label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
|---|---|---|---|
0 | public void executeQuery(Connection connection, String query) { action = null; updateCount = 0; resultsAvailable = false; metaAvailable = false; planAvailable = false; if (connection == null) { ide.setStatus("not connected"); return; } cleanUp(); try { ide.setStatus("Executing query"); stmt = connection.createStatement(); if (query.toLowerCase().startsWith("select")) { result = stmt.executeQuery(query); resultsAvailable = true; action = "select"; } else if (query.toLowerCase().startsWith("update")) { updateCount = stmt.executeUpdate(query); action = "update"; } else if (query.toLowerCase().startsWith("delete")) { updateCount = stmt.executeUpdate(query); action = "delete"; } else if (query.toLowerCase().startsWith("insert")) { updateCount = stmt.executeUpdate(query); action = "insert"; } else if (query.toLowerCase().startsWith("commit")) { connection.commit(); action = "commit"; } else if (query.toLowerCase().startsWith("rollback")) { connection.rollback(); action = "rollback"; } else if (query.toLowerCase().startsWith("create")) { updateCount = stmt.executeUpdate(query); action = "create"; } else if (query.toLowerCase().startsWith("drop")) { updateCount = stmt.executeUpdate(query); action = "drop"; } else if (query.toLowerCase().startsWith("desc ")) { String objectName = query.substring(query.indexOf(' '), query.length()); query = "select * from (" + objectName + ") where rownum < 1"; descQuery(connection, query); } else if (query.toLowerCase().startsWith("explain plan for ")) { explainQuery(connection, query); } else { result = stmt.executeQuery(query); resultsAvailable = true; action = "select"; } ide.setStatus("executed query"); } catch (Exception e) { ide.setStatus(e.getMessage()); } } | public RandomGUID() { MessageDigest md5 = null; try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e.getClass().getName() + ": " + e.getMessage()); } try { long time = System.currentTimeMillis(); long rand = 0; rand = myRand.nextLong(); StringBuffer sb = new StringBuffer(); sb.append(s_id); sb.append(":"); sb.append(Long.toString(time)); sb.append(":"); sb.append(Long.toString(rand)); md5.update(sb.toString().getBytes()); byte[] array = md5.digest(); sb.setLength(0); 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) { throw new RuntimeException(e.getClass().getName() + ": " + e.getMessage()); } } | 896,900 |
1 | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | @Override public void run() { long timeout = 10 * 1000L; long start = (new Date()).getTime(); try { InputStream is = socket.getInputStream(); boolean available = false; while (!available && !socket.isClosed()) { try { if (is.available() != 0) { available = true; } else { Thread.sleep(100); } } catch (Exception e) { LOG.error("Error checking socket", e); } long curr = (new Date()).getTime(); if ((curr - start) >= timeout) { break; } } if (socket.isClosed()) { } else { ByteArrayOutputStream baos = new ByteArrayOutputStream(); IOUtils.copy(is, baos); baos.flush(); baos.close(); data = baos.toByteArray(); } String msg = FtpResponse.ReadComplete.asString() + ClientCommand.SP + "Read Complete" + ClientCommand.CRLF; List<String> list = new ArrayList<String>(); list.add(msg); ClientResponse response = new ClientResponse(list); ftpClient.notifyListeners(response); } catch (Exception e) { LOG.error("Error reading server response", e); } } | 896,901 |
0 | public static void exportDB(String input, String output) { try { Class.forName("org.sqlite.JDBC"); String fileName = input + File.separator + G.databaseName; File dataBase = new File(fileName); if (!dataBase.exists()) { JOptionPane.showMessageDialog(null, "No se encuentra el fichero DB", "Error", JOptionPane.ERROR_MESSAGE); } else { G.conn = DriverManager.getConnection("jdbc:sqlite:" + fileName); HashMap<Integer, String> languageIDs = new HashMap<Integer, String>(); HashMap<Integer, String> typeIDs = new HashMap<Integer, String>(); long tiempoInicio = System.currentTimeMillis(); Element dataBaseXML = new Element("database"); Element languages = new Element("languages"); Statement stat = G.conn.createStatement(); ResultSet rs = stat.executeQuery("select * from language order by id"); while (rs.next()) { int id = rs.getInt("id"); String name = rs.getString("name"); languageIDs.put(id, name); Element language = new Element("language"); language.setText(name); languages.addContent(language); } dataBaseXML.addContent(languages); rs = stat.executeQuery("select * from type order by id"); while (rs.next()) { int id = rs.getInt("id"); String name = rs.getString("name"); typeIDs.put(id, name); } rs = stat.executeQuery("select distinct name from main order by name"); while (rs.next()) { String name = rs.getString("name"); Element image = new Element("image"); image.setAttribute("id", name); Statement stat2 = G.conn.createStatement(); ResultSet rs2 = stat2.executeQuery("select distinct idL from main where name = \"" + name + "\" order by idL"); while (rs2.next()) { int idL = rs2.getInt("idL"); Element language = new Element("language"); language.setAttribute("id", languageIDs.get(idL)); Statement stat3 = G.conn.createStatement(); ResultSet rs3 = stat3.executeQuery("select * from main where name = \"" + name + "\" and idL = " + idL + " order by idT"); while (rs3.next()) { int idT = rs3.getInt("idT"); String word = rs3.getString("word"); Element wordE = new Element("word"); wordE.setAttribute("type", typeIDs.get(idT)); wordE.setText(word); language.addContent(wordE); String pathSrc = input + File.separator + name.substring(0, 1).toUpperCase() + File.separator + name; String pathDst = output + File.separator + 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()); } } rs3.close(); stat3.close(); image.addContent(language); } rs2.close(); stat2.close(); dataBaseXML.addContent(image); } rs.close(); stat.close(); XMLOutputter out = new XMLOutputter(Format.getPrettyFormat()); FileOutputStream f = new FileOutputStream(output + File.separator + G.imagesName); out.output(dataBaseXML, f); f.flush(); f.close(); long totalTiempo = System.currentTimeMillis() - tiempoInicio; System.out.println("El tiempo total es :" + totalTiempo / 1000 + " segundos"); } } catch (Exception e) { e.printStackTrace(); } } | private boolean loadSymbol(QuoteCache quoteCache, Symbol symbol, TradingDate startDate, TradingDate endDate) { boolean success = true; String URLString = constructURL(symbol, startDate, endDate); PreferencesManager.ProxyPreferences proxyPreferences = PreferencesManager.loadProxySettings(); try { URL url; url = new URL(URLString); InputStreamReader input = new InputStreamReader(url.openStream()); BufferedReader bufferedInput = new BufferedReader(input); String line; while ((line = bufferedInput.readLine()) != null) { Class cl = null; Constructor cnst = null; QuoteFilter filter = null; try { cl = Class.forName("org.mov.quote." + name + "QuoteFilter"); try { cnst = cl.getConstructor(new Class[] { Symbol.class }); } catch (SecurityException e2) { e2.printStackTrace(); } catch (NoSuchMethodException e2) { e2.printStackTrace(); } try { filter = (QuoteFilter) cnst.newInstance(new Object[] { symbol }); } catch (IllegalArgumentException e3) { e3.printStackTrace(); } catch (InstantiationException e3) { e3.printStackTrace(); } catch (IllegalAccessException e3) { e3.printStackTrace(); } catch (InvocationTargetException e3) { e3.printStackTrace(); } } catch (ClassNotFoundException e1) { e1.printStackTrace(); } Quote quote = filter.toQuote(line); if (quote != null) quoteCache.load(quote); } bufferedInput.close(); } catch (BindException e) { DesktopManager.showErrorMessage(Locale.getString("UNABLE_TO_CONNECT_ERROR", e.getMessage())); success = false; } catch (ConnectException e) { DesktopManager.showErrorMessage(Locale.getString("UNABLE_TO_CONNECT_ERROR", e.getMessage())); success = false; } catch (UnknownHostException e) { DesktopManager.showErrorMessage(Locale.getString("UNKNOWN_HOST_ERROR", e.getMessage())); success = false; } catch (NoRouteToHostException e) { DesktopManager.showErrorMessage(Locale.getString("DESTINATION_UNREACHABLE_ERROR", e.getMessage())); success = false; } catch (MalformedURLException e) { DesktopManager.showErrorMessage(Locale.getString("INVALID_PROXY_ERROR", proxyPreferences.host, proxyPreferences.port)); success = false; } catch (FileNotFoundException e) { } catch (IOException e) { DesktopManager.showErrorMessage(Locale.getString("ERROR_DOWNLOADING_QUOTES")); success = false; } return success; } | 896,902 |
1 | private WikiSiteContentInfo createInfoIndexSite(Long domainId) { final UserInfo user = getSecurityService().getCurrentUser(); final Locale locale = new Locale(user.getLocale()); final String country = locale.getLanguage(); InputStream inStream = Thread.currentThread().getContextClassLoader().getResourceAsStream("wiki_index_" + country + ".xhtml"); if (inStream == null) { inStream = Thread.currentThread().getContextClassLoader().getResourceAsStream("wiki_index.xhtml"); } if (inStream == null) { inStream = new ByteArrayInputStream(DEFAULT_WIKI_INDEX_SITE_TEXT.getBytes()); } if (inStream != null) { ByteArrayOutputStream out = new ByteArrayOutputStream(); try { IOUtils.copyLarge(inStream, out); return createIndexVersion(domainId, out.toString(), user); } catch (IOException exception) { LOGGER.error("Error creating info page.", exception); } finally { try { inStream.close(); out.close(); } catch (IOException exception) { LOGGER.error("Error reading wiki_index.xhtml", exception); } } } return null; } | public void copyFile(File sourceFile, String toDir, boolean create, boolean overwrite) throws FileNotFoundException, IOException { FileInputStream source = null; FileOutputStream destination = null; byte[] buffer; int bytes_read; File toFile = new File(toDir); if (create && !toFile.exists()) toFile.mkdirs(); if (toFile.exists()) { File destFile = new File(toDir + "/" + sourceFile.getName()); try { if (!destFile.exists() || overwrite) { source = new FileInputStream(sourceFile); destination = new FileOutputStream(destFile); buffer = new byte[1024]; while (true) { bytes_read = source.read(buffer); if (bytes_read == -1) break; destination.write(buffer, 0, bytes_read); } } } catch (Exception exx) { exx.printStackTrace(); } finally { if (source != null) try { source.close(); } catch (IOException e) { } if (destination != null) try { destination.close(); } catch (IOException e) { } } } } | 896,903 |
0 | @Override public void run() { try { URL url = new URL(this.uri); String data = "tags=" + this.tags + "&mbox=" + this.mbox + "&_method=put"; HttpURLConnection huc = (HttpURLConnection) url.openConnection(); huc.setRequestMethod("POST"); huc.setDoOutput(true); huc.setRequestProperty("Content-type", "application/x-www-form-urlencoded"); huc.setRequestProperty("Content-Length", "" + data.length()); huc.getOutputStream().write(data.getBytes()); huc.getOutputStream().flush(); huc.connect(); if (huc.getResponseCode() == 200) { System.out.println("Harvested: " + this.uri); } else if (huc.getResponseCode() > 200) { System.out.println("Not Harvested: " + this.uri + " error: " + huc.getResponseCode()); } huc.disconnect(); } catch (MalformedURLException e) { e.printStackTrace(); } catch (ProtocolException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } | private void delay(HttpServletRequest request, HttpServletResponse response, FilterChain chain) throws IOException, ServletException { String url = request.getRequestURL().toString(); if (delayed.contains(url)) { delayed.remove(url); LOGGER.info(MessageFormat.format("Loading delayed resource at url = [{0}]", url)); chain.doFilter(request, response); } else { LOGGER.info("Returning resource = [LoaderApplication.swf]"); InputStream input = null; OutputStream output = null; try { input = getClass().getResourceAsStream("LoaderApplication.swf"); output = response.getOutputStream(); delayed.add(url); response.setHeader("Cache-Control", "no-cache"); IOUtils.copy(input, output); } finally { IOUtils.closeQuietly(output); IOUtils.closeQuietly(input); } } } | 896,904 |
1 | private void parseExternalCss(Document d) throws XPathExpressionException, IOException { InputStream is = null; try { XPath xp = xpf.newXPath(); XPathExpression xpe = xp.compile("//link[@type='text/css']/@href"); NodeList nl = (NodeList) xpe.evaluate(d, XPathConstants.NODESET); for (int i = 0; i < nl.getLength(); i++) { Attr a = (Attr) nl.item(i); String url = a.getValue(); URL u = new URL(url); is = new BufferedInputStream(u.openStream()); ByteArrayOutputStream baos = new ByteArrayOutputStream(); IOUtils.copy(is, baos); parser.add(new String(baos.toByteArray(), "UTF-8")); Element linkNode = a.getOwnerElement(); Element parent = (Element) linkNode.getParentNode(); parent.removeChild(linkNode); IOUtils.closeQuietly(is); is = null; } } finally { IOUtils.closeQuietly(is); } } | 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(); } } | 896,905 |
