY EXCEPTION] Not enough privilegies to create " + "folder and copy NexOpen weaving jar at location " + getWeavingFolder()); Logger.logException(e); } finally { if (out != null) { out.flush(); out.close(); } } } | 13,263 |
0 | private String hashPassword(String password) { if (password != null && password.trim().length() > 0) { try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(password.trim().getBytes()); BigInteger hash = new BigInteger(1, md5.digest()); return hash.toString(16); } catch (NoSuchAlgorithmException nsae) { } } return null; } | public static String download(String address, String outputFolder) { URL url = null; String fileName = ""; try { url = new URL(address); System.err.println("Indirizzo valido!"); } catch (MalformedURLException ex) { System.err.println("Indirizzo non valido!"); } try { HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setRequestProperty("Range", "bytes=0-"); connection.connect(); int contentLength = connection.getContentLength(); if (contentLength < 1) { System.err.println("Errore, c'e' qualcosa che non va!"); return ""; } fileName = url.getFile(); fileName = fileName.substring(url.getFile().lastIndexOf('/') + 1); RandomAccessFile file = new RandomAccessFile(outputFolder + fileName, "rw"); file.seek(0); InputStream stream = connection.getInputStream(); byte[] buffer = new byte[1024]; while (true) { int read = stream.read(buffer); if (read == -1) { break; } file.write(buffer, 0, read); } file.close(); } catch (IOException ioe) { System.err.println("I/O error!"); } return outputFolder + fileName; } | 13,264 |
1 | public static String getTextFromUrl(final String url) throws IOException { final String lineSeparator = System.getProperty("line.separator"); InputStreamReader inputStreamReader = null; BufferedReader bufferedReader = null; try { final StringBuilder result = new StringBuilder(); inputStreamReader = new InputStreamReader(new URL(url).openStream()); bufferedReader = new BufferedReader(inputStreamReader); String line; while ((line = bufferedReader.readLine()) != null) { result.append(line).append(lineSeparator); } return result.toString(); } finally { InputOutputUtil.close(bufferedReader, inputStreamReader); } } | private ExamModel(URL urlQuestions) throws IOException, DataCoherencyException { BufferedReader in = new BufferedReader(new InputStreamReader(urlQuestions.openStream())); String line; questions = new ArrayList<Question>(); questionsMap = new HashMap<String, Question>(); in = new BufferedReader(new InputStreamReader(urlQuestions.openStream(), "UTF-8")); int questionNumber = 0; Question question; String questText = ""; String hash = ""; int lookingFor = ExamModel.READING_HASH; while ((line = in.readLine()) != null) { switch(lookingFor) { case ExamModel.READING_HASH: if (line.length() == 0 || line.trim().length() == 0) continue; hash = line; questionNumber++; lookingFor = ExamModel.READING_QUESTION; break; case ExamModel.READING_QUESTION: if (line.equals("--")) { question = new Question(questionNumber, hash, questText); questions.add(question); questionsMap.put(question.getHash(), question); questText = ""; hash = null; lookingFor = ExamModel.READING_HASH; } else { questText = questText.concat(line + Constants.nl); } break; default: throw new DataCoherencyException("Neočekávaný konec souboru!"); } } questions.trimToSize(); in.close(); } | 13,265 |
0 | 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); } } } | @SmallTest public void testSha1() throws Exception { MessageDigest digest = MessageDigest.getInstance("SHA-1"); int numTests = mTestData.length; for (int i = 0; i < numTests; i++) { digest.update(mTestData[i].input.getBytes()); byte[] hash = digest.digest(); String encodedHash = encodeHex(hash); assertEquals(encodedHash, mTestData[i].result); } } | 13,266 |
0 | private void processAlignmentsFromAlignmentSource(String name, Alignment reference, String alignmentSource) throws AlignmentParserException, IllegalArgumentException, KADMOSCMDException, IOException { if (alignmentSource == null) throw new IllegalArgumentException("alignmentSource is null"); URL url; String st; BufferedReader reader; Alignment alignment; try { try { alignment = parseAlignment(alignmentSource); addAlignmentWrapper(new AlignmentWrapper(name, reference, alignmentSource, alignment)); } catch (AlignmentParserException e1) { url = new URL(alignmentSource); reader = new BufferedReader(new InputStreamReader(url.openStream())); st = ""; while (((st = reader.readLine()) != null)) { alignment = parseAlignment(st); addAlignmentWrapper(new AlignmentWrapper(name, reference, alignmentSource, alignment)); } } } catch (Exception e1) { File itemFile = new File(alignmentSource); if (itemFile.exists()) { if (itemFile.isDirectory() && !itemFile.isHidden()) { File[] files = itemFile.listFiles(); for (int i = 0; i < files.length; i++) { if (files[i].isFile() && !files[i].isHidden()) { processAlignmentsFromAlignmentSource(name, reference, files[i].getPath()); } else if (files[i].isDirectory() && !files[i].isHidden() && deepScan) { processAlignmentsFromAlignmentSource(name, reference, files[i].getPath()); } } } else if (itemFile.isFile() && !itemFile.isHidden()) { try { alignment = parseAlignment(alignmentSource); addAlignmentWrapper(new AlignmentWrapper(name, reference, alignmentSource, alignment)); } catch (Exception e2) { reader = new BufferedReader(new FileReader(alignmentSource)); st = ""; while (((st = reader.readLine()) != null)) { alignment = parseAlignment(st); addAlignmentWrapper(new AlignmentWrapper(name, reference, st, alignment)); } } } else { throw new FileNotFoundException("File " + alignmentSource + " is neither directory nor file, or it is hidden."); } } else { throw new FileNotFoundException("File " + alignmentSource + " does not exists."); } } } | public final String hashRealmPassword(String username, String realm, String password) throws GeneralSecurityException { MessageDigest md = null; md = MessageDigest.getInstance("MD5"); md.update(username.getBytes()); md.update(":".getBytes()); md.update(realm.getBytes()); md.update(":".getBytes()); md.update(password.getBytes()); byte[] hash = md.digest(); return toHex(hash, hash.length); } | 13,267 |
1 | public static String getMD5Str(String str) { MessageDigest messageDigest = null; try { messageDigest = MessageDigest.getInstance("MD5"); messageDigest.reset(); messageDigest.update(str.getBytes("UTF-8")); } catch (NoSuchAlgorithmException e) { System.out.println("NoSuchAlgorithmException caught!"); System.exit(-1); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } byte[] byteArray = messageDigest.digest(); StringBuffer md5StrBuff = new StringBuffer(); for (int i = 0; i < byteArray.length; i++) { if (Integer.toHexString(0xFF & byteArray[i]).length() == 1) md5StrBuff.append("0").append(Integer.toHexString(0xFF & byteArray[i])); else md5StrBuff.append(Integer.toHexString(0xFF & byteArray[i])); } return md5StrBuff.substring(8, 24).toString().toUpperCase(); } | @Override public String getMD5(String host) { String res = ""; Double randNumber = Math.random() + System.currentTimeMillis(); try { MessageDigest algorithm = MessageDigest.getInstance("MD5"); algorithm.reset(); algorithm.update(randNumber.toString().getBytes()); byte[] md5 = algorithm.digest(); String tmp = ""; for (int i = 0; i < md5.length; i++) { tmp = (Integer.toHexString(0xFF & md5[i])); if (tmp.length() == 1) { res += "0" + tmp; } else { res += tmp; } } } catch (Exception ex) { } return res; } | 13,268 |