1 | public static void main(String[] args) throws IOException { String paramFileName = args[0]; BufferedReader inFile_params = new BufferedReader(new FileReader(paramFileName)); String cands_fileName = (inFile_params.readLine().split("\\s+"))[0]; String alignSrcCand_phrasal_fileName = (inFile_params.readLine().split("\\s+"))[0]; String alignSrcCand_word_fileName = (inFile_params.readLine().split("\\s+"))[0]; String source_fileName = (inFile_params.readLine().split("\\s+"))[0]; String trainSrc_fileName = (inFile_params.readLine().split("\\s+"))[0]; String trainTgt_fileName = (inFile_params.readLine().split("\\s+"))[0]; String trainAlign_fileName = (inFile_params.readLine().split("\\s+"))[0]; String alignCache_fileName = (inFile_params.readLine().split("\\s+"))[0]; String alignmentsType = "AlignmentGrids"; int maxCacheSize = 1000; inFile_params.close(); int numSentences = countLines(source_fileName); InputStream inStream_src = new FileInputStream(new File(source_fileName)); BufferedReader srcFile = new BufferedReader(new InputStreamReader(inStream_src, "utf8")); String[] srcSentences = new String[numSentences]; for (int i = 0; i < numSentences; ++i) { srcSentences[i] = srcFile.readLine(); } srcFile.close(); println("Creating src vocabulary @ " + (new Date())); srcVocab = new Vocabulary(); int[] sourceWordsSentences = Vocabulary.initializeVocabulary(trainSrc_fileName, srcVocab, true); int numSourceWords = sourceWordsSentences[0]; int numSourceSentences = sourceWordsSentences[1]; println("Reading src corpus @ " + (new Date())); srcCorpusArray = SuffixArrayFactory.createCorpusArray(trainSrc_fileName, srcVocab, numSourceWords, numSourceSentences); println("Creating src SA @ " + (new Date())); srcSA = SuffixArrayFactory.createSuffixArray(srcCorpusArray, maxCacheSize); println("Creating tgt vocabulary @ " + (new Date())); tgtVocab = new Vocabulary(); int[] targetWordsSentences = Vocabulary.initializeVocabulary(trainTgt_fileName, tgtVocab, true); int numTargetWords = targetWordsSentences[0]; int numTargetSentences = targetWordsSentences[1]; println("Reading tgt corpus @ " + (new Date())); tgtCorpusArray = SuffixArrayFactory.createCorpusArray(trainTgt_fileName, tgtVocab, numTargetWords, numTargetSentences); println("Creating tgt SA @ " + (new Date())); tgtSA = SuffixArrayFactory.createSuffixArray(tgtCorpusArray, maxCacheSize); int trainingSize = srcCorpusArray.getNumSentences(); if (trainingSize != tgtCorpusArray.getNumSentences()) { throw new RuntimeException("Source and target corpora have different number of sentences. This is bad."); } println("Reading alignment data @ " + (new Date())); alignments = null; if ("AlignmentArray".equals(alignmentsType)) { alignments = SuffixArrayFactory.createAlignments(trainAlign_fileName, srcSA, tgtSA); } else if ("AlignmentGrids".equals(alignmentsType) || "AlignmentsGrid".equals(alignmentsType)) { alignments = new AlignmentGrids(new Scanner(new File(trainAlign_fileName)), srcCorpusArray, tgtCorpusArray, trainingSize, true); } else if ("MemoryMappedAlignmentGrids".equals(alignmentsType)) { alignments = new MemoryMappedAlignmentGrids(trainAlign_fileName, srcCorpusArray, tgtCorpusArray); } if (!fileExists(alignCache_fileName)) { alreadyResolved_srcSet = new HashMap<String, TreeSet<Integer>>(); alreadyResolved_tgtSet = new HashMap<String, TreeSet<Integer>>(); } else { try { ObjectInputStream in = new ObjectInputStream(new FileInputStream(alignCache_fileName)); alreadyResolved_srcSet = (HashMap<String, TreeSet<Integer>>) in.readObject(); alreadyResolved_tgtSet = (HashMap<String, TreeSet<Integer>>) in.readObject(); in.close(); } catch (FileNotFoundException e) { System.err.println("FileNotFoundException in AlignCandidates.main(String[]): " + e.getMessage()); System.exit(99901); } catch (IOException e) { System.err.println("IOException in AlignCandidates.main(String[]): " + e.getMessage()); System.exit(99902); } catch (ClassNotFoundException e) { System.err.println("ClassNotFoundException in AlignCandidates.main(String[]): " + e.getMessage()); System.exit(99904); } } println("Processing candidates @ " + (new Date())); PrintWriter outFile_alignSrcCand_phrasal = new PrintWriter(alignSrcCand_phrasal_fileName); PrintWriter outFile_alignSrcCand_word = new PrintWriter(alignSrcCand_word_fileName); InputStream inStream_cands = new FileInputStream(new File(cands_fileName)); BufferedReader candsFile = new BufferedReader(new InputStreamReader(inStream_cands, "utf8")); String line = ""; String cand = ""; line = candsFile.readLine(); int countSatisfied = 0; int countAll = 0; int countSatisfied_sizeOne = 0; int countAll_sizeOne = 0; int prev_i = -1; String srcSent = ""; String[] srcWords = null; int candsRead = 0; int C50count = 0; while (line != null) { ++candsRead; println("Read candidate on line #" + candsRead); int i = toInt((line.substring(0, line.indexOf("|||"))).trim()); if (i != prev_i) { srcSent = srcSentences[i]; srcWords = srcSent.split("\\s+"); prev_i = i; println("New value for i: " + i + " seen @ " + (new Date())); C50count = 0; } else { ++C50count; } line = (line.substring(line.indexOf("|||") + 3)).trim(); cand = (line.substring(0, line.indexOf("|||"))).trim(); cand = cand.substring(cand.indexOf(" ") + 1, cand.length() - 1); JoshuaDerivationTree DT = new JoshuaDerivationTree(cand, 0); String candSent = DT.toSentence(); String[] candWords = candSent.split("\\s+"); String alignSrcCand = DT.alignments(); outFile_alignSrcCand_phrasal.println(alignSrcCand); println(" i = " + i + ", alignSrcCand: " + alignSrcCand); String alignSrcCand_res = ""; String[] linksSrcCand = alignSrcCand.split("\\s+"); for (int k = 0; k < linksSrcCand.length; ++k) { String link = linksSrcCand[k]; if (link.indexOf(',') == -1) { alignSrcCand_res += " " + link.replaceFirst("--", "-"); } else { alignSrcCand_res += " " + resolve(link, srcWords, candWords); } } alignSrcCand_res = alignSrcCand_res.trim(); println(" i = " + i + ", alignSrcCand_res: " + alignSrcCand_res); outFile_alignSrcCand_word.println(alignSrcCand_res); if (C50count == 50) { println("50C @ " + (new Date())); C50count = 0; } line = candsFile.readLine(); } outFile_alignSrcCand_phrasal.close(); outFile_alignSrcCand_word.close(); candsFile.close(); println("Finished processing candidates @ " + (new Date())); try { ObjectOutputStream out = new ObjectOutputStream(new FileOutputStream(alignCache_fileName)); out.writeObject(alreadyResolved_srcSet); out.writeObject(alreadyResolved_tgtSet); out.flush(); out.close(); } catch (IOException e) { System.err.println("IOException in AlignCandidates.main(String[]): " + e.getMessage()); System.exit(99902); } } | public static void notify(String msg) throws Exception { String url = "http://api.clickatell.com/http/sendmsg?"; url = add(url, "user", user); url = add(url, "password", password); url = add(url, "api_id", apiId); url = add(url, "to", to); url = add(url, "text", msg); URL u = new URL(url); URLConnection c = u.openConnection(); InputStream is = c.getInputStream(); IOUtils.copy(is, System.out); IOUtils.closeQuietly(is); System.out.println(); } | 896,906 |
1 | 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); } } | private 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.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) { ; } } } | 896,907 |
0 | public ArrayList<Jane16Results> callExternalService(ServiceType type, HashMap<String, String> params) throws Exception { URL url = initURL(type, params); XMLParser parser = initParser(type); InputStream in = url.openStream(); ArrayList<Jane16Results> results = new ArrayList<Jane16Results>(); byte[] buf = new byte[1024]; ArrayList<Byte> arrByte = new ArrayList<Byte>(); int len; while ((len = in.read(buf)) > 0) { for (int i = 0; i < len; i++) { arrByte.add(buf[i]); } } in.close(); byte[] data = new byte[arrByte.size()]; int i = 0; for (Byte b : arrByte) { data[i++] = b; } results = parser.parse(data); return results; } | private void show(String fileName, HttpServletResponse response) throws IOException { TelnetInputStream ftpIn = ftpClient_sun.get(fileName); OutputStream out = null; try { out = response.getOutputStream(); IOUtils.copy(ftpIn, out); } finally { if (ftpIn != null) { ftpIn.close(); } } } | 896,908 |
1 | private void fileCopy(final File src, final File dest) throws IOException { final FileChannel srcChannel = new FileInputStream(src).getChannel(); final FileChannel dstChannel = new FileOutputStream(dest).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } | public void xtestFile2() throws Exception { InputStream inputStream = new FileInputStream(IOTest.FILE); OutputStream outputStream = new FileOutputStream("C:/Temp/testFile2.mp4"); IOUtils.copy(inputStream, outputStream); inputStream.close(); outputStream.close(); } | 896,909 |
0 | public String getNextObjectId() throws SQLException { long nextserial = 1; String s0 = "lock table serials in exclusive mode"; String s1 = "SELECT nextserial FROM serials WHERE tablename = 'SERVER_OIDS'"; String s2; try { Statement stmt = dbconnect.connection.createStatement(); stmt.executeUpdate(s0); ResultSet rs = stmt.executeQuery(s1); if (!rs.next()) { s2 = "insert into serials (tablename,nextserial) values ('SERVER_OIDS', " + (nextserial) + ")"; } else { nextserial = rs.getLong(1) + 1; s2 = "update serials set nextserial=" + (nextserial) + " where tablename='SERVER_OIDS'"; } stmt.executeUpdate(s2); dbconnect.connection.commit(); rs.close(); stmt.close(); return "" + nextserial; } catch (SQLException e) { dbconnect.connection.rollback(); throw e; } } | public void run() { try { Socket socket = getSocket(); System.out.println("opening socket to " + address + " on " + port); InputStream in = socket.getInputStream(); for (; ; ) { FileTransferHeader header = FileTransferHeader.readHeader(in); if (header == null) break; System.out.println("header: " + header); String[] parts = header.getFilename().getSegments(); String filename; if (parts.length > 0) filename = "dl-" + parts[parts.length - 1]; else filename = "dl-" + session.getScreenname(); System.out.println("writing to file " + filename); long sum = 0; if (new File(filename).exists()) { FileInputStream fis = new FileInputStream(filename); byte[] block = new byte[10]; for (int i = 0; i < block.length; ) { int count = fis.read(block); if (count == -1) break; i += count; } FileTransferChecksum summer = new FileTransferChecksum(); summer.update(block, 0, 10); sum = summer.getValue(); } FileChannel fileChannel = new FileOutputStream(filename).getChannel(); FileTransferHeader outHeader = new FileTransferHeader(header); outHeader.setHeaderType(FileTransferHeader.HEADERTYPE_ACK); outHeader.setIcbmMessageId(cookie); outHeader.setBytesReceived(0); outHeader.setReceivedChecksum(sum); OutputStream socketOut = socket.getOutputStream(); System.out.println("sending header: " + outHeader); outHeader.write(socketOut); for (int i = 0; i < header.getFileSize(); ) { long transferred = fileChannel.transferFrom(Channels.newChannel(in), 0, header.getFileSize() - i); System.out.println("transferred " + transferred); if (transferred == -1) return; i += transferred; } System.out.println("finished transfer!"); fileChannel.close(); FileTransferHeader doneHeader = new FileTransferHeader(header); doneHeader.setHeaderType(FileTransferHeader.HEADERTYPE_RECEIVED); doneHeader.setFlags(doneHeader.getFlags() | FileTransferHeader.FLAG_DONE); doneHeader.setBytesReceived(doneHeader.getBytesReceived() + 1); doneHeader.setIcbmMessageId(cookie); doneHeader.setFilesLeft(doneHeader.getFilesLeft() - 1); doneHeader.write(socketOut); if (doneHeader.getFilesLeft() - 1 <= 0) { socket.close(); break; } } } catch (IOException e) { e.printStackTrace(); return; } } | 896,910 |
1 | 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)); } } | 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()); } | 896,911 |
1 | public static final boolean copy(File source, File target, boolean overwrite) { if (!overwrite && target.exists()) { LOGGER.error("Target file exist and it not permitted to overwrite it !"); return false; } FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(source).getChannel(); out = new FileOutputStream(target).getChannel(); in.transferTo(0, in.size(), out); } catch (FileNotFoundException e) { LOGGER.error(e.getLocalizedMessage()); if (LOGGER.isDebugEnabled()) e.printStackTrace(); return false; } catch (IOException e) { LOGGER.error(e.getLocalizedMessage()); if (LOGGER.isDebugEnabled()) e.printStackTrace(); return false; } finally { try { in.close(); } catch (Exception e) { } try { out.close(); } catch (Exception e) { } } return true; } | @Deprecated public boolean backupLuceneIndex(int indexLocation, int backupLocation) { boolean result = false; try { System.out.println("lucene backup started"); String indexPath = this.getIndexFolderPath(indexLocation); String backupPath = this.getIndexFolderPath(backupLocation); File inDir = new File(indexPath); boolean flag = true; if (inDir.exists() && inDir.isDirectory()) { File filesList[] = inDir.listFiles(); if (filesList != null) { File parDirBackup = new File(backupPath); if (!parDirBackup.exists()) parDirBackup.mkdir(); String date = this.getDate(); backupPath += "/" + date; File dirBackup = new File(backupPath); if (!dirBackup.exists()) dirBackup.mkdir(); else { File files[] = dirBackup.listFiles(); if (files != null) { for (int i = 0; i < files.length; i++) { if (files[i] != null) { files[i].delete(); } } } dirBackup.delete(); dirBackup.mkdir(); } for (int i = 0; i < filesList.length; i++) { if (filesList[i].isFile()) { try { File destFile = new File(backupPath + "/" + filesList[i].getName()); if (!destFile.exists()) destFile.createNewFile(); FileInputStream in = new FileInputStream(filesList[i]); FileOutputStream out = new FileOutputStream(destFile); FileChannel fcIn = in.getChannel(); FileChannel fcOut = out.getChannel(); fcIn.transferTo(0, fcIn.size(), fcOut); } catch (FileNotFoundException ex) { System.out.println("FileNotFoundException ---->" + ex); flag = false; } catch (IOException excIO) { System.out.println("IOException ---->" + excIO); flag = false; } } } } } System.out.println("lucene backup finished"); System.out.println("flag ========= " + flag); if (flag) { result = true; } } catch (Exception e) { System.out.println("Exception in backupLuceneIndex Method : " + e); e.printStackTrace(); } return result; } | 896,912 |
0 | public static String getDocumentAsString(URL url) throws IOException { StringBuffer result = new StringBuffer(); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream(), "UTF8")); String line = ""; while (line != null) { result.append(line); line = in.readLine(); } return result.toString(); } | @Override public int run() { Enumeration<?> e; try { e = About.class.getClassLoader().getResources("META-INF/MANIFEST.MF"); while (e.hasMoreElements()) { final URL url = (URL) e.nextElement(); if (url.toString().indexOf("renaissance") != -1) { final InputStream is = url.openStream(); Properties p = new Properties(); p.load(is); for (Entry<?, ?> entry : p.entrySet()) { System.err.println(entry); } } } } catch (IOException e1) { logger.fatal("Caught an exception " + e1); return 1; } System.err.println("Classpath is " + System.getProperty("java.class.path")); return 0; } | 896,913 |
0 | private static File copyFileTo(File file, File directory) throws IOException { File newFile = new File(directory, file.getName()); FileInputStream fis = null; FileOutputStream fos = null; try { fis = new FileInputStream(file); fos = new FileOutputStream(newFile); byte buff[] = new byte[1024]; int val; while ((val = fis.read(buff)) > 0) fos.write(buff, 0, val); } finally { if (fis != null) fis.close(); if (fos != null) fos.close(); } return newFile; } | public static InputStream getInputStream(String path) throws ResourceException { URL url = getURL(path); if (url != null) { try { return url.openConnection().getInputStream(); } catch (IOException e) { throw new ResourceException(e); } } else { throw new ResourceException("Error obtaining resource, invalid path: " + path); } } | 896,914 |