1 | private void output(HttpServletResponse resp, InputStream is, long length, String fileName) throws Exception { resp.reset(); String mimeType = "image/jpeg"; resp.setContentType(mimeType); resp.setContentLength((int) length); resp.setHeader("Content-Disposition", "inline; filename=\"" + fileName + "\""); resp.setHeader("Cache-Control", "must-revalidate"); ServletOutputStream sout = resp.getOutputStream(); IOUtils.copy(is, sout); sout.flush(); resp.flushBuffer(); } | @RequestMapping(value = "/image/{fileName}", method = RequestMethod.GET) public void getImage(@PathVariable String fileName, HttpServletRequest req, HttpServletResponse res) throws Exception { File file = new File(STORAGE_PATH + fileName + ".jpg"); res.setHeader("Cache-Control", "no-store"); res.setHeader("Pragma", "no-cache"); res.setDateHeader("Expires", 0); res.setContentType("image/jpg"); ServletOutputStream ostream = res.getOutputStream(); IOUtils.copy(new FileInputStream(file), ostream); ostream.flush(); ostream.close(); } | 13,269 |
0 | 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(); } | private static void loadQueryProcessorFactories() { qpFactoryMap = new HashMap<String, QueryProcessorFactoryIF>(); Enumeration<URL> resources = null; try { resources = QueryUtils.class.getClassLoader().getResources(RESOURCE_STRING); } catch (IOException e) { log.error("Error while trying to look for " + "QueryProcessorFactoryIF implementations.", e); } while (resources != null && resources.hasMoreElements()) { URL url = resources.nextElement(); InputStream is = null; try { is = url.openStream(); } catch (IOException e) { log.warn("Error opening stream to QueryProcessorFactoryIF service description.", e); } if (is != null) { BufferedReader rdr = new BufferedReader(new InputStreamReader(is)); String line; try { while ((line = rdr.readLine()) != null) { try { ClassLoader classLoader = Thread.currentThread().getContextClassLoader(); Class<?> c = Class.forName(line, true, classLoader); if (QueryProcessorFactoryIF.class.isAssignableFrom(c)) { QueryProcessorFactoryIF factory = (QueryProcessorFactoryIF) c.newInstance(); qpFactoryMap.put(factory.getQueryLanguage().toUpperCase(), factory); } else { log.warn("Wrong entry for QueryProcessorFactoryIF service " + "description, '" + line + "' is not implementing the " + "correct interface."); } } catch (Exception e) { log.warn("Could not create an instance for " + "QueryProcessorFactoryIF service '" + line + "'."); } } } catch (IOException e) { log.warn("Could not read from QueryProcessorFactoryIF " + "service descriptor.", e); } } } if (!qpFactoryMap.containsKey(DEFAULT_LANGUAGE)) { qpFactoryMap.put(DEFAULT_LANGUAGE, new TologQueryProcessorFactory()); } } | 13,270 |
1 | private void checkRoundtrip(byte[] content) throws Exception { InputStream in = new ByteArrayInputStream(content); ByteArrayOutputStream out = new ByteArrayOutputStream(); CodecUtil.encodeQuotedPrintableBinary(in, out); in = new QuotedPrintableInputStream(new ByteArrayInputStream(out.toByteArray())); out = new ByteArrayOutputStream(); IOUtils.copy(in, out); assertEquals(content, out.toByteArray()); } | public static void copyFile(File srcFile, File destFolder) { try { File destFile = new File(destFolder, srcFile.getName()); if (destFile.exists()) { throw new BuildException("Could not copy " + srcFile + " to " + destFolder + " as " + destFile + " already exists"); } FileChannel srcChannel = null; FileChannel destChannel = null; try { srcChannel = new FileInputStream(srcFile).getChannel(); destChannel = new FileOutputStream(destFile).getChannel(); destChannel.transferFrom(srcChannel, 0, srcChannel.size()); } finally { if (srcChannel != null) { srcChannel.close(); } if (destChannel != null) { destChannel.close(); } } destFile.setLastModified((srcFile.lastModified())); } catch (IOException e) { throw new BuildException("Could not copy " + srcFile + " to " + destFolder + ": " + e, e); } } | 13,271 |
0 | private boolean serverOK(String serverAddress, String serverPort) { boolean status = false; String serverString = serverAddress + ":" + serverPort + MolConvertInNodeModel.SERVER_WSDL_PATH; System.out.println("connecting to " + serverString + "..."); try { java.net.URL url = new java.net.URL(serverString); try { java.net.HttpURLConnection connection = (java.net.HttpURLConnection) url.openConnection(); status = readContents(connection); if (status) { JOptionPane.showMessageDialog(this.getPanel(), "Connection to Server is OK"); } } catch (Exception connEx) { JOptionPane.showMessageDialog(this.getPanel(), connEx.getMessage()); logger.error(connEx.getMessage()); } } catch (java.net.MalformedURLException urlEx) { JOptionPane.showMessageDialog(this.getPanel(), urlEx.getMessage()); logger.error(urlEx.getMessage()); } return status; } | public static byte[] encode(String origin, String algorithm) throws NoSuchAlgorithmException { String resultStr = null; resultStr = new String(origin); MessageDigest md = MessageDigest.getInstance(algorithm); md.update(resultStr.getBytes()); return md.digest(); } | 13,272 |
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 void xtestFile1() throws Exception { InputStream inputStream = new FileInputStream(IOTest.FILE); OutputStream outputStream = new FileOutputStream("C:/Temp/testFile1.mp4"); IOUtils.copy(inputStream, outputStream); inputStream.close(); outputStream.close(); } | 13,273 |
1 | public static void copyFile3(File srcFile, File destFile) throws IOException { InputStream in = new FileInputStream(srcFile); OutputStream out = new FileOutputStream(destFile); byte[] buf = new byte[1024]; int len; while((len = in.read(buf)) > 0) { out.write(buf, 0, len); } in.close(); out.close(); } | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | 13,274 |
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.B64InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | 13,275 |
0 | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | public static String generateToken(ClientInfo clientInfo) { try { MessageDigest md5 = MessageDigest.getInstance("MD5"); Random rand = new Random(); String random = clientInfo.getIpAddress() + ":" + clientInfo.getPort() + ":" + rand.nextInt(); md5.update(random.getBytes()); String token = toHexString(md5.digest((new Date()).toString().getBytes())); clientInfo.setToken(token); return token; } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return null; } | 13,276 |
0 | public ActionForward dbExecute(ActionMapping pMapping, ActionForm pForm, HttpServletRequest pRequest, HttpServletResponse pResponse) throws DatabaseException { String email = pRequest.getParameter("email"); MessageDigest md; try { md = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException e) { throw new DatabaseException("Could not hash password for storage: no such algorithm"); } md.update(pRequest.getParameter("password").getBytes()); String password = (new BASE64Encoder()).encode(md.digest()); String remember = pRequest.getParameter("rememberLogin"); User user = database.acquireUserByEmail(email); if (user == null || user.equals(User.anonymous()) || !user.getActive()) { return pMapping.findForward("invalid"); } else if (user.getPassword().equals(password)) { pRequest.getSession().setAttribute("login", user); if (remember != null) { Cookie usercookie = new Cookie("bib.username", email); Cookie passcookie = new Cookie("bib.password", password.toString()); usercookie.setPath("/"); passcookie.setPath("/"); usercookie.setMaxAge(60 * 60 * 24 * 365); passcookie.setMaxAge(60 * 60 * 24 * 365); pResponse.addCookie(usercookie); pResponse.addCookie(passcookie); } return pMapping.findForward("success"); } else { return pMapping.findForward("invalid"); } } | private static void executeDBPatchFile() throws Exception { Connection con = null; PreparedStatement pre_stmt = null; ResultSet rs = null; try { InputStream is = null; URL url = new URL("http://www.hdd-player.de/umc/UMC-DB-Update-Script.sql"); is = url.openStream(); BufferedReader br = new BufferedReader(new InputStreamReader(is)); Class.forName("org.sqlite.JDBC"); con = DriverManager.getConnection("jdbc:sqlite:database/umc.db", "", ""); double dbVersion = -1; pre_stmt = con.prepareStatement("SELECT * FROM DB_VERSION WHERE ID_MODUL = 0"); rs = pre_stmt.executeQuery(); if (rs.next()) { dbVersion = rs.getDouble("VERSION"); } String line = ""; con.setAutoCommit(false); boolean collectSQL = false; ArrayList<String> sqls = new ArrayList<String>(); double patchVersion = 0; while ((line = br.readLine()) != null) { if (line.startsWith("[")) { Pattern p = Pattern.compile("\\[.*\\]"); Matcher m = p.matcher(line); m.find(); String value = m.group(); value = value.substring(1, value.length() - 1); patchVersion = Double.parseDouble(value); } if (patchVersion == dbVersion + 1) collectSQL = true; if (collectSQL) { if (!line.equals("") && !line.startsWith("[") && !line.startsWith("--") && !line.contains("--")) { if (line.endsWith(";")) line = line.substring(0, line.length() - 1); sqls.add(line); } } } if (pre_stmt != null) pre_stmt.close(); if (rs != null) rs.close(); for (String sql : sqls) { log.debug("Führe SQL aus Patch Datei aus: " + sql); pre_stmt = con.prepareStatement(sql); pre_stmt.execute(); } if (patchVersion > 0) { log.debug("aktualisiere Versionsnummer in DB"); if (pre_stmt != null) pre_stmt.close(); if (rs != null) rs.close(); pre_stmt = con.prepareStatement("UPDATE DB_VERSION SET VERSION = ? WHERE ID_MODUL = 0"); pre_stmt.setDouble(1, patchVersion); pre_stmt.execute(); } con.commit(); } catch (MalformedURLException exc) { log.error(exc.toString()); throw new Exception("SQL Patch Datei konnte nicht online gefunden werden", exc); } catch (IOException exc) { log.error(exc.toString()); throw new Exception("SQL Patch Datei konnte nicht gelesen werden", exc); } catch (Throwable exc) { log.error("Fehler bei Ausführung der SQL Patch Datei", exc); try { con.rollback(); } catch (SQLException exc1) { } throw new Exception("SQL Patch Datei konnte nicht ausgeführt werden", exc); } finally { try { if (pre_stmt != null) pre_stmt.close(); if (con != null) con.close(); } catch (SQLException exc2) { log.error("Fehler bei Ausführung von SQL Patch Datei", exc2); } } } | 13,277 |
1 | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public File createFileFromClasspathResource(String resourceUrl) throws IOException { File fichierTest = File.createTempFile("xmlFieldTestFile", ""); FileOutputStream fos = new FileOutputStream(fichierTest); InputStream is = XmlFieldDomSelectorTest.class.getResourceAsStream(resourceUrl); IOUtils.copy(is, fos); is.close(); fos.close(); return fichierTest; } | 13,278 |
1 | public static void copyFile(String fromFile, String toFile) { FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } | public File takeFile(File f, String prefix, String suffix) throws IOException { File nf = createNewFile(prefix, suffix); FileInputStream fis = new FileInputStream(f); FileChannel fic = fis.getChannel(); FileOutputStream fos = new FileOutputStream(nf); FileChannel foc = fos.getChannel(); foc.transferFrom(fic, 0, fic.size()); foc.close(); fic.close(); f.delete(); return nf; } | 13,279 |
0 | public static String SHA512(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-512"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("UTF-8"), 0, text.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | 13,280 |
0 | public void delete(String language, String tag, int row) throws FidoDatabaseException { try { Connection conn = null; Statement stmt = null; try { String sql = "delete from LanguageMorphologies " + "where LanguageName = '" + language + "' and MorphologyTag = '" + tag + "' and " + " Rank = " + row; conn = fido.util.FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); stmt.executeUpdate(sql); bumpAllRowsUp(stmt, language, tag, row); conn.commit(); } catch (SQLException e) { if (conn != null) conn.rollback(); throw e; } finally { if (stmt != null) stmt.close(); if (conn != null) conn.close(); } } catch (SQLException e) { throw new FidoDatabaseException(e); } } | public DataSet guessAtUnknowns(String filename) { TasselFileType guess = TasselFileType.Sequence; DataSet tds = null; try { BufferedReader br = null; if (filename.startsWith("http")) { URL url = new URL(filename); br = new BufferedReader(new InputStreamReader(url.openStream())); } else { br = new BufferedReader(new FileReader(filename)); } String line1 = br.readLine().trim(); String[] sval1 = line1.split("\\s"); String line2 = br.readLine().trim(); String[] sval2 = line2.split("\\s"); boolean lociMatchNumber = false; if (!sval1[0].startsWith("<") && (sval1.length == 2) && (line1.indexOf(':') < 0)) { int countLoci = Integer.parseInt(sval1[1]); if (countLoci == sval2.length) { lociMatchNumber = true; } } if (sval1[0].equalsIgnoreCase("<Annotated>")) { guess = TasselFileType.Annotated; } else if (line1.startsWith("<") || line1.startsWith("#")) { boolean isTrait = false; boolean isMarker = false; boolean isNumeric = false; boolean isMap = false; Pattern tagPattern = Pattern.compile("[<>\\s]+"); String[] info1 = tagPattern.split(line1); String[] info2 = tagPattern.split(line2); if (info1.length > 1) { if (info1[1].toUpperCase().startsWith("MARKER")) { isMarker = true; } else if (info1[1].toUpperCase().startsWith("TRAIT")) { isTrait = true; } else if (info1[1].toUpperCase().startsWith("NUMER")) { isNumeric = true; } else if (info1[1].toUpperCase().startsWith("MAP")) { isMap = true; } } if (info2.length > 1) { if (info2[1].toUpperCase().startsWith("MARKER")) { isMarker = true; } else if (info2[1].toUpperCase().startsWith("TRAIT")) { isTrait = true; } else if (info2[1].toUpperCase().startsWith("NUMER")) { isNumeric = true; } else if (info2[1].toUpperCase().startsWith("MAP")) { isMap = true; } } else { guess = null; String inline = br.readLine(); while (guess == null && inline != null && (inline.startsWith("#") || inline.startsWith("<"))) { if (inline.startsWith("<")) { String[] info = tagPattern.split(inline); if (info[1].toUpperCase().startsWith("MARKER")) { isMarker = true; } else if (info[1].toUpperCase().startsWith("TRAIT")) { isTrait = true; } else if (info[1].toUpperCase().startsWith("NUMER")) { isNumeric = true; } else if (info[1].toUpperCase().startsWith("MAP")) { isMap = true; } } } } if (isTrait || (isMarker && isNumeric)) { guess = TasselFileType.Phenotype; } else if (isMarker) { guess = TasselFileType.Polymorphism; } else if (isMap) { guess = TasselFileType.GeneticMap; } else { throw new IOException("Improperly formatted header. Data will not be imported."); } } else if ((line1.startsWith(">")) || (line1.startsWith(";"))) { guess = TasselFileType.Fasta; } else if (sval1.length == 1) { guess = TasselFileType.SqrMatrix; } else if (line1.indexOf(':') > 0) { guess = TasselFileType.Polymorphism; } else if ((sval1.length == 2) && (lociMatchNumber)) { guess = TasselFileType.Polymorphism; } else if ((line1.startsWith("#Nexus")) || (line1.startsWith("#NEXUS")) || (line1.startsWith("CLUSTAL")) || ((sval1.length == 2) && (sval2.length == 2))) { guess = TasselFileType.Sequence; } else if (sval1.length == 3) { guess = TasselFileType.Numerical; } myLogger.info("guessAtUnknowns: type: " + guess); tds = processDatum(filename, guess); br.close(); } catch (Exception e) { } return tds; } | 13,281 |
0 | public static void main(String[] args) throws IOException { httpclient = new DefaultHttpClient(); httpclient.getParams().setParameter(CoreProtocolPNames.PROTOCOL_VERSION, HttpVersion.HTTP_1_1); loginLocalhostr(); initialize(); HttpOptions httpoptions = new HttpOptions(localhostrurl); HttpResponse myresponse = httpclient.execute(httpoptions); HttpEntity myresEntity = myresponse.getEntity(); System.out.println(EntityUtils.toString(myresEntity)); fileUpload(); } | public static String hash(String plainTextPwd) { MessageDigest hashAlgo; try { hashAlgo = java.security.MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new QwickException(e); } hashAlgo.update(plainTextPwd.getBytes()); return new String(hashAlgo.digest()); } | 13,282 |
1 | public void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { try { String act = request.getParameter("act"); if (null == act) { } else if ("down".equalsIgnoreCase(act)) { String vest = request.getParameter("vest"); String id = request.getParameter("id"); if (null == vest) { t_attach_Form attach = null; t_attach_QueryMap query = new t_attach_QueryMap(); attach = query.getByID(id); if (null != attach) { String filename = attach.getAttach_name(); String fullname = attach.getAttach_fullname(); response.addHeader("Content-Disposition", "attachment;filename=" + filename + ""); File file = new File(fullname); if (file.exists()) { java.io.FileInputStream in = new FileInputStream(file); org.apache.commons.io.IOUtils.copy(in, response.getOutputStream()); } } } else if ("review".equalsIgnoreCase(vest)) { t_infor_review_QueryMap reviewQuery = new t_infor_review_QueryMap(); t_infor_review_Form review = reviewQuery.getByID(id); String seq = request.getParameter("seq"); String name = null, fullname = null; if ("1".equals(seq)) { name = review.getAttachname1(); fullname = review.getAttachfullname1(); } else if ("2".equals(seq)) { name = review.getAttachname2(); fullname = review.getAttachfullname2(); } else if ("3".equals(seq)) { name = review.getAttachname3(); fullname = review.getAttachfullname3(); } String downTypeStr = DownType.getInst().getDownTypeByFileName(name); logger.debug("filename=" + name + " downtype=" + downTypeStr); response.setContentType(downTypeStr); response.addHeader("Content-Disposition", "attachment;filename=" + name + ""); File file = new File(fullname); if (file.exists()) { java.io.FileInputStream in = new FileInputStream(file); org.apache.commons.io.IOUtils.copy(in, response.getOutputStream()); in.close(); } } } else if ("upload".equalsIgnoreCase(act)) { String infoId = request.getParameter("inforId"); logger.debug("infoId=" + infoId); } } catch (Exception e) { } } | public static void copyFile(File fromFile, File toFile) throws OWFileCopyException { try { FileChannel src = new FileInputStream(fromFile).getChannel(); FileChannel dest = new FileOutputStream(toFile).getChannel(); dest.transferFrom(src, 0, src.size()); src.close(); dest.close(); } catch (IOException e) { throw (new OWFileCopyException("An error occurred while copying a file", e)); } } | 13,283 |
1 | private void copyFile(File src_file, File dest_file) { InputStream src_stream = null; OutputStream dest_stream = null; try { int b; src_stream = new BufferedInputStream(new FileInputStream(src_file)); dest_stream = new BufferedOutputStream(new FileOutputStream(dest_file)); while ((b = src_stream.read()) != -1) dest_stream.write(b); } catch (Exception e) { XRepository.getLogger().warning(this, "Error on copying the plugin file!"); XRepository.getLogger().warning(this, e); } finally { try { src_stream.close(); dest_stream.close(); } catch (Exception ex2) { } } } | private static String getSummaryText(File packageFile) { String retVal = null; Reader in = null; try { in = new FileReader(packageFile); StringWriter out = new StringWriter(); IOUtils.copy(in, out); StringBuffer buf = out.getBuffer(); int pos1 = buf.indexOf("<body>"); int pos2 = buf.lastIndexOf("</body>"); if (pos1 >= 0 && pos1 < pos2) { retVal = buf.substring(pos1 + 6, pos2); } else { retVal = ""; } } catch (FileNotFoundException e) { LOG.error(e.getMessage(), e); } catch (IOException e) { LOG.error(e.getMessage(), e); } finally { if (in != null) { try { in.close(); } catch (IOException e) { LOG.error(e.getMessage(), e); } } } return retVal; } | 13,284 |
0 | @SuppressWarnings("unchecked") public static void createInstance(ExternProtoDeclare externProtoDeclare) { ExternProtoDeclareImport epdi = new ExternProtoDeclareImport(); HashMap<String, ProtoDeclareImport> protoMap = X3DImport.getTheImport().getCurrentParser().getProtoMap(); boolean loadedFromWeb = false; File f = null; URL url = null; List<String> urls = externProtoDeclare.getUrl(); String tmpUrls = urls.toString(); urls = Util.splitStringToListOfStrings(tmpUrls); String protoName = null; int urlCount = urls.size(); for (int urlIndex = 0; urlIndex < urlCount; urlIndex++) { try { String path = urls.get(urlIndex); if (path.startsWith("\"") && path.endsWith("\"")) path = path.substring(1, path.length() - 1); int hashMarkPos = path.indexOf("#"); int urlLength = path.length(); if (hashMarkPos == -1) path = path.substring(0, urlLength); else { protoName = path.substring(hashMarkPos + 1, urlLength); path = path.substring(0, hashMarkPos); } if (path.toLowerCase().startsWith("http://")) { String filename = path.substring(path.lastIndexOf("/") + 1, path.lastIndexOf(".")); String fileext = path.substring(path.lastIndexOf("."), path.length()); f = File.createTempFile(filename, fileext); url = new URL(path); InputStream is = url.openStream(); FileOutputStream os = new FileOutputStream(f); byte[] buffer = new byte[0xFFFF]; for (int len; (len = is.read(buffer)) != -1; ) os.write(buffer, 0, len); is.close(); os.close(); url = f.toURI().toURL(); loadedFromWeb = true; } else { if (path.startsWith("/") || (path.charAt(1) == ':')) { } else { File x3dfile = X3DImport.getTheImport().getCurrentParser().getFile(); path = Util.getRealPath(x3dfile) + path; } f = new File(path); url = f.toURI().toURL(); Object