0 | public Savable loadResource(String name, PrimitiveLoader loader) { Savable objeto = null; URL url = ResourceLocator.locateFile(loader.getBaseFolder(), name, loader.getCompiledExtension()); if (url == null) { url = ResourceLocator.locateFile(loader.getBaseFolder(), name, loader.getPrimitiveExtension()); if (url != null) { try { objeto = loader.loadResource(name, url.openStream()); File file = ResourceLocator.replaceExtension(url, loader.getCompiledExtension()); BinaryExporter.getInstance().save(objeto, file); } catch (IOException e) { e.printStackTrace(); } catch (URISyntaxException e) { e.printStackTrace(); } } } else { try { objeto = BinaryImporter.getInstance().load(url.openStream()); } catch (IOException e) { e.printStackTrace(); } } return objeto; } | public String getLongToken(String md5Str) { MessageDigest md5 = null; try { md5 = MessageDigest.getInstance("MD5"); md5.update(md5Str.getBytes(JspRunConfig.charset)); } catch (Exception e) { e.printStackTrace(); } StringBuffer token = toHex(md5.digest()); return token.toString(); } | 896,915 |
0 | public boolean validatePassword(UserType nameMatch, String password) { try { MessageDigest md = MessageDigest.getInstance(HASH_ALGORITHM); md.reset(); md.update(nameMatch.getSalt().getBytes("UTF-8")); md.update(password.getBytes("UTF-8")); String encodedString = new String(Base64.encode(md.digest())); return encodedString.equals(nameMatch.getPassword()); } catch (UnsupportedEncodingException ex) { logger.fatal("Your computer does not have UTF-8 support for Java installed.", ex); logger.fatal("Shutting down..."); GlobalUITools.displayFatalExceptionMessage(null, "UTF-8 for Java not installed", ex, true); assert false : "This should never happen"; return false; } catch (NoSuchAlgorithmException ex) { String errorMessage = "Could not use algorithm " + HASH_ALGORITHM; logger.fatal(ex.getMessage()); logger.fatal(errorMessage); GlobalUITools.displayFatalExceptionMessage(null, "Could not use algorithm " + HASH_ALGORITHM, ex, true); assert false : "This could should never be reached"; return false; } } | private static void doCopyFile(File srcFile, File destFile, boolean preserveFileDate) throws IOException { if (destFile.exists() && destFile.isDirectory()) { throw new IOException("Destination '" + destFile + "' exists but is a directory"); } long time = System.currentTimeMillis(); FileInputStream fis = null; FileOutputStream fos = null; FileChannel input = null; FileChannel output = null; try { fis = new FileInputStream(srcFile); fos = new FileOutputStream(destFile); input = fis.getChannel(); output = fos.getChannel(); long size = input.size(); long pos = 0; long count = 0; while (pos < size && continueWriting(pos, size)) { count = (size - pos) > FIFTY_MB ? FIFTY_MB : (size - pos); pos += output.transferFrom(input, pos, count); } } finally { output.close(); IOUtils.closeQuietly(fos); input.close(); IOUtils.closeQuietly(fis); } if (srcFile.length() != destFile.length()) { if (DiskManager.isLocked()) throw new IOException("Copy stopped since VtM was working"); else throw new IOException("Failed to copy full contents from '" + srcFile + "' to '" + destFile + "'"); } else { time = System.currentTimeMillis() - time; long speed = (destFile.length() / time) / 1000; DiskManager.addDiskSpeed(speed); } if (preserveFileDate) { destFile.setLastModified(srcFile.lastModified()); } } | 896,916 |
1 | public void writeTo(File f) throws IOException { if (state != STATE_OK) throw new IllegalStateException("Upload failed"); if (tempLocation == null) throw new IllegalStateException("File already saved"); if (f.isDirectory()) f = new File(f, filename); FileInputStream fis = new FileInputStream(tempLocation); FileOutputStream fos = new FileOutputStream(f); byte[] buf = new byte[BUFFER_SIZE]; try { int i = 0; while ((i = fis.read(buf)) != -1) fos.write(buf, 0, i); } finally { deleteTemporaryFile(); fis.close(); fos.close(); } } | public void xtest12() throws Exception { PDFManager manager = new ITextManager(); InputStream pdf = new FileInputStream("/tmp/090237098008f637.pdf"); InputStream page1 = manager.cut(pdf, 36, 36); OutputStream outputStream = new FileOutputStream("/tmp/090237098008f637-1.pdf"); IOUtils.copy(page1, outputStream); outputStream.close(); pdf.close(); } | 896,917 |
1 | private void dumpFile(File repository, File copy) { try { if (copy.exists() && !copy.delete()) { throw new RuntimeException("can't delete copy: " + copy); } printFile("Real Archive File", repository); new ZipArchive(repository.getPath()); IOUtils.copyFiles(repository, copy); printFile("Copy Archive File", copy); new ZipArchive(copy.getPath()); } catch (IOException e) { e.printStackTrace(); } } | private void createWikiPages(WikiContext context) throws PluginException { OntologyWikiPageName owpn = new OntologyWikiPageName(omemo.getFormDataAlias().toUpperCase(), omemo.getFormDataVersionDate()); String wikiPageFullFileName = WikiPageName2FullFileName(context, owpn.toString()); String rdfFileNameWithPath = getWorkDir(context) + File.separator + owpn.toFileName(); FileOutputStream fos = null; FileInputStream fis = null; try { fos = new FileOutputStream(wikiPageFullFileName); fis = new FileInputStream(rdfFileNameWithPath); InfoExtractor infoe = new InfoExtractor(fis, omemo.getFormDataNS(), omemo.getFormDataOntLang()); infoe.writePage(getWorkDir(context), owpn, Omemo.checksWikiPageName); fis.close(); fos.close(); } catch (Exception e) { log.error("Can not read local rdf file or can not write wiki page"); throw new PluginException("Error creating wiki pages. See logs"); } } | 896,918 |
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.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; } | private String fazHttpRequest(String u) { StringBuilder str = new StringBuilder(); URL url = null; URLConnection urlC = null; try { url = new URL(u.toString()); urlC = url.openConnection(); BufferedReader in = new BufferedReader(new InputStreamReader(urlC.getInputStream())); String inputLine; while ((inputLine = in.readLine()) != null) { str.append(inputLine); } in.close(); } catch (Exception e) { System.out.println("[fazHttpRequest]" + e); } return (str.length() > 0) ? str.toString() : null; } | 896,919 |
1 | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public void command() { JFileChooser chooser = new JFileChooser(); chooser.setCurrentDirectory(new File(dir)); int returnVal = chooser.showOpenDialog(null); if (returnVal == JFileChooser.APPROVE_OPTION) { filename = chooser.getSelectedFile().getAbsolutePath(); String f2 = ""; for (int i = 0; i < filename.length(); ++i) { if (filename.charAt(i) != '\\') { f2 = f2 + filename.charAt(i); } else f2 = f2 + '/'; } filename = f2; if (filename.contains(dir)) { filename = filename.substring(dir.length()); } else { try { FileChannel srcFile = new FileInputStream(filename).getChannel(); FileChannel dstFile; filename = "ueditor_files/" + chooser.getSelectedFile().getName(); File newFile; if (!(newFile = new File(dir + filename)).createNewFile()) { dstFile = new FileInputStream(dir + filename).getChannel(); newFile = null; } else { dstFile = new FileOutputStream(newFile).getChannel(); } dstFile.transferFrom(srcFile, 0, srcFile.size()); srcFile.close(); dstFile.close(); System.out.println("file copyed to: " + dir + filename); } catch (Exception e) { e.printStackTrace(); label.setIcon(InputText.iconX); filename = null; for (Group g : groups) { g.updateValidity(true); } return; } } label.setIcon(InputText.iconV); for (Group g : groups) { g.updateValidity(true); } } } | 896,920 |
1 | public static void copyFile(File sourceFile, File destFile, boolean overwrite) throws IOException, DirNotFoundException, FileNotFoundException, FileExistsAlreadyException { File destDir = new File(destFile.getParent()); if (!destDir.exists()) { throw new DirNotFoundException(destDir.getAbsolutePath()); } if (!sourceFile.exists()) { throw new FileNotFoundException(sourceFile.getAbsolutePath()); } if (!overwrite && destFile.exists()) { throw new FileExistsAlreadyException(destFile.getAbsolutePath()); } FileInputStream in = new FileInputStream(sourceFile); FileOutputStream out = new FileOutputStream(destFile); byte[] buffer = new byte[8 * 1024]; int count = 0; do { out.write(buffer, 0, count); count = in.read(buffer, 0, buffer.length); } while (count != -1); in.close(); out.close(); } | public static void copyFiles(String strPath, String trgPath) { File src = new File(strPath); File trg = new File(trgPath); if (src.isDirectory()) { if (trg.exists() != true) trg.mkdirs(); String list[] = src.list(); for (int i = 0; i < list.length; i++) { String strPath_1 = src.getAbsolutePath() + SEPARATOR + list[i]; String trgPath_1 = trg.getAbsolutePath() + SEPARATOR + list[i]; copyFiles(strPath_1, trgPath_1); } } else { try { FileChannel srcChannel = new FileInputStream(strPath).getChannel(); FileChannel dstChannel = new FileOutputStream(trgPath).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (FileNotFoundException e) { System.out.println("[Error] File not found: " + e.getMessage()); } catch (IOException e) { System.out.println("[Error] " + e.getMessage()); } } } | 896,921 |
0 | public static String hash(String text) throws Exception { StringBuffer hexString; MessageDigest mdAlgorithm = MessageDigest.getInstance("MD5"); mdAlgorithm.update(text.getBytes()); byte[] digest = mdAlgorithm.digest(); hexString = new StringBuffer(); for (int i = 0; i < digest.length; i++) { text = Integer.toHexString(0xFF & digest[i]); if (text.length() < 2) { text = "0" + text; } hexString.append(text); } return hexString.toString(); } | public static void copyFile(File src, String srcEncoding, File dest, String destEncoding) throws IOException { InputStreamReader in = new InputStreamReader(new FileInputStream(src), srcEncoding); OutputStreamWriter out = new OutputStreamWriter(new RobustFileOutputStream(dest), destEncoding); int c; while ((c = in.read()) != -1) out.write(c); out.flush(); in.close(); out.close(); } | 896,922 |
0 | 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) { } } | @Override public String addUserIdentity(OpenIDItem identity, long userId) throws DatabaseException { if (identity == null) throw new NullPointerException("identity"); if (identity.getIdentity() == null || "".equals(identity.getIdentity())) throw new NullPointerException("identity.getIdentity()"); try { getConnection().setAutoCommit(false); } catch (SQLException e) { LOGGER.warn("Unable to set autocommit off", e); } String retID = "exist"; PreparedStatement insSt = null, seqSt = null; try { int modified = 0; insSt = getConnection().prepareStatement(INSERT_IDENTITY_STATEMENT); insSt.setLong(1, userId); insSt.setString(2, identity.getIdentity()); modified = insSt.executeUpdate(); seqSt = getConnection().prepareStatement(USER_IDENTITY_VALUE); ResultSet rs = seqSt.executeQuery(); while (rs.next()) { retID = rs.getString(1); } if (modified == 1) { getConnection().commit(); LOGGER.debug("DB has been updated. Queries: \"" + seqSt + "\" and \"" + insSt + "\""); } else { getConnection().rollback(); LOGGER.debug("DB has not been updated -> rollback! Queries: \"" + seqSt + "\" and \"" + insSt + "\""); retID = "error"; } } catch (SQLException e) { LOGGER.error(e); retID = "error"; } finally { closeConnection(); } return retID; } | 896,923 |
1 | public static String hash(String value) { MessageDigest md = null; try { md = MessageDigest.getInstance(HASH_ALGORITHM); } catch (NoSuchAlgorithmException e) { throw new CryptoException(e); } try { md.update(value.getBytes(INPUT_ENCODING)); } catch (UnsupportedEncodingException e) { throw new CryptoException(e); } return new BASE64Encoder().encode(md.digest()); } | private boolean setupDatabase() { if (DoInstallationTasks.DEBUG_DB) { System.out.println("About to setup database"); } if (installer.getRootDBUsername() != null && installer.getRootDBUsername().length() > 1 && installer.getRootDBPassword() != null && installer.getRootDBPassword().length() > 1) { if (DoInstallationTasks.DEBUG_DB) { System.out.println("Going to call doDBRootPortions"); } if (!doDBRootPortions(installer.getPachyDBHost(), installer.getPachyDBPort(), installer.getPachyDBName(), installer.getPachyDBUsername(), installer.getPachyDBPassword(), installer.getRootDBUsername(), installer.getRootDBPassword())) { System.err.println("Root work not able to be completed, " + "not continuing."); return false; } if (DoInstallationTasks.DEBUG_DB) { System.out.println("Back from call to doDBRootPortions"); } } if (DoInstallationTasks.DEBUG_DB) { System.out.println("Going to open SQL files"); } Connection conn = getDBConnection(installer.getPachyDBHost(), installer.getPachyDBPort(), installer.getPachyDBName(), installer.getPachyDBUsername(), installer.getPachyDBPassword()); if (conn == null) { return false; } Statement stmt = null; boolean havePachy20 = false; try { stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery("SELECT * FROM PRESENTATION LIMIT 1"); if (rs.next()) { havePachy20 = true; } if (!havePachy20) { rs = stmt.executeQuery("SELECT * FROM SCREEN LIMIT 1"); if (rs.next()) { havePachy20 = true; } } } catch (SQLException sqle) { System.err.println("Error doing check for presentation, means " + "2.0 doesn't exist"); System.out.println("SQLException: " + sqle.getMessage()); System.out.println("SQLState: " + sqle.getSQLState()); System.out.println("VendorError: " + sqle.getErrorCode()); } finally { try { stmt.close(); } catch (SQLException sqlex) { } } if (havePachy20) { Object[] options = { Pachyderm21Installer.ISTRINGS.getString("dialog.abort"), Pachyderm21Installer.ISTRINGS.getString("dialog.keep"), Pachyderm21Installer.ISTRINGS.getString("dialog.overwrite") }; int result = JOptionPane.showOptionDialog(this.installer, Pachyderm21Installer.ISTRINGS.getString("dit.pachy20msg"), Pachyderm21Installer.ISTRINGS.getString("dit.pachy20title"), JOptionPane.DEFAULT_OPTION, JOptionPane.QUESTION_MESSAGE, null, options, options[0]); if (result == 0) { System.out.println("Aborted by user before doing database"); return false; } else if (result == 2) { havePachy20 = false; } } else { Object[] options = { Pachyderm21Installer.ISTRINGS.getString("dialog.continue"), Pachyderm21Installer.ISTRINGS.getString("dialog.abort") }; int result = JOptionPane.showOptionDialog(this.installer, Pachyderm21Installer.ISTRINGS.getString("dit.nopachy20msg"), Pachyderm21Installer.ISTRINGS.getString("dit.nopachy20title"), JOptionPane.DEFAULT_OPTION, JOptionPane.QUESTION_MESSAGE, null, options, options[0]); if (result == 1) { System.out.println("Aborted by user before doing database"); return false; } } boolean dbError = false; if (havePachy20) { try { java.util.Date d = new java.util.Date(); stmt = conn.createStatement(); stmt.executeUpdate("RENAME TABLE APDEFAULT TO APDEFAULT_2_0_" + d.getTime()); } catch (SQLException sqle) { System.err.println("Error doing check for presentation, " + "means 2.0 doesn't exist"); System.out.println("SQLException: " + sqle.getMessage()); System.out.println("SQLState: " + sqle.getSQLState()); System.out.println("VendorError: " + sqle.getErrorCode()); dbError = true; } finally { try { stmt.close(); } catch (SQLException sqlex) { } } } if (dbError) { return false; } try { stmt = conn.createStatement(); stmt.executeUpdate("START TRANSACTION"); InputStreamReader isr = new InputStreamReader(getClass().getResourceAsStream("apdefaults.sql")); LineNumberReader lnr = new LineNumberReader(isr); String linein; while ((linein = lnr.readLine()) != null) { if (linein.trim().length() > 0) { String lineout = replaceTemplateVariables(linein); stmt.executeUpdate(lineout); } } stmt.executeUpdate("COMMIT"); lnr.close(); } catch (SQLException sqle) { System.err.println("error doing apdefaults.sql template"); System.out.println("sqlexception: " + sqle.getMessage()); System.out.println("sqlstate: " + sqle.getSQLState()); System.out.println("vendorerror: " + sqle.getErrorCode()); if (stmt != null) { try { stmt.executeUpdate("ROLLBACK"); } catch (SQLException sqlex) { } } dbError = true; } catch (Exception e) { System.err.println("Error doing apdefaults.sql template"); e.printStackTrace(System.err); if (stmt != null) { try { stmt.executeUpdate("ROLLBACK"); } catch (SQLException sqlex) { } } dbError = true; } finally { try { stmt.close(); } catch (SQLException sqlex) { } } if (dbError) { return false; } try { stmt = conn.createStatement(); stmt.executeUpdate("START TRANSACTION"); InputStreamReader isr = new InputStreamReader(getClass().getResourceAsStream("Pachyderm21.sql")); LineNumberReader lnr = new LineNumberReader(isr); String linein; while ((linein = lnr.readLine()) != null) { if (linein.trim().length() > 0) { String lineout = replaceTemplateVariables(linein); if (DoInstallationTasks.DEBUG) { System.out.println("line #" + lnr.getLineNumber()); } stmt.executeUpdate(lineout); } } stmt.executeUpdate("COMMIT"); lnr.close(); } catch (SQLException sqle) { System.err.println("error doing pachyderm21.sql template"); System.out.println("sqlexception: " + sqle.getMessage()); System.out.println("sqlstate: " + sqle.getSQLState()); System.out.println("vendorerror: " + sqle.getErrorCode()); if (stmt != null) { try { stmt.executeUpdate("ROLLBACK"); } catch (SQLException sqlex) { } } dbError = true; } catch (Exception e) { System.err.println("error doing pachyderm21.sql template"); e.printStackTrace(System.err); if (stmt != null) { try { stmt.executeUpdate("ROLLBACK"); } catch (SQLException sqlex) { } } dbError = true; } finally { try { stmt.close(); } catch (SQLException sqlex) { } } if (dbError) { return false; } if (!havePachy20) { try { stmt = conn.createStatement(); stmt.executeUpdate("START TRANSACTION"); InputStreamReader isr = new InputStreamReader(getClass().getResourceAsStream("Pachyderm" + "21new.sql")); LineNumberReader lnr = new LineNumberReader(isr); String linein; while ((linein = lnr.readLine()) != null) { if (linein.trim().length() > 0) { String lineout = replaceTemplateVariables(linein); if (DoInstallationTasks.DEBUG) { System.out.println("Line #" + lnr.getLineNumber()); } stmt.executeUpdate(lineout); } } stmt.executeUpdate("COMMIT"); lnr.close(); } catch (SQLException sqle) { System.err.println("Error doing Pachyderm21new.sql template"); System.out.println("SQLException: " + sqle.getMessage()); System.out.println("SQLState: " + sqle.getSQLState()); System.out.println("VendorError: " + sqle.getErrorCode()); if (stmt != null) { try { stmt.executeUpdate("ROLLBACK"); } catch (SQLException sqlex) { } } dbError = true; } catch (Exception e) { System.err.println("Error doing Pachyderm21.sql template"); e.printStackTrace(System.err); if (stmt != null) { try { stmt.executeUpdate("ROLLBACK"); } catch (SQLException sqlex) { } } dbError = true; } finally { try { stmt.close(); } catch (SQLException sqlex) { } } } PreparedStatement ps = null; PreparedStatement ps1 = null; PreparedStatement ps2 = null; PreparedStatement ps3 = null; try { String adminPassword = installer.getAdminPassword(); MessageDigest _md = MessageDigest.getInstance("MD5"); _md.update(adminPassword.getBytes("UTF-8")); byte[] md5 = _md.digest(); ps = conn.prepareStatement("UPDATE AUTHRECORD set PASSWORD=? " + "WHERE USERNAME='administrator'"); ps.setBytes(1, md5); int numupdates = ps.executeUpdate(); if (DEBUG) System.out.println("Changing admin password, " + "numUpdates = " + numupdates); Vector<AdminData> v = installer.getAdditionalAdminAccounts(); String customPropertiesSPFPre = "{\n \"CXMultiValueArchive\" = {" + "\n \"class\" = " + "\"ca.ucalgary.apollo.core." + "CXMutableMultiValue\";\n " + "\"values\" = (\n " + "{\n \"class\" = \"ca.ucalgary." + "apollo.core.CXMultiValue$Value\";\n" + " \"identifier\" = \"0\";\n " + "\"label\" = \"work\";\n " + "\"value\" = \""; String customPropertiesSPFPost = "\";\n }\n );\n \"identCounter\" = \"1\";\n };\n}"; if (v.size() > 0) { ps = conn.prepareStatement("INSERT INTO `APPERSON` VALUES " + "(NULL,NULL,NULL,NOW(),NULL,NULL," + "?,?,NULL,NULL,NULL,NULL,NULL," + "NULL,?,NULL,NULL,NULL,NULL,NOW()," + "NULL,NULL,NULL,NULL,NULL,NULL,?," + "NULL,NULL,NULL,NULL,NULL)"); ps1 = conn.prepareStatement("INSERT INTO `AUTHRECORD` VALUES " + "(?,'pachyderm',?,NULL)"); ps2 = conn.prepareStatement("INSERT INTO `AUTHMAP` " + "(external_id,external_realm," + "map_id,person_id) " + "VALUES (?,'pachyderm',?,?)"); ps3 = conn.prepareStatement("INSERT INTO `GROUPPERSONJOIN` " + "(group_id,person_id) " + "VALUES(1, ?)"); } for (int i = 0; i < v.size(); ++i) { AdminData ad = (AdminData) v.elementAt(i); _md = MessageDigest.getInstance("MD5"); _md.update(ad.getPassword().getBytes("UTF-8")); md5 = _md.digest(); ps.setString(1, customPropertiesSPFPre + ad.getEmail() + customPropertiesSPFPost); ps.setString(2, ad.getFirstName()); ps.setString(3, ad.getLastName()); ps.setInt(4, i + 2); numupdates = ps.executeUpdate(); if (numupdates == 1) { ps1.setBytes(1, md5); ps1.setString(2, ad.getUsername()); ps1.executeUpdate(); ps2.setString(1, ad.getUsername() + "@pachyderm"); ps2.setInt(2, i + 2); ps2.setInt(3, i + 2); ps2.executeUpdate(); ps3.setInt(1, i + 2); ps3.executeUpdate(); } } } catch (SQLException sqle) { System.err.println("Error doing Pachyderm21new.sql template"); System.out.println("SQLException: " + sqle.getMessage()); System.out.println("SQLState: " + sqle.getSQLState()); System.out.println("VendorError: " + sqle.getErrorCode()); dbError = true; } catch (Exception e) { System.err.println("Error doing Pachyderm21.sql template"); e.printStackTrace(System.err); dbError = true; } finally { if (ps != null) { try { ps.close(); } catch (SQLException sqlex) { } } if (ps1 != null) { try { ps1.close(); } catch (SQLException sqlex) { } } if (ps2 != null) { try { ps2.close(); } catch (SQLException sqlex) { } } } return true; } | 896,924 |
1 | public Program createNewProgram(int projectID, String name, String description) throws AdaptationException { Program program = null; Connection connection = null; Statement statement = null; ResultSet resultSet = null; try { connection = DriverManager.getConnection(CONN_STR); connection.setAutoCommit(false); statement = connection.createStatement(); String query = "INSERT INTO Programs(projectID, name, " + "description, sourcePath) VALUES ( " + projectID + ", " + "'" + name + "', " + "'" + description + "', " + "'" + "[unknown]" + "')"; log.debug("SQL Query:\n" + query); statement.executeUpdate(query); query = "SELECT * FROM Programs WHERE " + " projectID = " + projectID + " AND " + " name = '" + name + "' AND " + " description = '" + description + "'"; resultSet = statement.executeQuery(query); if (!resultSet.next()) { connection.rollback(); String msg = "Attempt to create program failed"; log.error(msg); throw new AdaptationException(msg); } program = getProgram(resultSet); connection.commit(); } catch (SQLException ex) { try { connection.rollback(); } catch (Exception e) { } String msg = "SQLException in createNewProgram"; 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 program; } | public ProjectDeploymentConfiguration deleteProjectDeploymentConfig(int id) throws AdaptationException { ProjectDeploymentConfiguration config = null; Connection connection = null; Statement statement = null; ResultSet resultSet = null; try { String query = "SELECT * FROM ProjectDeploymentConfigurations " + "WHERE id = " + id; connection = DriverManager.getConnection(CONN_STR); statement = connection.createStatement(); resultSet = statement.executeQuery(query); if (!resultSet.next()) { connection.rollback(); String msg = "Attempt to delete project deployment " + "configuration failed."; log.error(msg); throw new AdaptationException(msg); } config = getProjectDeploymentConfiguration(resultSet); query = "DELETE FROM ProjectDeploymentConfigurations " + "WHERE id = " + id; statement.executeUpdate(query); connection.commit(); } catch (SQLException ex) { try { connection.rollback(); } catch (Exception e) { } String msg = "SQLException in deleteProjectDeploymentConfig"; 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 config; } | 896,925 |
0 | public void testCodingBeyondContentLimitFromFile() throws Exception { ByteArrayOutputStream baos = new ByteArrayOutputStream(); WritableByteChannel channel = newChannel(baos); HttpParams params = new BasicHttpParams(); SessionOutputBuffer outbuf = new SessionOutputBufferImpl(1024, 128, params); HttpTransportMetricsImpl metrics = new HttpTransportMetricsImpl(); LengthDelimitedEncoder encoder = new LengthDelimitedEncoder(channel, outbuf, metrics, 16); File tmpFile = File.createTempFile("testFile", "txt"); FileOutputStream fout = new FileOutputStream(tmpFile); OutputStreamWriter wrtout = new OutputStreamWriter(fout); wrtout.write("stuff;"); wrtout.write("more stuff; and a lot more stuff"); wrtout.flush(); wrtout.close(); FileChannel fchannel = new FileInputStream(tmpFile).getChannel(); encoder.transfer(fchannel, 0, 20); String s = baos.toString("US-ASCII"); assertTrue(encoder.isCompleted()); assertEquals("stuff;more stuff", s); tmpFile.delete(); } | private Bitmap fetchImage(String urlstr) throws Exception { URL url; url = new URL(urlstr); HttpURLConnection c = (HttpURLConnection) url.openConnection(); c.setDoInput(true); c.setRequestProperty("User-Agent", "Agent"); c.connect(); InputStream is = c.getInputStream(); Bitmap img; img = BitmapFactory.decodeStream(is); return img; } | 896,926 |
0 | public static void main(String[] args) throws IOException { FileChannel fc = new FileOutputStream("src/com/aaron/nio/data.txt").getChannel(); fc.write(ByteBuffer.wrap("dfsdf ".getBytes())); fc.close(); fc = new RandomAccessFile("src/com/aaron/nio/data.txt", "rw").getChannel(); fc.position(fc.size()); fc.write(ByteBuffer.wrap("中文的 ".getBytes())); fc.close(); fc = new FileInputStream("src/com/aaron/nio/data.txt").getChannel(); ByteBuffer buff = ByteBuffer.allocate(1024); fc.read(buff); buff.flip(); while (buff.hasRemaining()) { System.out.print(buff.getChar()); } fc.close(); } | public RTUser getUserInfo(final String username) { getSession(); Map<String, String> attributes = Collections.emptyMap(); final HttpGet get = new HttpGet(m_baseURL + "/REST/1.0/user/" + username); try { final HttpResponse response = getClient().execute(get); int responseCode = response.getStatusLine().getStatusCode(); if (responseCode != HttpStatus.SC_OK) { throw new RequestTrackerException("Received a non-200 response code from the server: " + responseCode); } else { if (response.getEntity() != null) { attributes = parseResponseStream(response.getEntity().getContent()); } } } catch (final Exception e) { LogUtils.errorf(this, e, "An exception occurred while getting user info for " + username); return null; } final String id = attributes.get("id"); final String realname = attributes.get("realname"); final String email = attributes.get("emailaddress"); if (id == null || "".equals(id)) { LogUtils.errorf(this, "Unable to retrieve ID from user info."); return null; } return new RTUser(Long.parseLong(id.replace("user/", "")), username, realname, email); } | 896,927 |
0 | private static List retrieveQuotes(Report report, Symbol symbol, String prefix, TradingDate startDate, TradingDate endDate) throws ImportExportException { List quotes = new ArrayList(); String URLString = constructURL(symbol, prefix, startDate, endDate); EODQuoteFilter filter = new GoogleEODQuoteFilter(symbol); PreferencesManager.ProxyPreferences proxyPreferences = PreferencesManager.getProxySettings(); try { URL url = new URL(URLString); InputStreamReader input = new InputStreamReader(url.openStream()); BufferedReader bufferedInput = new BufferedReader(input); String line = bufferedInput.readLine(); while (line != null) { line = bufferedInput.readLine(); if (line != null) { try { EODQuote quote = filter.toEODQuote(line); quotes.add(quote); verify(report, quote); } catch (QuoteFormatException e) { report.addError(Locale.getString("GOOGLE_DISPLAY_URL") + ":" + symbol + ":" + Locale.getString("ERROR") + ": " + e.getMessage()); } } } bufferedInput.close(); } catch (BindException e) { throw new ImportExportException(Locale.getString("UNABLE_TO_CONNECT_ERROR", e.getMessage())); } catch (ConnectException e) { throw new ImportExportException(Locale.getString("UNABLE_TO_CONNECT_ERROR", e.getMessage())); } catch (UnknownHostException e) { throw new ImportExportException(Locale.getString("UNKNOWN_HOST_ERROR", e.getMessage())); } catch (NoRouteToHostException e) { throw new ImportExportException(Locale.getString("DESTINATION_UNREACHABLE_ERROR", e.getMessage())); } catch (MalformedURLException e) { throw new ImportExportException(Locale.getString("INVALID_PROXY_ERROR", proxyPreferences.host, proxyPreferences.port)); } catch (FileNotFoundException e) { } catch (IOException e) { throw new ImportExportException(Locale.getString("ERROR_DOWNLOADING_QUOTES")); } return quotes; } | 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); } } | 896,928 |