testContent = url.getContent(); if (testContent == null) continue; loadedFromWeb = false; } X3DDocument x3dDocument = null; try { x3dDocument = X3DDocument.Factory.parse(f); } catch (XmlException e) { e.printStackTrace(); return; } catch (IOException e) { e.printStackTrace(); return; } Scene scene = x3dDocument.getX3D().getScene(); ProtoDeclare[] protos = scene.getProtoDeclareArray(); ProtoDeclare protoDeclare = null; if (protoName == null) { protoDeclare = protos[0]; } else { for (ProtoDeclare proto : protos) { if (proto.getName().equals(protoName)) { protoDeclare = proto; break; } } } if (protoDeclare == null) continue; ProtoBody protoBody = protoDeclare.getProtoBody(); epdi.protoBody = protoBody; protoMap.put(externProtoDeclare.getName(), epdi); break; } catch (MalformedURLException e) { } catch (IOException e) { } finally { if (loadedFromWeb && f != null) { f.delete(); } } } } | public static String remove_tag(String sessionid, String absolutePathForTheSpesificTag) { String resultJsonString = "some problem existed inside the create_new_tag() function if you see this string"; try { Log.d("current running function name:", "remove_tag"); HttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost("https://mt0-app.cloud.cm/rpc/json"); List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(2); nameValuePairs.add(new BasicNameValuePair("c", "Storage")); nameValuePairs.add(new BasicNameValuePair("m", "remove_tag")); nameValuePairs.add(new BasicNameValuePair("absolute_tags", absolutePathForTheSpesificTag)); httppost.setEntity(new UrlEncodedFormEntity(nameValuePairs)); httppost.setHeader("Cookie", "PHPSESSID=" + sessionid); HttpResponse response = httpclient.execute(httppost); resultJsonString = EntityUtils.toString(response.getEntity()); Log.d("jsonStringReturned:", resultJsonString); return resultJsonString; } catch (Exception e) { e.printStackTrace(); } return resultJsonString; } | 13,285 |
0 | public void processDeleteCompany(Company companyBean, AuthSession authSession) { if (authSession == null) { return; } DatabaseAdapter dbDyn = null; PreparedStatement ps = null; try { dbDyn = DatabaseAdapter.getInstance(); if (companyBean.getId() == null) throw new IllegalArgumentException("companyId is null"); String sql = "update WM_LIST_COMPANY set is_deleted = 1 " + "where ID_FIRM = ? and ID_FIRM in "; switch(dbDyn.getFamaly()) { case DatabaseManager.MYSQL_FAMALY: String idList = authSession.getGrantedCompanyId(); sql += " (" + idList + ") "; break; default: sql += "(select z1.ID_FIRM from v$_read_list_firm z1 where z1.user_login = ?)"; break; } ps = dbDyn.prepareStatement(sql); RsetTools.setLong(ps, 1, companyBean.getId()); switch(dbDyn.getFamaly()) { case DatabaseManager.MYSQL_FAMALY: break; default: ps.setString(2, authSession.getUserLogin()); break; } int i1 = ps.executeUpdate(); if (log.isDebugEnabled()) log.debug("Count of deleted records - " + i1); dbDyn.commit(); } catch (Exception e) { try { if (dbDyn != null) dbDyn.rollback(); } catch (Exception e001) { } String es = "Error delete company"; log.error(es, e); throw new IllegalStateException(es, e); } finally { DatabaseManager.close(dbDyn, ps); dbDyn = null; ps = null; } } | public static byte[] decrypt(byte[] ciphertext, byte[] key) throws IOException { CryptInputStream in = new CryptInputStream(new ByteArrayInputStream(ciphertext), new SerpentEngine(), key); ByteArrayOutputStream bout = new ByteArrayOutputStream(); IOUtils.copy(in, bout); return bout.toByteArray(); } | 13,286 |
1 | private static void copyFile(File source, File destination) throws IOException, SecurityException { if (!destination.exists()) destination.createNewFile(); FileChannel sourceChannel = null; FileChannel destinationChannel = null; try { sourceChannel = new FileInputStream(source).getChannel(); destinationChannel = new FileOutputStream(destination).getChannel(); long count = 0; long size = sourceChannel.size(); while ((count += destinationChannel.transferFrom(sourceChannel, 0, size - count)) < size) ; } finally { if (sourceChannel != null) sourceChannel.close(); if (destinationChannel != null) destinationChannel.close(); } } | private void copyFile(File file, File targetFile) { try { BufferedInputStream bis = new BufferedInputStream(new FileInputStream(file)); BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(targetFile)); byte[] tmp = new byte[8192]; int read = -1; while ((read = bis.read(tmp)) > 0) { bos.write(tmp, 0, read); } bis.close(); bos.close(); } catch (Exception e) { if (!targetFile.delete()) { System.err.println("Ups, created copy cant be deleted (" + targetFile.getAbsolutePath() + ")"); } } } | 13,287 |
0 | private File downloadPDB(String pdbId) { File tempFile = new File(path + "/" + pdbId + ".pdb.gz"); File pdbHome = new File(path); if (!pdbHome.canWrite()) { System.err.println("can not write to " + pdbHome); return null; } String ftp = String.format("ftp://ftp.ebi.ac.uk/pub/databases/msd/pdb_uncompressed/pdb%s.ent", pdbId.toLowerCase()); System.out.println("Fetching " + ftp); try { URL url = new URL(ftp); InputStream conn = url.openStream(); System.out.println("writing to " + tempFile); FileOutputStream outPut = new FileOutputStream(tempFile); GZIPOutputStream gzOutPut = new GZIPOutputStream(outPut); PrintWriter pw = new PrintWriter(gzOutPut); BufferedReader fileBuffer = new BufferedReader(new InputStreamReader(conn)); String line; while ((line = fileBuffer.readLine()) != null) { pw.println(line); } pw.flush(); pw.close(); outPut.close(); conn.close(); } catch (Exception e) { e.printStackTrace(); return null; } return tempFile; } | public Atividade insertAtividade(Atividade atividade) throws SQLException { Connection conn = null; String insert = "insert into Atividade (idatividade, requerente_idrequerente, datacriacao, datatermino, valor, tipoatividade, descricao, fase_idfase, estado) " + "values " + "(nextval('seq_atividade'), " + atividade.getRequerente().getIdRequerente() + ", " + "'" + atividade.getDataCriacao() + "', '" + atividade.getDataTermino() + "', '" + atividade.getValor() + "', '" + atividade.getTipoAtividade().getIdTipoAtividade() + "', '" + atividade.getDescricao() + "', " + atividade.getFaseIdFase() + ", " + atividade.getEstado() + ")"; try { conn = connectionFactory.getConnection(true); conn.setAutoCommit(false); Statement stmt = conn.createStatement(); Integer result = stmt.executeUpdate(insert); if (result == 1) { String sqlSelect = "select last_value from seq_atividade"; ResultSet rs = stmt.executeQuery(sqlSelect); while (rs.next()) { atividade.setIdAtividade(rs.getInt("last_value")); } } conn.commit(); } catch (SQLException e) { conn.rollback(); throw e; } finally { conn.close(); } return null; } | 13,288 |
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); } } | protected void doProxyInternally(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException { HttpRequestBase proxyReq = buildProxyRequest(req); URI reqUri = proxyReq.getURI(); String cookieDomain = reqUri.getHost(); DefaultHttpClient httpClient = new DefaultHttpClient(); HttpContext httpContext = new BasicHttpContext(); httpContext.setAttribute("org.atricorel.idbus.kernel.main.binding.http.HttpServletRequest", req); int intIdx = 0; for (int i = 0; i < httpClient.getRequestInterceptorCount(); i++) { if (httpClient.getRequestInterceptor(i) instanceof RequestAddCookies) { intIdx = i; break; } } IDBusRequestAddCookies interceptor = new IDBusRequestAddCookies(cookieDomain); httpClient.removeRequestInterceptorByClass(RequestAddCookies.class); httpClient.addRequestInterceptor(interceptor, intIdx); httpClient.getParams().setParameter(ClientPNames.HANDLE_REDIRECTS, false); httpClient.getParams().setParameter(ClientPNames.COOKIE_POLICY, CookiePolicy.BROWSER_COMPATIBILITY); if (logger.isTraceEnabled()) logger.trace("Staring to follow redirects for " + req.getPathInfo()); HttpResponse proxyRes = null; List<Header> storedHeaders = new ArrayList<Header>(40); boolean followTargetUrl = true; byte[] buff = new byte[1024]; while (followTargetUrl) { if (logger.isTraceEnabled()) logger.trace("Sending internal request " + proxyReq); proxyRes = httpClient.execute(proxyReq, httpContext); String targetUrl = null; Header[] headers = proxyRes.getAllHeaders(); for (Header header : headers) { if (header.getName().equals("Server")) continue; if (header.getName().equals("Transfer-Encoding")) continue; if (header.getName().equals("Location")) continue; if (header.getName().equals("Expires")) continue; if (header.getName().equals("Content-Length")) continue; if (header.getName().equals("Content-Type")) continue; storedHeaders.add(header); } if (logger.isTraceEnabled()) logger.trace("HTTP/STATUS:" + proxyRes.getStatusLine().getStatusCode() + "[" + proxyReq + "]"); switch(proxyRes.getStatusLine().getStatusCode()) { case 200: followTargetUrl = false; break; case 404: followTargetUrl = false; break; case 500: followTargetUrl = false; break; case 302: Header location = proxyRes.getFirstHeader("Location"); targetUrl = location.getValue(); if (!internalProcessingPolicy.match(req, targetUrl)) { if (logger.isTraceEnabled()) logger.trace("Do not follow HTTP 302 to [" + location.getValue() + "]"); Collections.addAll(storedHeaders, proxyRes.getHeaders("Location")); followTargetUrl = false; } else { if (logger.isTraceEnabled()) logger.trace("Do follow HTTP 302 to [" + location.getValue() + "]"); followTargetUrl = true; } break; default: followTargetUrl = false; break; } HttpEntity entity = proxyRes.getEntity(); if (entity != null) { InputStream instream = entity.getContent(); try { if (!followTargetUrl) { for (Header header : headers) { if (header.getName().equals("Content-Type")) res.setHeader(header.getName(), header.getValue()); if (header.getName().equals("Content-Length")) res.setHeader(header.getName(), header.getValue()); } res.setStatus(proxyRes.getStatusLine().getStatusCode()); for (Header header : storedHeaders) { if (header.getName().startsWith("Set-Cookie")) res.addHeader(header.getName(), header.getValue()); else res.setHeader(header.getName(), header.getValue()); } IOUtils.copy(instream, res.getOutputStream()); res.getOutputStream().flush(); } else { int r = instream.read(buff); int total = r; while (r > 0) { r = instream.read(buff); total += r; } if (total > 0) logger.warn("Ignoring response content size : " + total); } } catch (IOException ex) { throw ex; } catch (RuntimeException ex) { proxyReq.abort(); throw ex; } finally { try { instream.close(); } catch (Exception ignore) { } } } else { if (!followTargetUrl) { res.setStatus(proxyRes.getStatusLine().getStatusCode()); for (Header header : headers) { if (header.getName().equals("Content-Type")) res.setHeader(header.getName(), header.getValue()); if (header.getName().equals("Content-Length")) res.setHeader(header.getName(), header.getValue()); } for (Header header : storedHeaders) { if (header.getName().startsWith("Set-Cookie")) res.addHeader(header.getName(), header.getValue()); else res.setHeader(header.getName(), header.getValue()); } } } if (followTargetUrl) { proxyReq = buildProxyRequest(targetUrl); httpContext = null; } } if (logger.isTraceEnabled()) logger.trace("Ended following redirects for " + req.getPathInfo()); } | 13,289 |
1 | public static void main(String[] args) throws Exception { if (args.length != 2) { System.out.println("arguments: sourcefile destfile"); System.exit(1); } FileChannel in = new FileInputStream(args[0]).getChannel(), out = new FileOutputStream(args[1]).getChannel(); in.transferTo(0, in.size(), out); } | private void process(String zipFileName, String directory, String db) throws SQLException { InputStream in = null; try { if (!FileUtils.exists(zipFileName)) { throw new IOException("File not found: " + zipFileName); } String originalDbName = null; int originalDbLen = 0; if (db != null) { originalDbName = getOriginalDbName(zipFileName, db); if (originalDbName == null) { throw new IOException("No database named " + db + " found"); } if (originalDbName.startsWith(File.separator)) { originalDbName = originalDbName.substring(1); } originalDbLen = originalDbName.length(); } in = FileUtils.openFileInputStream(zipFileName); ZipInputStream zipIn = new ZipInputStream(in); while (true) { ZipEntry entry = zipIn.getNextEntry(); if (entry == null) { break; } String fileName = entry.getName(); fileName = fileName.replace('\\', File.separatorChar); fileName = fileName.replace('/', File.separatorChar); if (fileName.startsWith(File.separator)) { fileName = fileName.substring(1); } boolean copy = false; if (db == null) { copy = true; } else if (fileName.startsWith(originalDbName + ".")) { fileName = db + fileName.substring(originalDbLen); copy = true; } if (copy) { OutputStream out = null; try { out = FileUtils.openFileOutputStream(directory + File.separator + fileName, false); IOUtils.copy(zipIn, out); out.close(); } finally { IOUtils.closeSilently(out); } } zipIn.closeEntry(); } zipIn.closeEntry(); zipIn.close(); } catch (IOException e) { throw Message.convertIOException(e, zipFileName); } finally { IOUtils.closeSilently(in); } } | 13,290 |
1 | public GetMyDocuments() { String urlString = dms_url + "/servlet/com.ufnasoft.dms.server.ServerGetMyDocuments"; String rvalue = ""; String filename = dms_home + FS + "temp" + FS + username + "mydocuments.xml"; try { String urldata = urlString + "?username=" + URLEncoder.encode(username, "UTF-8") + "&key=" + URLEncoder.encode(key, "UTF-8") + "&filename=" + URLEncoder.encode(username, "UTF-8") + "mydocuments.xml"; ; DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); URL u = new URL(urldata); DataInputStream is = new DataInputStream(u.openStream()); FileOutputStream os = new FileOutputStream(filename); int iBufSize = is.available(); byte inBuf[] = new byte[20000 * 1024]; int iNumRead; while ((iNumRead = is.read(inBuf, 0, iBufSize)) > 0) os.write(inBuf, 0, iNumRead); os.close(); is.close(); File f = new File(filename); InputStream inputstream = new FileInputStream(f); Document document = parser.parse(inputstream); NodeList nodelist = document.getElementsByTagName("document"); int num = nodelist.getLength(); myDocsData = new String[num][4]; myDocsToolTip = new String[num]; myDocumentImageName = new String[num]; myDocIds = new int[num]; for (int i = 0; i < num; i++) { myDocsData[i][0] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "filename")); myDocsData[i][1] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "project")); myDocsData[i][2] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "deadline")); myDocsData[i][3] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "workingfolder")); myDocsToolTip[i] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "title")); myDocumentImageName[i] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "imagename")); myDocIds[i] = (new Integer(new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "documentid")))).intValue(); } } catch (MalformedURLException ex) { System.out.println(ex); } catch (ParserConfigurationException ex) { System.out.println(ex); } catch (NullPointerException ex) { } catch (Exception ex) { System.out.println(ex); } } | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | 13,291 |