0 | private void loadFile(File file) throws Exception { Edl edl = new Edl("file:///" + file.getAbsolutePath()); URL url = ExtractaHelper.retrieveUrl(edl.getUrlRetrievalDescriptor()); String sUrlString = url.toExternalForm(); if (sUrlString.startsWith("file:/") && (sUrlString.charAt(6) != '/')) { sUrlString = sUrlString.substring(0, 6) + "//" + sUrlString.substring(6); } Document document = DomHelper.parseHtml(url.openStream()); m_inputPanel.setDocument(document); m_resultPanel.setContext(new ResultContext(edl, document, url)); initNameCounters(edl.getItemDescriptors()); m_outputFile = file; m_sUrlString = sUrlString; m_urlTF.setText(m_sUrlString); updateHistroy(m_outputFile); setModified(false); } | private static String getHash(char[] passwd, String algorithm) throws NoSuchAlgorithmException { MessageDigest alg = MessageDigest.getInstance(algorithm); alg.reset(); alg.update(new String(passwd).getBytes()); byte[] digest = alg.digest(); StringBuilder sb = new StringBuilder(); for (int i = 0; i < digest.length; i++) { String hex = Integer.toHexString(0xff & digest[i]); if (hex.length() == 1) { sb.append('0'); } sb.append(hex); } return sb.toString(); } | 896,929 |
1 | 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 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); } | 896,930 |
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 static int save(File inputFile, File outputFile) throws IOException { InputStream in = null; OutputStream out = null; try { in = new FileInputStream(inputFile); outputFile.getParentFile().mkdirs(); out = new FileOutputStream(outputFile); } catch (Exception e) { e.getMessage(); } try { return IOUtils.copy(in, out); } finally { IOUtils.closeQuietly(in); IOUtils.closeQuietly(out); try { if (out != null) { out.close(); } } catch (IOException ioe) { ioe.getMessage(); } try { if (in != null) { in.close(); } } catch (IOException ioe) { ioe.getMessage(); } } } | 896,931 |
1 | private String createCSVFile(String fileName) throws FileNotFoundException, IOException { String csvFile = fileName + ".csv"; BufferedReader buf = new BufferedReader(new FileReader(fileName)); BufferedWriter out = new BufferedWriter(new FileWriter(csvFile)); String line; while ((line = buf.readLine()) != null) out.write(line + "\n"); buf.close(); out.close(); return csvFile; } | public long copyDirAllFilesToDirectoryRecursive(String baseDirStr, String destDirStr, boolean copyOutputsRtIDsDirs) throws Exception { long plussQuotaSize = 0; if (baseDirStr.endsWith(sep)) { baseDirStr = baseDirStr.substring(0, baseDirStr.length() - 1); } if (destDirStr.endsWith(sep)) { destDirStr = destDirStr.substring(0, destDirStr.length() - 1); } FileUtils.getInstance().createDirectory(destDirStr); BufferedInputStream in = null; BufferedOutputStream out = null; byte dataBuff[] = new byte[bufferSize]; File baseDir = new File(baseDirStr); baseDir.mkdirs(); if (!baseDir.exists()) { createDirectory(baseDirStr); } if ((baseDir.exists()) && (baseDir.isDirectory())) { String[] entryList = baseDir.list(); if (entryList.length > 0) { for (int pos = 0; pos < entryList.length; pos++) { String entryName = entryList[pos]; String oldPathFileName = baseDirStr + sep + entryName; File entryFile = new File(oldPathFileName); if (entryFile.isFile()) { String newPathFileName = destDirStr + sep + entryName; File newFile = new File(newPathFileName); if (newFile.exists()) { plussQuotaSize -= newFile.length(); newFile.delete(); } in = new BufferedInputStream(new FileInputStream(oldPathFileName), bufferSize); out = new BufferedOutputStream(new FileOutputStream(newPathFileName), bufferSize); int readLen; while ((readLen = in.read(dataBuff)) > 0) { out.write(dataBuff, 0, readLen); plussQuotaSize += readLen; } out.flush(); in.close(); out.close(); } if (entryFile.isDirectory()) { boolean enableCopyDir = false; if (copyOutputsRtIDsDirs) { enableCopyDir = true; } else { if (entryFile.getParentFile().getName().equals("outputs")) { enableCopyDir = false; } else { enableCopyDir = true; } } if (enableCopyDir) { plussQuotaSize += this.copyDirAllFilesToDirectoryRecursive(baseDirStr + sep + entryName, destDirStr + sep + entryName, copyOutputsRtIDsDirs); } } } } } else { throw new Exception("Base dir not exist ! baseDirStr = (" + baseDirStr + ")"); } return plussQuotaSize; } | 896,932 |
1 | private void copy(File sourceFile, File destinationFile) { try { FileChannel in = new FileInputStream(sourceFile).getChannel(); FileChannel out = new FileOutputStream(destinationFile).getChannel(); try { in.transferTo(0, in.size(), out); in.close(); out.close(); } catch (IOException e) { GTLogger.getInstance().error(e); } } catch (FileNotFoundException e) { GTLogger.getInstance().error(e); } } | private static boolean unzipWithWarning(File source, File targetDirectory, OverwriteValue policy) { try { if (!source.exists()) return false; ZipInputStream input = new ZipInputStream(new FileInputStream(source)); ZipEntry zipEntry = null; byte[] buffer = new byte[1024]; while ((zipEntry = input.getNextEntry()) != null) { if (zipEntry.isDirectory()) continue; File newFile = new File(targetDirectory, zipEntry.getName()); if (newFile.exists()) { switch(policy.value) { case NO_TO_ALL: continue; case YES_TO_ALL: break; default: switch(policy.value = confirmOverwrite(zipEntry.getName())) { case NO_TO_ALL: case NO: continue; default: } } } newFile.getParentFile().mkdirs(); int bytesRead; FileOutputStream output = new FileOutputStream(newFile); while ((bytesRead = input.read(buffer)) != -1) output.write(buffer, 0, bytesRead); output.close(); input.closeEntry(); } input.close(); } catch (Exception exc) { exc.printStackTrace(); return false; } return true; } | 896,933 |
1 | public static void copyFile(File in, File outDir) throws IOException { FileChannel sourceChannel = null; FileChannel destinationChannel = null; try { sourceChannel = new FileInputStream(in).getChannel(); File out = new File(outDir, in.getName()); destinationChannel = new FileOutputStream(out).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); } finally { try { if (sourceChannel != null) { sourceChannel.close(); } } finally { if (destinationChannel != null) { destinationChannel.close(); } } } } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 896,934 |
1 | private static void copy(String srcFilename, String dstFilename, boolean override) throws IOException, XPathFactoryConfigurationException, SAXException, ParserConfigurationException, XPathExpressionException { File fileToCopy = new File(rootDir + "test-output/" + srcFilename); if (fileToCopy.exists()) { File newFile = new File(rootDir + "test-output/" + dstFilename); if (!newFile.exists() || override) { try { FileChannel srcChannel = new FileInputStream(rootDir + "test-output/" + srcFilename).getChannel(); FileChannel dstChannel = new FileOutputStream(rootDir + "test-output/" + dstFilename).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException e) { } } } } | private void copyOneFile(String oldPath, String newPath) { File copiedFile = new File(newPath); try { FileInputStream source = new FileInputStream(oldPath); FileOutputStream destination = new FileOutputStream(copiedFile); FileChannel sourceFileChannel = source.getChannel(); FileChannel destinationFileChannel = destination.getChannel(); long size = sourceFileChannel.size(); sourceFileChannel.transferTo(0, size, destinationFileChannel); source.close(); destination.close(); } catch (Exception exc) { exc.printStackTrace(); } } | 896,935 |
1 | private void writeAndCheckFile(DataFileReader reader, String base, String path, String hash, Reference ref, boolean hashall) throws Exception { Data data = ref.data; File file = new File(base + path); file.getParentFile().mkdirs(); if (Debug.level > 1) System.err.println("read file " + data.file + " at index " + data.index); OutputStream output = new FileOutputStream(file); if (hashall) output = new DigestOutputStream(output, MessageDigest.getInstance("MD5")); reader.read(output, data.index, data.file); output.close(); if (hashall) { String filehash = StringUtils.toHex(((DigestOutputStream) output).getMessageDigest().digest()); if (!hash.equals(filehash)) throw new RuntimeException("hash wasn't equal for " + file); } file.setLastModified(ref.lastmod); if (file.length() != data.size) throw new RuntimeException("corrupted file " + file); } | public Boolean compress(String sSourceDir, ArrayList<String> aFiles, String sDestinationFilename) { logger.debug("compress(%s, %s, %s)", sSourceDir, aFiles, sDestinationFilename); BufferedInputStream oOrigin = null; FileOutputStream oDestination; ZipOutputStream oOutput = null; Iterator<String> oIterator; byte[] aData; try { oDestination = new FileOutputStream(sDestinationFilename); oOutput = new ZipOutputStream(new BufferedOutputStream(oDestination)); aData = new byte[BUFFER_SIZE]; oIterator = aFiles.iterator(); while (oIterator.hasNext()) { try { String sFilename = (String) oIterator.next(); FileInputStream fisInput = new FileInputStream(sSourceDir + File.separator + sFilename); oOrigin = new BufferedInputStream(fisInput, BUFFER_SIZE); ZipEntry oEntry = new ZipEntry(sFilename.replace('\\', '/')); oOutput.putNextEntry(oEntry); int iCount; while ((iCount = oOrigin.read(aData, 0, BUFFER_SIZE)) != -1) oOutput.write(aData, 0, iCount); } finally { StreamHelper.close(oOrigin); } } } catch (Exception oException) { logger.error(oException.getMessage(), oException); return false; } finally { StreamHelper.close(oOutput); } return true; } | 896,936 |
0 | public void render(final HttpServletRequest request, final HttpServletResponse response, InputStream inputStream, final Throwable t, final String contentType, final String encoding) throws Exception { if (contentType != null) { response.setContentType(contentType); } if (encoding != null) { response.setCharacterEncoding(encoding); } IOUtils.copy(inputStream, response.getOutputStream()); } | private void openConnection() throws IOException { connection = (HttpURLConnection) url.openConnection(); connection.setDoInput(true); connection.setDoOutput(true); connection.setRequestMethod("POST"); connection.setRequestProperty("Content-Type", "text/xml"); } | 896,937 |
0 | public final void loadAllData(final String ticker, final File output, final CSVFormat outputFormat, final Date from, final Date to) { try { final URL url = buildURL(ticker, from, to); final InputStream is = url.openStream(); final ReadCSV csv = new ReadCSV(is, true, CSVFormat.ENGLISH); final PrintWriter tw = new PrintWriter(new FileWriter(output)); tw.println("date,time,open price,high price,low price," + "close price,volume,adjusted price"); while (csv.next() && !shouldStop()) { final Date date = csv.getDate("date"); final double adjClose = csv.getDouble("adj close"); final double open = csv.getDouble("open"); final double close = csv.getDouble("close"); final double high = csv.getDouble("high"); final double low = csv.getDouble("low"); final double volume = csv.getDouble("volume"); final NumberFormat df = NumberFormat.getInstance(); df.setGroupingUsed(false); final StringBuilder line = new StringBuilder(); line.append(NumericDateUtil.date2Long(date)); line.append(outputFormat.getSeparator()); line.append(NumericDateUtil.time2Int(date)); line.append(outputFormat.getSeparator()); line.append(outputFormat.format(open, this.precision)); line.append(outputFormat.getSeparator()); line.append(outputFormat.format(high, this.precision)); line.append(outputFormat.getSeparator()); line.append(outputFormat.format(low, this.precision)); line.append(outputFormat.getSeparator()); line.append(outputFormat.format(close, this.precision)); line.append(outputFormat.getSeparator()); line.append(df.format(volume)); line.append(outputFormat.getSeparator()); line.append(outputFormat.format(adjClose, this.precision)); tw.println(line.toString()); } tw.close(); } catch (final IOException ex) { throw new LoaderError(ex); } } | public void doPost(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException { PrintWriter out = null; ServletOutputStream outstream = null; try { String action = req.getParameter("nmrshiftdbaction"); String relativepath = ServletUtils.expandRelative(this.getServletConfig(), "/WEB-INF"); TurbineConfig tc = new TurbineConfig(relativepath + "..", relativepath + getServletConfig().getInitParameter("properties")); tc.init(); int spectrumId = -1; DBSpectrum spectrum = null; Export export = null; String format = req.getParameter("format"); if (action.equals("test")) { try { res.setContentType("text/plain"); out = res.getWriter(); List l = DBSpectrumPeer.executeQuery("select SPECTRUM_ID from SPECTRUM limit 1"); if (l.size() > 0) spectrumId = ((Record) l.get(0)).getValue(1).asInt(); out.write("success"); } catch (Exception ex) { out.write("failure"); } } else if (action.equals("rss")) { int numbertoexport = 10; out = res.getWriter(); if (req.getParameter("numbertoexport") != null) { try { numbertoexport = Integer.parseInt(req.getParameter("numbertoexport")); if (numbertoexport < 1 || numbertoexport > 20) throw new NumberFormatException("Number to small/large"); } catch (NumberFormatException ex) { out.println("The parameter <code>numbertoexport</code>must be an integer from 1 to 20"); } } res.setContentType("text/xml"); RssWriter rssWriter = new RssWriter(); rssWriter.setWriter(res.getWriter()); AtomContainerSet soac = new AtomContainerSet(); String query = "select distinct MOLECULE.MOLECULE_ID from MOLECULE, SPECTRUM where SPECTRUM.MOLECULE_ID = MOLECULE.MOLECULE_ID and SPECTRUM.REVIEW_FLAG =\"true\" order by MOLECULE.DATE desc;"; List l = NmrshiftdbUserPeer.executeQuery(query); for (int i = 0; i < numbertoexport; i++) { if (i == l.size()) break; DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(((Record) l.get(i)).getValue(1).asInt())); IMolecule cdkmol = mol.getAsCDKMoleculeAsEntered(1); soac.addAtomContainer(cdkmol); rssWriter.getLinkmap().put(cdkmol, mol.getEasylink(req)); rssWriter.getDatemap().put(cdkmol, mol.getDate()); rssWriter.getTitlemap().put(cdkmol, mol.getChemicalNamesAsOneStringWithFallback()); rssWriter.getCreatormap().put(cdkmol, mol.getNmrshiftdbUser().getUserName()); rssWriter.setCreator(GeneralUtils.getAdminEmail(getServletConfig())); Vector v = mol.getDBCanonicalNames(); for (int k = 0; k < v.size(); k++) { DBCanonicalName canonName = (DBCanonicalName) v.get(k); if (canonName.getDBCanonicalNameType().getCanonicalNameType() == "INChI") { rssWriter.getInchimap().put(cdkmol, canonName.getName()); break; } } rssWriter.setTitle("NMRShiftDB"); rssWriter.setLink("http://www.nmrshiftdb.org"); rssWriter.setDescription("NMRShiftDB