1 | protected String decrypt(final String data, final String key) throws CryptographicFailureException { Validate.notNull(data, "Provided data cannot be null."); Validate.notNull(key, "Provided key name cannot be null."); final PrivateKey pk = getPrivateKey(key); if (pk == null) { throw new CryptographicFailureException("PrivateKeyNotFound", String.format("Cannot find private key '%s'", key)); } try { final Cipher cipher = Cipher.getInstance(pk.getAlgorithm()); cipher.init(Cipher.DECRYPT_MODE, pk); final ByteArrayInputStream bin = new ByteArrayInputStream(Base64.decodeBase64(data.getBytes())); final CipherInputStream cin = new CipherInputStream(bin, cipher); final ByteArrayOutputStream bout = new ByteArrayOutputStream(); IOUtils.copy(cin, bout); return new String(bout.toByteArray()); } catch (NoSuchAlgorithmException e) { throw new IllegalStateException(String.format("Cannot find instance of algorithm '%s'", pk.getAlgorithm()), e); } catch (NoSuchPaddingException e) { throw new IllegalStateException(String.format("Cannot build instance of algorithm '%s'", pk.getAlgorithm()), e); } catch (InvalidKeyException e) { throw new IllegalStateException(String.format("Cannot build instance of algorithm '%s'", pk.getAlgorithm()), e); } catch (IOException e) { throw new IllegalStateException("Cannot build in-memory cipher copy", e); } } | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | 13,292 |
0 | public boolean renameTo(File dest) throws IOException { if (dest == null) { throw new NullPointerException("dest"); } if (!file.renameTo(dest)) { FileInputStream inputStream = new FileInputStream(file); FileOutputStream outputStream = new FileOutputStream(dest); FileChannel in = inputStream.getChannel(); FileChannel out = outputStream.getChannel(); long destsize = in.transferTo(0, size, out); in.close(); out.close(); if (destsize == size) { file.delete(); file = dest; isRenamed = true; return true; } else { dest.delete(); return false; } } file = dest; isRenamed = true; return true; } | public void doUpdateByIP() throws Exception { if (!isValidate()) { throw new CesSystemException("User_session.doUpdateByIP(): Illegal data values for update"); } Connection con = null; PreparedStatement ps = null; String strQuery = "UPDATE " + Common.USER_SESSION_TABLE + " SET " + "session_id = ?, user_id = ?, begin_date = ? , " + " mac_no = ?, login_id= ? " + "WHERE ip_address = ?"; DBOperation dbo = factory.createDBOperation(POOL_NAME); try { con = dbo.getConnection(); con.setAutoCommit(false); ps = con.prepareStatement(strQuery); ps.setString(1, this.sessionID); ps.setInt(2, this.user.getUserID()); ps.setTimestamp(3, this.beginDate); ps.setString(4, this.macNO); ps.setString(5, this.loginID); ps.setString(6, this.ipAddress); int resultCount = ps.executeUpdate(); if (resultCount != 1) { con.rollback(); throw new CesSystemException("User_session.doUpdateByIP(): ERROR updating data in T_SYS_USER_SESSION!! " + "resultCount = " + resultCount); } con.commit(); } catch (SQLException se) { if (con != null) { con.rollback(); } throw new CesSystemException("User_session.doUpdateByIP(): SQLException while updating user_session; " + "session_id = " + this.sessionID + " :\n\t" + se); } finally { con.setAutoCommit(true); closePreparedStatement(ps); closeConnection(dbo); } } | 13,293 |
0 | public void addFinance(int clubid, int quarterid, String date, String desc, String loc, BigDecimal amount) throws FinanceException, SQLException { String budgetQuery = "SELECT used, available FROM Budget WHERE club_id=" + clubid + " and quarter_id=" + quarterid + ";"; String financeUpdate = "INSERT INTO Finance (`club_id`, `transaction_date`, `description`, `location`, `amount`) VALUES ('" + clubid + "', '" + date + "', '" + desc + "', '" + "', '" + loc + "', '" + amount + "');"; Budget b = new Budget(); try { cn.setAutoCommit(false); Statement sm = cn.createStatement(); ResultSet rs = sm.executeQuery(budgetQuery); if (rs.first()) { b.used = rs.getBigDecimal(1); b.available = rs.getBigDecimal(2); } else { throw new FinanceException("No budget exists for this club!!"); } if (b.available.compareTo(amount.negate()) >= 0) { if (amount.equals(new BigDecimal(0))) ; { b.used = b.used.subtract(amount); } b.available = b.available.add(amount); sm = cn.createStatement(); sm.executeUpdate(financeUpdate); sm = cn.createStatement(); sm.executeUpdate("Update Budget SET used = " + b.used + ", amount = " + b.available + " WHERE club_id=" + clubid + " and quarter_id=" + quarterid + ";"); cn.commit(); } else { throw new FinanceException("The proposed expenditure is not within the club's budget."); } } catch (SQLException e) { cn.rollback(); throw e; } finally { cn.setAutoCommit(true); } } | private void packageDestZip(File tmpFile) throws FileNotFoundException, IOException { log("Creating launch profile package " + destfile); ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(destfile))); ZipEntry e = new ZipEntry(RESOURCE_JAR_FILENAME); e.setMethod(ZipEntry.STORED); e.setSize(tmpFile.length()); e.setCompressedSize(tmpFile.length()); e.setCrc(calcChecksum(tmpFile, new CRC32())); out.putNextEntry(e); InputStream in = new BufferedInputStream(new FileInputStream(tmpFile)); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.closeEntry(); out.finish(); out.close(); } | 13,294 |
0 | public Configuration(URL url) { InputStream in = null; try { load(in = url.openStream()); } catch (Exception e) { throw new RuntimeException("Could not load configuration from " + url, e); } finally { if (in != null) { try { in.close(); } catch (IOException ignore) { } } } } | public void deployDir(File srcDir, String destDir) { File[] dirFiles = srcDir.listFiles(); for (int k = 0; dirFiles != null && k < dirFiles.length; k++) { if (!dirFiles[k].getName().startsWith(".")) { if (dirFiles[k].isFile()) { File deployFile = new File(destDir + File.separator + dirFiles[k].getName()); if (dirFiles[k].lastModified() != deployFile.lastModified() || dirFiles[k].length() != deployFile.length()) { IOUtils.copy(dirFiles[k], deployFile); } } else if (dirFiles[k].isDirectory()) { String newDestDir = destDir + File.separator + dirFiles[k].getName(); deployDir(dirFiles[k], newDestDir); } } } } | 13,295 |
1 | public int next() { int sequenceValue = current(); try { Update update = dbi.getUpdate(); update.setTableName(sequenceTable); update.assignValue("SEQUENCE_VALUE", --sequenceValue); Search search = new Search(); search.addAttributeCriteria(sequenceTable, "SEQUENCE_NAME", Search.EQUAL, sequenceName); update.where(search); int affectedRows = dbi.getConnection().createStatement().executeUpdate(update.toString()); if (affectedRows == 1) { dbi.getConnection().commit(); } else { dbi.getConnection().rollback(); } } catch (SQLException sqle) { System.err.println("SQLException occurred in current(): " + sqle.getMessage()); } return sequenceValue; } | @Override public boolean delete(String consulta, boolean autocommit, int transactionIsolation, Connection cx) throws SQLException { filasDelete = 0; if (!consulta.contains(";")) { this.tipoConsulta = new Scanner(consulta); if (this.tipoConsulta.hasNext()) { execConsulta = this.tipoConsulta.next(); if (execConsulta.equalsIgnoreCase("delete")) { Connection conexion = cx; Statement st = null; try { conexion.setAutoCommit(autocommit); if (transactionIsolation == 1 || transactionIsolation == 2 || transactionIsolation == 4 || transactionIsolation == 8) { conexion.setTransactionIsolation(transactionIsolation); } else { throw new IllegalArgumentException("Valor invalido sobre TransactionIsolation,\n TRANSACTION_NONE no es soportado por MySQL"); } st = (Statement) conexion.createStatement(ResultSetImpl.TYPE_SCROLL_SENSITIVE, ResultSetImpl.CONCUR_UPDATABLE); conexion.setReadOnly(false); filasDelete = st.executeUpdate(consulta.trim(), Statement.RETURN_GENERATED_KEYS); if (filasDelete > -1) { if (autocommit == false) { conexion.commit(); } return true; } else { return false; } } catch (MySQLIntegrityConstraintViolationException e) { if (autocommit == false) { try { conexion.rollback(); System.out.println("Se ejecuto un Rollback"); } catch (MySQLTransactionRollbackException sqlE) { System.out.println("No se ejecuto un Rollback"); sqlE.printStackTrace(); } catch (SQLException se) { se.printStackTrace(); } } e.printStackTrace(); return false; } catch (MySQLNonTransientConnectionException e) { if (autocommit == false) { try { conexion.rollback(); System.out.println("Se ejecuto un Rollback"); } catch (MySQLTransactionRollbackException sqlE) { System.out.println("No se ejecuto un Rollback"); sqlE.printStackTrace(); } catch (SQLException se) { se.printStackTrace(); } } e.printStackTrace(); return false; } catch (MySQLDataException e) { System.out.println("Datos incorrectos"); if (autocommit == false) { try { conexion.rollback(); System.out.println("Se ejecuto un Rollback"); } catch (MySQLTransactionRollbackException sqlE) { System.out.println("No se ejecuto un Rollback"); sqlE.printStackTrace(); } catch (SQLException se) { se.printStackTrace(); } } return false; } catch (MySQLSyntaxErrorException e) { System.out.println("Error en la sintaxis de la Consulta en MySQL"); if (autocommit == false) { try { conexion.rollback(); System.out.println("Se ejecuto un Rollback"); } catch (MySQLTransactionRollbackException sqlE) { System.out.println("No se ejecuto un Rollback"); sqlE.printStackTrace(); } catch (SQLException se) { se.printStackTrace(); } } return false; } catch (SQLException e) { if (autocommit == false) { try { conexion.rollback(); System.out.println("Se ejecuto un Rollback"); } catch (MySQLTransactionRollbackException sqlE) { System.out.println("No se ejecuto un Rollback"); sqlE.printStackTrace(); } catch (SQLException se) { se.printStackTrace(); } } e.printStackTrace(); return false; } finally { try { if (st != null) { if (!st.isClosed()) { st.close(); } } if (!conexion.isClosed()) { conexion.close(); } } catch (NullPointerException ne) { ne.printStackTrace(); } catch (SQLException e) { e.printStackTrace(); } } } else { throw new IllegalArgumentException("No es una instruccion Delete"); } } else { try { throw new JMySQLException("Error Grave , notifique al departamento de Soporte Tecnico \n" + email); } catch (JMySQLException ex) { Logger.getLogger(JMySQL.class.getName()).log(Level.SEVERE, null, ex); return false; } } } else { throw new IllegalArgumentException("No estan permitidas las MultiConsultas en este metodo"); } } | 13,296 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | private void doDecrypt(boolean createOutput) throws IOException { FileInputStream input = null; FileOutputStream output = null; File tempOutput = null; try { input = new FileInputStream(infile); String cipherBaseFilename = basename(infile); byte[] magic = new byte[MAGIC.length]; input.read(magic); for (int i = 0; i < MAGIC.length; i++) { if (MAGIC[i] != magic[i]) throw new IOException("Not a BORK file (bad magic number)"); } short version = readShort(input); if (version / 1000 > VERSION / 1000) throw new IOException("File created by an incompatible future version: " + version + " > " + VERSION); String cipherName = readString(input); Cipher cipher = createCipher(cipherName, createSessionKey(password, cipherBaseFilename)); CipherInputStream decryptedInput = new CipherInputStream(input, cipher); long headerCrc = Unsigned.promote(readInt(decryptedInput)); decryptedInput.resetCRC(); outfile = new File(outputDir, readString(decryptedInput)); if (!createOutput || outfile.exists()) { skipped = true; return; } tempOutput = File.createTempFile("bork", null, outputDir); tempOutput.deleteOnExit(); byte[] buffer = new byte[BUFFER_SIZE]; output = new FileOutputStream(tempOutput); int bytesRead; while ((bytesRead = decryptedInput.read(buffer)) != -1) output.write(buffer, 0, bytesRead); output.close(); output = null; if (headerCrc != decryptedInput.getCRC()) { outfile = null; throw new IOException("CRC mismatch: password is probably incorrect"); } if (!tempOutput.renameTo(outfile)) throw new IOException("Failed to rename temp output file " + tempOutput + " to " + outfile); outfile.setLastModified(infile.lastModified()); } finally { close(input); close(output); if (tempOutput != null) tempOutput.delete(); } } | 13,297 |
1 | public static String hashPassword(String password) { String hashword = null; try { MessageDigest md5 = MessageDigest.getInstance(MESSAGE_DIGEST_ALGORITHM_MD5); md5.update(password.getBytes()); BigInteger hash = new BigInteger(1, md5.digest()); hashword = hash.toString(16); } catch (NoSuchAlgorithmException e) { logger.error("Cannot find algorithm = '" + MESSAGE_DIGEST_ALGORITHM_MD5 + "'", e); throw new IllegalStateException(e); } return pad(hashword, 32, '0'); } | public static String hash(String str) { MessageDigest summer; try { summer = MessageDigest.getInstance("md5"); summer.update(str.getBytes()); } catch (NoSuchAlgorithmException ex) { return null; } BigInteger hash = new BigInteger(1, summer.digest()); String hashword = hash.toString(16); return hashword; } | 13,298 |
0 | @Override public String encodePassword(String rawPass, Object salt) throws DataAccessException { try { MessageDigest digest = MessageDigest.getInstance(digestAlgorithm); digest.reset(); digest.update(((String) salt).getBytes("UTF-8")); return new String(digest.digest(rawPass.getBytes("UTF-8"))); } catch (Throwable e) { throw new DataAccessException("Error al codificar la contrase�a", e) { private static final long serialVersionUID = 3880106673612870103L; }; } } | 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(); } } | 13,299 |
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