is an open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data"); rssWriter.setPublisher("NMRShiftDB.org"); rssWriter.setImagelink("http://www.nmrshiftdb.org/images/nmrshift-logo.gif"); rssWriter.setAbout("http://www.nmrshiftdb.org/NmrshiftdbServlet?nmrshiftdbaction=rss"); Collection coll = new ArrayList(); Vector spectra = mol.selectSpectra(null); for (int k = 0; k < spectra.size(); k++) { Element el = ((DBSpectrum) spectra.get(k)).getCmlSpect(); Element el2 = el.getChildElements().get(0); el.removeChild(el2); coll.add(el2); } rssWriter.getMultiMap().put(cdkmol, coll); } rssWriter.write(soac); } else if (action.equals("getattachment")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); DBSample sample = DBSamplePeer.retrieveByPK(new NumberKey(req.getParameter("sampleid"))); outstream.write(sample.getAttachment()); } else if (action.equals("createreport")) { res.setContentType("application/pdf"); outstream = res.getOutputStream(); boolean yearly = req.getParameter("style").equals("yearly"); int yearstart = Integer.parseInt(req.getParameter("yearstart")); int yearend = Integer.parseInt(req.getParameter("yearend")); int monthstart = 0; int monthend = 0; if (!yearly) { monthstart = Integer.parseInt(req.getParameter("monthstart")); monthend = Integer.parseInt(req.getParameter("monthend")); } int type = Integer.parseInt(req.getParameter("type")); JasperReport jasperReport = (JasperReport) JRLoader.loadObject(relativepath + "/reports/" + (yearly ? "yearly" : "monthly") + "_report_" + type + ".jasper"); Map parameters = new HashMap(); if (yearly) parameters.put("HEADER", "Report for years " + yearstart + " - " + yearend); else parameters.put("HEADER", "Report for " + monthstart + "/" + yearstart + " - " + monthend + "/" + yearend); DBConnection dbconn = TurbineDB.getConnection(); Connection conn = dbconn.getConnection(); Statement stmt = conn.createStatement(); ResultSet rs = null; if (type == 1) { rs = stmt.executeQuery("select YEAR(DATE) as YEAR, " + (yearly ? "" : " MONTH(DATE) as MONTH, ") + "AFFILIATION_1, AFFILIATION_2, MACHINE.NAME as NAME, count(*) as C, sum(WISHED_SPECTRUM like '%13C%' or WISHED_SPECTRUM like '%variable temperature%' or WISHED_SPECTRUM like '%ID sel. NOE%' or WISHED_SPECTRUM like '%solvent suppression%' or WISHED_SPECTRUM like '%standard spectrum%') as 1_D, sum(WISHED_SPECTRUM like '%H,H-COSY%' or WISHED_SPECTRUM like '%NOESY%' or WISHED_SPECTRUM like '%HMQC%' or WISHED_SPECTRUM like '%HMBC%') as 2_D, sum(OTHER_WISHED_SPECTRUM!='') as SPECIAL, sum(OTHER_NUCLEI!='') as HETERO, sum(PROCESS='self') as SELF, sum(PROCESS='robot') as ROBOT, sum(PROCESS='worker') as OPERATOR from (SAMPLE join TURBINE_USER using (USER_ID)) join MACHINE on MACHINE.MACHINE_ID=SAMPLE.MACHINE where YEAR(DATE)>=" + yearstart + " and YEAR(DATE)<=" + yearend + " and LOGIN_NAME<>'testuser' group by YEAR, " + (yearly ? "" : "MONTH, ") + "AFFILIATION_1, AFFILIATION_2, MACHINE.NAME"); } else if (type == 2) { rs = stmt.executeQuery("select YEAR(DATE) as YEAR, " + (yearly ? "" : " MONTH(DATE) as MONTH, ") + "MACHINE.NAME as NAME, count(*) as C, sum(WISHED_SPECTRUM like '%13C%' or WISHED_SPECTRUM like '%variable temperature%' or WISHED_SPECTRUM like '%ID sel. NOE%' or WISHED_SPECTRUM like '%solvent suppression%' or WISHED_SPECTRUM like '%standard spectrum%') as 1_D, sum(WISHED_SPECTRUM like '%H,H-COSY%' or WISHED_SPECTRUM like '%NOESY%' or WISHED_SPECTRUM like '%HMQC%' or WISHED_SPECTRUM like '%HMBC%') as 2_D, sum(OTHER_WISHED_SPECTRUM!='') as SPECIAL, sum(OTHER_NUCLEI!='') as HETERO, sum(PROCESS='self') as SELF, sum(PROCESS='robot') as ROBOT, sum(PROCESS='worker') as OPERATOR from (SAMPLE join TURBINE_USER using (USER_ID)) join MACHINE on MACHINE.MACHINE_ID=SAMPLE.MACHINE group by YEAR, " + (yearly ? "" : "MONTH, ") + "MACHINE.NAME"); } JasperPrint jasperPrint = JasperFillManager.fillReport(jasperReport, parameters, new JRResultSetDataSource(rs)); JasperExportManager.exportReportToPdfStream(jasperPrint, outstream); dbconn.close(); } else if (action.equals("exportcmlbyinchi")) { res.setContentType("text/xml"); out = res.getWriter(); String inchi = req.getParameter("inchi"); String spectrumtype = req.getParameter("spectrumtype"); Criteria crit = new Criteria(); crit.add(DBCanonicalNamePeer.NAME, inchi); crit.addJoin(DBCanonicalNamePeer.MOLECULE_ID, DBSpectrumPeer.MOLECULE_ID); crit.addJoin(DBSpectrumPeer.SPECTRUM_TYPE_ID, DBSpectrumTypePeer.SPECTRUM_TYPE_ID); crit.add(DBSpectrumTypePeer.NAME, spectrumtype); try { GeneralUtils.logToSql(crit.toString(), null); } catch (Exception ex) { } Vector spectra = DBSpectrumPeer.doSelect(crit); if (spectra.size() == 0) { out.write("No such molecule or spectrum"); } else { Element cmlElement = new Element("cml"); cmlElement.addAttribute(new Attribute("convention", "nmrshiftdb-convention")); cmlElement.setNamespaceURI("http://www.xml-cml.org/schema"); Element parent = ((DBSpectrum) spectra.get(0)).getDBMolecule().getCML(1); nu.xom.Node cmldoc = parent.getChild(0); ((Element) cmldoc).setNamespaceURI("http://www.xml-cml.org/schema"); parent.removeChildren(); cmlElement.appendChild(cmldoc); for (int k = 0; k < spectra.size(); k++) { Element parentspec = ((DBSpectrum) spectra.get(k)).getCmlSpect(); Node spectrumel = parentspec.getChild(0); parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ((Element) spectrumel).setNamespaceURI("http://www.xml-cml.org/schema"); } out.write(cmlElement.toXML()); } } else if (action.equals("namelist")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ZipOutputStream zipout = new ZipOutputStream(baos); Criteria crit = new Criteria(); crit.addJoin(DBMoleculePeer.MOLECULE_ID, DBSpectrumPeer.MOLECULE_ID); crit.add(DBSpectrumPeer.REVIEW_FLAG, "true"); Vector v = DBMoleculePeer.doSelect(crit); for (int i = 0; i < v.size(); i++) { if (i % 500 == 0) { if (i != 0) { zipout.write(new String("<p>The list is continued <a href=\"nmrshiftdb.names." + i + ".html\">here</a></p></body></html>").getBytes()); zipout.closeEntry(); } zipout.putNextEntry(new ZipEntry("nmrshiftdb.names." + i + ".html")); zipout.write(new String("<html><body><h1>This is a list of strcutures in <a href=\"http://www.nmrshiftdb.org\">NMRShiftDB</a>, starting at " + i + ", Its main purpose is to be found by search engines</h1>").getBytes()); } DBMolecule mol = (DBMolecule) v.get(i); zipout.write(new String("<p><a href=\"" + mol.getEasylink(req) + "\">").getBytes()); Vector cannames = mol.getDBCanonicalNames(); for (int k = 0; k < cannames.size(); k++) { zipout.write(new String(((DBCanonicalName) cannames.get(k)).getName() + " ").getBytes()); } Vector chemnames = mol.getDBChemicalNames(); for (int k = 0; k < chemnames.size(); k++) { zipout.write(new String(((DBChemicalName) chemnames.get(k)).getName() + " ").getBytes()); } zipout.write(new String("</a>. Information we have got: NMR spectra").getBytes()); Vector spectra = mol.selectSpectra(); for (int k = 0; k < spectra.size(); k++) { zipout.write(new String(((DBSpectrum) spectra.get(k)).getDBSpectrumType().getName() + ", ").getBytes()); } if (mol.hasAny3d()) zipout.write(new String("3D coordinates, ").getBytes()); zipout.write(new String("File formats: CML, mol, png, jpeg").getBytes()); zipout.write(new String("</p>").getBytes()); } zipout.write(new String("</body></html>").getBytes()); zipout.closeEntry(); zipout.close(); InputStream is = new ByteArrayInputStream(baos.toByteArray()); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } else if (action.equals("predictor")) { if (req.getParameter("symbol") == null) { res.setContentType("text/plain"); out = res.getWriter(); out.write("please give the symbol to create the predictor for in the request with symbol=X (e. g. symbol=C"); } res.setContentType("application/zip"); outstream = res.getOutputStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ZipOutputStream zipout = new ZipOutputStream(baos); String filename = "org/openscience/nmrshiftdb/PredictionTool.class"; zipout.putNextEntry(new ZipEntry(filename)); JarInputStream jip = new JarInputStream(new FileInputStream(ServletUtils.expandRelative(getServletConfig(), "/WEB-INF/lib/nmrshiftdb-lib.jar"))); JarEntry entry = jip.getNextJarEntry(); while (entry.getName().indexOf("PredictionTool.class") == -1) { entry = jip.getNextJarEntry(); } for (int i = 0; i < entry.getSize(); i++) { zipout.write(jip.read()); } zipout.closeEntry(); zipout.putNextEntry(new ZipEntry("nmrshiftdb.csv")); int i = 0; org.apache.turbine.util.db.pool.DBConnection conn = TurbineDB.getConnection(); HashMap mapsmap = new HashMap(); while (true) { Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery("select HOSE_CODE, VALUE, SYMBOL from HOSE_CODES where CONDITION_TYPE='m' and WITH_RINGS=0 and SYMBOL='" + req.getParameter("symbol") + "' limit " + (i * 1000) + ", 1000"); int m = 0; while (rs.next()) { String code = rs.getString(1); Double value = new Double(rs.getString(2)); String symbol = rs.getString(3); if (mapsmap.get(symbol) == null) { mapsmap.put(symbol, new HashMap()); } for (int spheres = 6; spheres > 0; spheres--) { StringBuffer hoseCodeBuffer = new StringBuffer(); StringTokenizer st = new StringTokenizer(code, "()/"); for (int k = 0; k < spheres; k++) { if (st.hasMoreTokens()) { String partcode = st.nextToken(); hoseCodeBuffer.append(partcode); } if (k == 0) { hoseCodeBuffer.append("("); } else if (k == 3) { hoseCodeBuffer.append(")"); } else { hoseCodeBuffer.append("/"); } } String hoseCode = hoseCodeBuffer.toString(); if (((HashMap) mapsmap.get(symbol)).get(hoseCode) == null) { ((HashMap) mapsmap.get(symbol)).put(hoseCode, new ArrayList()); } ((ArrayList) ((HashMap) mapsmap.get(symbol)).get(hoseCode)).add(value); } m++; } i++; stmt.close(); if (m == 0) break; } Set keySet = mapsmap.keySet(); Iterator it = keySet.iterator(); while (it.hasNext()) { String symbol = (String) it.next(); HashMap hosemap = ((HashMap) mapsmap.get(symbol)); Set keySet2 = hosemap.keySet(); Iterator it2 = keySet2.iterator(); while (it2.hasNext()) { String hoseCode = (String) it2.next(); ArrayList list = ((ArrayList) hosemap.get(hoseCode)); double[] values = new double[list.size()]; for (int k = 0; k < list.size(); k++) { values[k] = ((Double) list.get(k)).doubleValue(); } zipout.write(new String(symbol + "|" + hoseCode + "|" + Statistics.minimum(values) + "|" + Statistics.average(values) + "|" + Statistics.maximum(values) + "\r\n").getBytes()); } } zipout.closeEntry(); zipout.close(); InputStream is = new ByteArrayInputStream(baos.toByteArray()); byte[] buf = new byte[32 * 1024]; int nRead = 0; i = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } else if (action.equals("exportspec") || action.equals("exportmol")) { if (spectrumId > -1) spectrum = DBSpectrumPeer.retrieveByPK(new NumberKey(spectrumId)); else spectrum = DBSpectrumPeer.retrieveByPK(new NumberKey(req.getParameter("spectrumid"))); export = new Export(spectrum); } else if (action.equals("exportmdl")) { res.setContentType("text/plain"); outstream = res.getOutputStream(); DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(req.getParameter("moleculeid"))); outstream.write(mol.getStructureFile(Integer.parseInt(req.getParameter("coordsetid")), false).getBytes()); } else if (action.equals("exportlastinputs")) { format = action; } else if (action.equals("printpredict")) { res.setContentType("text/html"); out = res.getWriter(); HttpSession session = req.getSession(); VelocityContext context = PredictPortlet.getContext(session, true, true, new StringBuffer(), getServletConfig(), req, true); StringWriter w = new StringWriter(); Velocity.mergeTemplate("predictprint.vm", "ISO-8859-1", context, w); out.println(w.toString()); } else { res.setContentType("text/html"); out = res.getWriter(); out.println("No valid action"); } if (format == null) format = ""; if (format.equals("pdf") || format.equals("rtf")) { res.setContentType("application/" + format); out = res.getWriter(); } if (format.equals("docbook")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); } if (format.equals("svg")) { res.setContentType("image/x-svg"); out = res.getWriter(); } if (format.equals("tiff")) { res.setContentType("image/tiff"); outstream = res.getOutputStream(); } if (format.equals("jpeg")) { res.setContentType("image/jpeg"); outstream = res.getOutputStream(); } if (format.equals("png")) { res.setContentType("image/png"); outstream = res.getOutputStream(); } if (format.equals("mdl") || format.equals("txt") || format.equals("cml") || format.equals("cmlboth") || format.indexOf("exsection") == 0) { res.setContentType("text/plain"); out = res.getWriter(); } if (format.equals("simplehtml") || format.equals("exportlastinputs")) { res.setContentType("text/html"); out = res.getWriter(); } if (action.equals("exportlastinputs")) { int numbertoexport = 4; if (req.getParameter("numbertoexport") != null) { try { numbertoexport = Integer.parseInt(req.getParameter("numbertoexport")); if (numbertoexport < 1 || numbertoexport > 20) throw new NumberFormatException("Number to small/large"); } catch (NumberFormatException ex) { out.println("The parameter <code>numbertoexport</code>must be an integer from 1 to 20"); } } NmrshiftdbUser user = null; try { user = NmrshiftdbUserPeer.getByName(req.getParameter("username")); } catch (NmrshiftdbException ex) { out.println("Seems <code>username</code> is not OK: " + ex.getMessage()); } if (user != null) { List l = NmrshiftdbUserPeer.executeQuery("SELECT LAST_DOWNLOAD_DATE FROM TURBINE_USER where LOGIN_NAME=\"" + user.getUserName() + "\";"); Date lastDownloadDate = ((Record) l.get(0)).getValue(1).asDate(); if (((new Date().getTime() - lastDownloadDate.getTime()) / 3600000) < 24) { out.println("Your last download was at " + lastDownloadDate + ". You may download your last inputs only once a day. Sorry for this, but we need to be carefull with resources. If you want to put your last inputs on your homepage best use some sort of cache (e. g. use wget for downlaod with crond and link to this static resource))!"); } else { NmrshiftdbUserPeer.executeStatement("UPDATE TURBINE_USER SET LAST_DOWNLOAD_DATE=NOW() where LOGIN_NAME=\"" + user.getUserName() + "\";"); Vector<String> parameters = new Vector<String>(); String query = "select distinct MOLECULE.MOLECULE_ID from MOLECULE, SPECTRUM where SPECTRUM.MOLECULE_ID = MOLECULE.MOLECULE_ID and SPECTRUM.REVIEW_FLAG =\"true\" and SPECTRUM.USER_ID=" + user.getUserId() + " order by MOLECULE.DATE desc;"; l = NmrshiftdbUserPeer.executeQuery(query); String url = javax.servlet.http.HttpUtils.getRequestURL(req).toString(); url = url.substring(0, url.length() - 17); for (int i = 0; i < numbertoexport; i++) { if (i == l.size()) break; DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(((Record) l.get(i)).getValue(1).asInt())); parameters.add(new String("<a href=\"" + url + "/portal/pane0/Results?nmrshiftdbaction=showDetailsFromHome&molNumber=" + mol.getMoleculeId() + "\"><img src=\"" + javax.servlet.http.HttpUtils.getRequestURL(req).toString() + "?nmrshiftdbaction=exportmol&spectrumid=" + ((DBSpectrum) mol.getDBSpectrums().get(0)).getSpectrumId() + "&format=jpeg&size=150x150&backcolor=12632256\"></a>")); } VelocityContext context = new VelocityContext(); context.put("results", parameters); StringWriter w = new StringWriter(); Velocity.mergeTemplate("lateststructures.vm", "ISO-8859-1", context, w); out.println(w.toString()); } } } if (action.equals("exportspec")) { if (format.equals("txt")) { String lastsearchtype = req.getParameter("lastsearchtype"); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { List l = ParseUtils.parseSpectrumFromSpecFile(req.getParameter("lastsearchvalues")); spectrum.initSimilarity(l, lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)); } Vector v = spectrum.getOptions(); DBMolecule mol = spectrum.getDBMolecule(); out.print(mol.getChemicalNamesAsOneString(false) + mol.getMolecularFormula(false) + "; " + mol.getMolecularWeight() + " Dalton\n\r"); out.print("\n\rAtom\t"); if (spectrum.getDBSpectrumType().getElementSymbol() == ("H")) out.print("Mult.\t"); out.print("Meas."); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\tInput\tDiff"); } out.print("\n\r"); out.print("No.\t"); if (spectrum.getDBSpectrumType().getElementSymbol() == ("H")) out.print("\t"); out.print("Shift"); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\tShift\tM-I"); } out.print("\n\r"); for (int i = 0; i < v.size(); i++) { out.print(((ValuesForVelocityBean) v.get(i)).getDisplayText() + "\t" + ((ValuesForVelocityBean) v.get(i)).getRange()); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\t" + ((ValuesForVelocityBean) v.get(i)).getNameForElements() + "\t" + ((ValuesForVelocityBean) v.get(i)).getDelta()); } out.print("\n\r"); } } if (format.equals("simplehtml")) { String i1 = export.getImage(false, "jpeg", ServletUtils.expandRelative(this.getServletConfig(), "/nmrshiftdbhtml") + "/tmp/" + System.currentTimeMillis(), true); export.pictures[0] = new File(i1).getName(); String i2 = export.getImage(true, "jpeg", ServletUtils.expandRelative(this.getServletConfig(), "/nmrshiftdbhtml") + "/tmp/" + System.currentTimeMillis(), true); export.pictures[1] = new File(i2).getName(); String docbook = export.getHtml(); out.print(docbook); } if (format.equals("pdf") || format.equals("rtf")) { String svgSpec = export.getSpecSvg(400, 200); String svgspecfile = relativepath + "/tmp/" + System.currentTimeMillis() + "s.svg"; new FileOutputStream(svgspecfile).write(svgSpec.getBytes()); export.pictures[1] = svgspecfile; String molSvg = export.getMolSvg(true); String svgmolfile = relativepath + "/tmp/" + System.currentTimeMillis() + "m.svg"; new FileOutputStream(svgmolfile).write(molSvg.getBytes()); export.pictures[0] = svgmolfile; String docbook = export.getDocbook("pdf", "SVG"); TransformerFactory tFactory = TransformerFactory.newInstance(); Transformer transformer = tFactory.newTransformer(new StreamSource("file:" + GeneralUtils.getNmrshiftdbProperty("docbookxslpath", getServletConfig()) + "/fo/docbook.xsl")); ByteArrayOutputStream baos = new ByteArrayOutputStream(); transformer.transform(new StreamSource(new StringReader(docbook)), new StreamResult(baos)); FopFactory fopFactory = FopFactory.newInstance(); FOUserAgent foUserAgent = fopFactory.newFOUserAgent(); OutputStream out2 = new ByteArrayOutputStream(); Fop fop = fopFactory.newFop(format.equals("rtf") ? MimeConstants.MIME_RTF : MimeConstants.MIME_PDF, foUserAgent, out2); TransformerFactory factory = TransformerFactory.newInstance(); transformer = factory.newTransformer(); Source src = new StreamSource(new StringReader(baos.toString())); Result res2 = new SAXResult(fop.getDefaultHandler()); transformer.transform(src, res2); out.print(out2.toString()); } if (format.equals("docbook")) { String i1 = relativepath + "/tmp/" + System.currentTimeMillis() + ".svg"; new FileOutputStream(i1).write(export.getSpecSvg(300, 200).getBytes()); export.pictures[0] = new File(i1).getName(); String i2 = relativepath + "/tmp/" + System.currentTimeMillis() + ".svg"; new FileOutputStream(i2).write(export.getMolSvg(true).getBytes()); export.pictures[1] = new File(i2).getName(); String docbook = export.getDocbook("pdf", "SVG"); String docbookfile = relativepath + "/tmp/" + System.currentTimeMillis() + ".xml"; new FileOutputStream(docbookfile).write(docbook.getBytes()); ByteArrayOutputStream baos = export.makeZip(new String[] { docbookfile, i1, i2 }); outstream.write(baos.toByteArray()); } if (format.equals("svg")) { out.print(export.getSpecSvg(400, 200)); } if (format.equals("tiff") || format.equals("jpeg") || format.equals("png")) { InputStream is = new FileInputStream(export.getImage(false, format, relativepath + "/tmp/" + System.currentTimeMillis(), true)); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } if (format.equals("cml")) { out.print(spectrum.getCmlSpect().toXML()); } if (format.equals("cmlboth")) { Element cmlElement = new Element("cml"); cmlElement.addAttribute(new Attribute("convention", "nmrshiftdb-convention")); cmlElement.setNamespaceURI("http://www.xml-cml.org/schema"); Element parent = spectrum.getDBMolecule().getCML(1, spectrum.getDBSpectrumType().getName().equals("1H")); nu.xom.Node cmldoc = parent.getChild(0); ((Element) cmldoc).setNamespaceURI("http://www.xml-cml.org/schema"); parent.removeChildren(); cmlElement.appendChild(cmldoc); Element parentspec = spectrum.getCmlSpect(); Node spectrumel = parentspec.getChild(0); parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ((Element) spectrumel).setNamespaceURI("http://www.xml-cml.org/schema"); out.write(cmlElement.toXML()); } if (format.indexOf("exsection") == 0) { StringTokenizer st = new StringTokenizer(format, "-"); st.nextToken(); String template = st.nextToken(); Criteria crit = new Criteria(); crit.add(DBSpectrumPeer.USER_ID, spectrum.getUserId()); Vector v = spectrum.getDBMolecule().getDBSpectrums(crit); VelocityContext context = new VelocityContext(); context.put("spectra", v); context.put("molecule", spectrum.getDBMolecule()); StringWriter w = new StringWriter(); Velocity.mergeTemplate("exporttemplates/" + template, "ISO-8859-1", context, w); out.write(w.toString()); } } if (action.equals("exportmol")) { int width = -1; int height = -1; if (req.getParameter("size") != null) { StringTokenizer st = new StringTokenizer(req.getParameter("size"), "x"); width = Integer.parseInt(st.nextToken()); height = Integer.parseInt(st.nextToken()); } boolean shownumbers = true; if (req.getParameter("shownumbers") != null && req.getParameter("shownumbers").equals("false")) { shownumbers = false; } if (req.getParameter("backcolor") != null) { export.backColor = new Color(Integer.parseInt(req.getParameter("backcolor"))); } if (req.getParameter("markatom") != null) { export.selected = Integer.parseInt(req.getParameter("markatom")) - 1; } if (format.equals("svg")) { out.print(export.getMolSvg(true)); } if (format.equals("tiff") || format.equals("jpeg") || format.equals("png")) { InputStream is = new FileInputStream(export.getImage(true, format, relativepath + "/tmp/" + System.currentTimeMillis(), width, height, shownumbers, null)); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } if (format.equals("mdl")) { out.println(spectrum.getDBMolecule().getStructureFile(1, false)); } if (format.equals("cml")) { out.println(spectrum.getDBMolecule().getCMLString(1)); } } if (out != null) out.flush(); else outstream.flush(); } catch (Exception ex) { ex.printStackTrace(); out.print(GeneralUtils.logError(ex, "NmrshiftdbServlet", null, true)); out.flush(); } } | 896,938 |
0 | void loadListFile(String listFileName, String majorType, String minorType, String languages, String annotationType) throws MalformedURLException, IOException { Lookup defaultLookup = new Lookup(listFileName, majorType, minorType, languages, annotationType); URL lurl = new URL(listsURL, listFileName); BufferedReader listReader = new BomStrippingInputStreamReader(lurl.openStream(), encoding); String line; int lines = 0; while (null != (line = listReader.readLine())) { GazetteerNode node = new GazetteerNode(line, unescapedSeparator, false); Lookup lookup = defaultLookup; Map<String, String> fm = node.getFeatureMap(); if (fm != null && fm.size() > 0) { lookup = new Lookup(listFileName, majorType, minorType, languages, annotationType); Set<String> keyset = fm.keySet(); if (keyset.size() <= 4) { Map<String, String> newfm = null; for (String key : keyset) { if (key.equals("majorType")) { String tmp = fm.get("majorType"); if (canonicalizeStrings) { tmp.intern(); } lookup.majorType = tmp; } else if (key.equals("minorType")) { String tmp = fm.get("minorType"); if (canonicalizeStrings) { tmp.intern(); } lookup.minorType = tmp; } else if (key.equals("languages")) { String tmp = fm.get("languages"); if (canonicalizeStrings) { tmp.intern(); } lookup.languages = tmp; } else if (key.equals("annotationType")) { String tmp = fm.get("annotationType"); if (canonicalizeStrings) { tmp.intern(); } lookup.annotationType = tmp; } else { if (newfm == null) { newfm = new HashMap<String, String>(); } String tmp = fm.get(key); if (canonicalizeStrings) { tmp.intern(); } newfm.put(key, tmp); } } if (newfm != null) { lookup.features = newfm; } } else { if (canonicalizeStrings) { for (String key : fm.keySet()) { String tmp = fm.get(key); tmp.intern(); fm.put(key, tmp); } } lookup.features = fm; } } addLookup(node.getEntry(), lookup); lines++; } logger.debug("Lines read: " + lines); } | protected InputStream openStreamInternal(String userAgent, Iterator mimeTypes, Iterator encodingTypes) throws IOException { if (stream != null) return stream; hasBeenOpened = true; URL url = null; try { url = buildURL(); } catch (MalformedURLException mue) { throw new IOException("Unable to make sense of URL for connection"); } if (url == null) return null; URLConnection urlC = url.openConnection(); if (urlC instanceof HttpURLConnection) { if (userAgent != null) urlC.setRequestProperty(HTTP_USER_AGENT_HEADER, userAgent); if (mimeTypes != null) { String acceptHeader = ""; while (mimeTypes.hasNext()) { acceptHeader += mimeTypes.next(); if (mimeTypes.hasNext()) acceptHeader += ","; } urlC.setRequestProperty(HTTP_ACCEPT_HEADER, acceptHeader); } if (encodingTypes != null) { String encodingHeader = ""; while (encodingTypes.hasNext()) { encodingHeader += encodingTypes.next(); if (encodingTypes.hasNext()) encodingHeader += ","; } urlC.setRequestProperty(HTTP_ACCEPT_ENCODING_HEADER, encodingHeader); } contentType = urlC.getContentType(); contentEncoding = urlC.getContentEncoding(); } return (stream = urlC.getInputStream()); } | 896,939 |
1 | @Override protected IStatus runCancelableRunnable(IProgressMonitor monitor) { IStatus returnValue = Status.OK_STATUS; monitor.beginTask(NLS.bind(Messages.SaveFileOnDiskHandler_SavingFiles, open), informationUnitsFromExecutionEvent.size()); for (InformationUnit informationUnit : informationUnitsFromExecutionEvent) { if (!monitor.isCanceled()) { monitor.setTaskName(NLS.bind(Messages.SaveFileOnDiskHandler_Saving, informationUnit.getLabel())); InformationStructureRead read = InformationStructureRead.newSession(informationUnit); read.getValueByNodeId(Activator.FILENAME); IFile binaryReferenceFile = InformationUtil.getBinaryReferenceFile(informationUnit); FileWriter writer = null; try { if (binaryReferenceFile != null) { File file = new File(open, (String) read.getValueByNodeId(Activator.FILENAME)); InputStream contents = binaryReferenceFile.getContents(); writer = new FileWriter(file); IOUtils.copy(contents, writer); monitor.worked(1); } } catch (Exception e) { returnValue = StatusCreator.newStatus(NLS.bind(Messages.SaveFileOnDiskHandler_ErrorSaving, informationUnit.getLabel(), e)); break; } finally { if (writer != null) { try { writer.flush(); writer.close(); } catch (IOException e) { } } } } } return returnValue; } | private static boolean prepareProbeFile(String completePath, String outputFile) { try { File inFile = new File(completePath + fSep + "probe.txt"); FileChannel inC = new FileInputStream(inFile).getChannel(); BufferedReader br = new BufferedReader(new FileReader(inFile)); File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + outputFile); FileChannel outC = new FileOutputStream(outFile, true).getChannel(); boolean endOfFile = true; short movieName = 0; int customer = 0; while (endOfFile) { String line = br.readLine(); if (line != null) { if (line.indexOf(":") >= 0) { movieName = new Short(line.substring(0, line.length() - 1)).shortValue(); } else { customer = new Integer(line).intValue(); ByteBuffer outBuf = ByteBuffer.allocate(6); outBuf.putShort(movieName); outBuf.putInt(customer); outBuf.flip(); outC.write(outBuf); } } else endOfFile = false; } br.close(); outC.close(); return true; } catch (IOException e) { System.err.println(e); return false; } } | 896,940 |
1 | public void write(File file) throws Exception { if (isInMemory()) { FileOutputStream fout = null; try { fout = new FileOutputStream(file); fout.write(get()); } finally { if (fout != null) { fout.close(); } } } else { File outputFile = getStoreLocation(); if (outputFile != null) { size = outputFile.length(); if (!outputFile.renameTo(file)) { BufferedInputStream in = null; BufferedOutputStream out = null; try { in = new BufferedInputStream(new FileInputStream(outputFile)); out = new BufferedOutputStream(new FileOutputStream(file)); IOUtils.copy(in, out); } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } if (out != null) { try { out.close(); } catch (IOException e) { } } } } } else { throw new FileUploadException("Cannot write uploaded file to disk!"); } } } | private FileLog(LOG_LEVEL displayLogLevel, LOG_LEVEL logLevel, String logPath) { this.logLevel = logLevel; this.displayLogLevel = displayLogLevel; if (null != logPath) { logFile = new File(logPath, "current.log"); log(LOG_LEVEL.DEBUG, "FileLog", "Initialising logfile " + logFile.getAbsolutePath() + " ."); try { if (logFile.exists()) { if (!logFile.renameTo(new File(logPath, System.currentTimeMillis() + ".log"))) { File newFile = new File(logPath, System.currentTimeMillis() + ".log"); if (newFile.exists()) { log(LOG_LEVEL.WARN, "FileLog", "The file (" + newFile.getAbsolutePath() + newFile.getName() + ") already exists, will overwrite it."); newFile.delete(); } newFile.createNewFile(); FileInputStream inStream = new FileInputStream(logFile); FileOutputStream outStream = new FileOutputStream(newFile); byte buffer[] = null; int offSet = 0; while (inStream.read(buffer, offSet, 2048) != -1) { outStream.write(buffer); offSet += 2048; } inStream.close(); outStream.close(); logFile.delete(); logFile = new File(logPath, "current.log"); } } logFile.createNewFile(); } catch (IOException e) { logFile = null; } } else { logFile = null; } } | 896,941 |
1 | private void copyFile(File sourceFile, File destFile) throws IOException { if (log.isDebugEnabled()) { log.debug("CopyFile : Source[" + sourceFile.getAbsolutePath() + "] Dest[" + destFile.getAbsolutePath() + "]"); } 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(); } } } | private void regattaBackup() { SwingWorker sw = new SwingWorker() { Regatta lRegatta = fRegatta; public Object construct() { String fullName = lRegatta.getSaveDirectory() + lRegatta.getSaveName(); System.out.println(MessageFormat.format(res.getString("MainMessageBackingUp"), new Object[] { fullName + BAK })); try { FileInputStream fis = new FileInputStream(new File(fullName)); FileOutputStream fos = new FileOutputStream(new File(fullName + BAK)); int bufsize = 1024; byte[] buffer = new byte[bufsize]; int n = 0; while ((n = fis.read(buffer, 0, bufsize)) >= 0) fos.write(buffer, 0, n); fos.flush(); fos.close(); } catch (java.io.IOException ex) { Util.showError(ex, true); } return null; } }; sw.start(); } | 896,942 |
1 | public static synchronized String getSequenceNumber(String SequenceName) { String result = "0"; Connection conn = null; Statement ps = null; ResultSet rs = null; try { conn = TPCW_Database.getConnection(); conn.setAutoCommit(false); String sql = "select num from sequence where name='" + SequenceName + "'"; ps = conn.createStatement(ResultSet.TYPE_SCROLL_INSENSITIVE, ResultSet.CONCUR_UPDATABLE); rs = ps.executeQuery(sql); long num = 0; while (rs.next()) { num = rs.getLong(1); result = new Long(num).toString(); } num++; sql = "update sequence set num=" + num + " where name='" + SequenceName + "'"; int res = ps.executeUpdate(sql); if (res == 1) { conn.commit(); } else conn.rollback(); } catch (Exception e) { System.out.println("Error Happens when trying to obtain the senquence number"); e.printStackTrace(); } finally { try { if (conn != null) conn.close(); if (rs != null) rs.close(); if (ps != null) ps.close(); } catch (SQLException se) { se.printStackTrace(); } } return result; } | public void addRegisterInfo(HttpServletRequest request) throws ApplicationException { String[] pids = request.getParameterValues("pid"); if (pids == null || pids.length <= 0) throw new ApplicationException("��ѡ��Ҫ���IJ�Ʒ"); RegisterDao registerDao = new RegisterDao(); Register register = registerDao.findPojoById(StrFun.getString(request, "rid"), Register.class); if (register.audit) throw new ApplicationException("��������Ѿ���ˣ��������µ���Ʒ"); DBConnect dbc = null; Connection conn = null; try { dbc = DBConnect.createDBConnect(); conn = dbc.getConnection(); conn.setAutoCommit(false); for (String pid : pids) { RegisterInfo pd = new RegisterInfo(); pd.rid = StrFun.getInt(request, "rid"); pd.pid = Integer.parseInt(pid); pd.productName = StrFun.getString(request, "productName_" + pid); pd.regAmount = StrFun.getInt(request, "regAmount_" + pid); pd.regPrice = StrFun.getInt(request, "regPrice_" + pid); pd.regSalePrice = StrFun.getInt(request, "regSalePrice_" + pid); pd.userNo = ServerUtil.getUserFromSession(request).userNo; if (pd.regAmount <= 0) throw new ApplicationException("�����������Ϊ��"); String sql = "insert into SS_RegisterInfo " + "(pid, rid, productName, regAmount, regPrice, regSalePrice, userNo) " + "values(" + "'" + pd.pid + "', " + "'" + pd.rid + "', " + "'" + pd.productName + "', " + "'" + pd.regAmount + "', " + "'" + pd.regPrice + "', " + "'" + pd.regSalePrice + "', " + "'" + pd.userNo + "' " + ")"; conn.createStatement().executeUpdate(sql); } conn.commit(); } catch (Exception e) { e.printStackTrace(); if (conn != null) { try { conn.rollback(); } catch (SQLException e1) { e1.printStackTrace(); } } throw new ApplicationException(e.getMessage(), e); } finally { if (dbc != null) try { dbc.close(); } catch (Exception e) { e.printStackTrace(); } } } | 896,943 |
1 | public static boolean predictDataSet(String completePath, String Type, String predictionOutputFileName, String slopeOneDataFolderName) { try { if (Type.equalsIgnoreCase("Qualifying")) { File inputFile = new File(completePath + fSep + "SmartGRAPE" + fSep + "CompleteQualifyingDataInByteFormat.txt"); FileChannel inC = new FileInputStream(inputFile).getChannel(); int filesize = (int) inC.size(); TShortObjectHashMap qualMap = new TShortObjectHashMap(17770, 1); ByteBuffer qualmappedfile = inC.map(FileChannel.MapMode.READ_ONLY, 0, filesize); while (qualmappedfile.hasRemaining()) { short movie = qualmappedfile.getShort(); int customer = qualmappedfile.getInt(); if (qualMap.containsKey(movie)) { TIntArrayList arr = (TIntArrayList) qualMap.get(movie); arr.add(customer); qualMap.put(movie, arr); } else { TIntArrayList arr = new TIntArrayList(); arr.add(customer); qualMap.put(movie, arr); } } System.out.println("Populated qualifying hashmap"); File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + predictionOutputFileName); FileChannel outC = new FileOutputStream(outFile).getChannel(); ByteBuffer buf; TShortObjectHashMap movieDiffStats; double finalPrediction; short[] movies = qualMap.keys(); Arrays.sort(movies); for (int i = 0; i < movies.length; i++) { short movieToProcess = movies[i]; movieDiffStats = loadMovieDiffStats(completePath, movieToProcess, slopeOneDataFolderName); System.out.println(movieDiffStats.size()); TIntArrayList customersToProcess = (TIntArrayList) qualMap.get(movieToProcess); for (int j = 0; j < customersToProcess.size(); j++) { int customerToProcess = customersToProcess.getQuick(j); finalPrediction = predictSlopeOneRating(customerToProcess, movieDiffStats); if (finalPrediction == finalPrediction) { if (finalPrediction < 1.0) finalPrediction = 1.0; else if (finalPrediction > 5.0) finalPrediction = 5.0; } else finalPrediction = GetAveragePrediction(movieToProcess); buf = ByteBuffer.allocate(10); buf.putShort(movieToProcess); buf.putInt(customerToProcess); buf.putFloat(new Double(finalPrediction).floatValue()); buf.flip(); outC.write(buf); } } outC.close(); return true; } else if (Type.equalsIgnoreCase("Probe")) { File inputFile = new File(completePath + fSep + "SmartGRAPE" + fSep + "CompleteProbeDataInByteFormat.txt"); FileChannel inC = new FileInputStream(inputFile).getChannel(); int filesize = (int) inC.size(); TShortObjectHashMap probeMap = new TShortObjectHashMap(17770, 1); ByteBuffer probemappedfile = inC.map(FileChannel.MapMode.READ_ONLY, 0, filesize); while (probemappedfile.hasRemaining()) { short movie = probemappedfile.getShort(); int customer = probemappedfile.getInt(); byte rating = probemappedfile.get(); if (probeMap.containsKey(movie)) { TIntByteHashMap actualRatings = (TIntByteHashMap) probeMap.get(movie); actualRatings.put(customer, rating); probeMap.put(movie, actualRatings); } else { TIntByteHashMap actualRatings = new TIntByteHashMap(); actualRatings.put(customer, rating); probeMap.put(movie, actualRatings); } } System.out.println("Populated probe hashmap"); File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + predictionOutputFileName); FileChannel outC = new FileOutputStream(outFile).getChannel(); ByteBuffer buf; double finalPrediction; TShortObjectHashMap movieDiffStats; short[] movies = probeMap.keys(); Arrays.sort(movies); for (int i = 0; i < movies.length; i++) { short movieToProcess = movies[i]; movieDiffStats = loadMovieDiffStats(completePath, movieToProcess, slopeOneDataFolderName); TIntByteHashMap custRatingsToProcess = (TIntByteHashMap) probeMap.get(movieToProcess); TIntArrayList customersToProcess = new TIntArrayList(custRatingsToProcess.keys()); for (int j = 0; j < customersToProcess.size(); j++) { int customerToProcess = customersToProcess.getQuick(j); byte rating = custRatingsToProcess.get(customerToProcess); finalPrediction = predictSlopeOneRating(customerToProcess, movieDiffStats); if (finalPrediction == finalPrediction) { if (finalPrediction < 1.0) finalPrediction = 1.0; else if (finalPrediction > 5.0) finalPrediction = 5.0; } else finalPrediction = GetAveragePrediction(movieToProcess); buf = ByteBuffer.allocate(11); buf.putShort(movieToProcess); buf.putInt(customerToProcess); buf.put(rating); buf.putFloat(new Double(finalPrediction).floatValue()); buf.flip(); outC.write(buf); } } outC.close(); return true; } else return false; } catch (Exception e) { e.printStackTrace(); return false; } } | public void merge(VMImage image, VMSnapShot another) throws VMException { if (path == null || another.getPath() == null) throw new VMException("EmuVMSnapShot is NULL!"); logging.debug(LOG_NAME, "merge images " + path + " and " + another.getPath()); File target = new File(path); File src = new File(another.getPath()); if (target.isDirectory() || src.isDirectory()) return; try { FileInputStream in = new FileInputStream(another.getPath()); FileChannel inChannel = in.getChannel(); FileOutputStream out = new FileOutputStream(path, true); FileChannel outChannel = out.getChannel(); outChannel.transferFrom(inChannel, 0, inChannel.size()); outChannel.close(); inChannel.close(); } catch (IOException e) { throw new VMException(e); } } | 896,944 |
1 | public static String md5(String text) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(text.getBytes()); return convertToHex(md.digest()); } catch (Exception e) { throw new RuntimeException(e.getMessage(), e); } } | public static byte[] createAuthenticator(ByteBuffer data, String secret) { assert data.isDirect() == false : "must not a direct ByteBuffer"; int pos = data.position(); if (pos < RadiusPacket.MIN_PACKET_LENGTH) { System.err.println("packet too small"); return null; } try { MessageDigest md5 = MessageDigest.getInstance("MD5"); byte[] arr = data.array(); md5.reset(); md5.update(arr, 0, pos); md5.update(secret.getBytes()); return md5.digest(); } catch (NoSuchAlgorithmException nsaex) { throw new RuntimeException("Could not access MD5 algorithm, fatal error"); } } | 896,945 |
0 | public String Hash(String plain) { try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(plain.getBytes(), 0, plain.length()); return new BigInteger(1, md5.digest()).toString(16); } catch (Exception ex) { Log.serverlogger.warn("No such Hash algorithm", ex); return ""; } } | @Test public void requestWebapp() throws Exception { final HttpClient client = new DefaultHttpClient(); final String echoValue = "ShrinkWrap>Tomcat Integration"; final List<NameValuePair> params = new ArrayList<NameValuePair>(); params.add(new BasicNameValuePair("to", PATH_ECHO_SERVLET)); params.add(new BasicNameValuePair("echo", echoValue)); final URI uri = URIUtils.createURI("http", BIND_HOST, HTTP_BIND_PORT, NAME_SIPAPP + SEPARATOR + servletClass.getSimpleName(), URLEncodedUtils.format(params, "UTF-8"), null); final HttpGet request = new HttpGet(uri); log.info("Executing request to: " + request.getURI()); final HttpResponse response = client.execute(request); System.out.println(response.getStatusLine()); final HttpEntity entity = response.getEntity(); if (entity == null) { Assert.fail("Request returned no entity"); } final BufferedReader reader = new BufferedReader(new InputStreamReader(entity.getContent())); final String line = reader.readLine(); Assert.assertEquals("Unexpected response from Servlet", echoValue + NAME_SIPAPP, line); } | 896,946 |
1 | public void copyFile(String source_name, String dest_name) throws IOException { File source_file = new File(source_name); File destination_file = new File(dest_name); FileInputStream source = null; FileOutputStream destination = null; byte[] buffer; int bytes_read; try { if (!source_file.exists() || !source_file.isFile()) throw new FileCopyException(MM.PHRASES.getPhrase("25") + " " + source_name); if (!source_file.canRead()) throw new FileCopyException(MM.PHRASES.getPhrase("26") + " " + MM.PHRASES.getPhrase("27") + ": " + source_name); if (destination_file.exists()) { if (destination_file.isFile()) { DataInputStream in = new DataInputStream(System.in); String response; if (!destination_file.canWrite()) throw new FileCopyException(MM.PHRASES.getPhrase("28") + " " + MM.PHRASES.getPhrase("29") + ": " + dest_name); System.out.print(MM.PHRASES.getPhrase("19") + dest_name + MM.PHRASES.getPhrase("30") + ": "); System.out.flush(); response = in.readLine(); if (!response.equals("Y") && !response.equals("y")) throw new FileCopyException(MM.PHRASES.getPhrase("31")); } else throw new FileCopyException(MM.PHRASES.getPhrase("28") + " " + MM.PHRASES.getPhrase("32") + ": " + dest_name); } else { File parentdir = parent(destination_file); if (!parentdir.exists()) throw new FileCopyException(MM.PHRASES.getPhrase("28") + " " + MM.PHRASES.getPhrase("33") + ": " + dest_name); if (!parentdir.canWrite()) throw new FileCopyException(MM.PHRASES.getPhrase("28") + " " + MM.PHRASES.getPhrase("34") + ": " + dest_name); } source = new FileInputStream(source_file); destination = new FileOutputStream(destination_file); buffer = new byte[1024]; while (true) { bytes_read = source.read(buffer); if (bytes_read == -1) break; destination.write(buffer, 0, bytes_read); } } finally { if (source != null) try { source.close(); } catch (IOException e) { ; } if (destination != null) try { destination.close(); } catch (IOException e) { ; } } } | private synchronized File gzipTempFile(File tempFile) throws BlogunityException { try { File gzippedFile = new File(BlogunityManager.getSystemConfiguration().getTempDir(), tempFile.getName() + ".gz"); GZIPOutputStream zos = new GZIPOutputStream(new FileOutputStream(gzippedFile)); byte[] readBuffer = new byte[2156]; int bytesIn = 0; FileInputStream fis = new FileInputStream(tempFile); while ((bytesIn = fis.read(readBuffer)) != -1) { zos.write(readBuffer, 0, bytesIn); } fis.close(); zos.close(); return gzippedFile; } catch (Exception e) { throw new BlogunityException(I18NStatusFactory.create(I18N.ERRORS.FEED_GZIP_FAILED, e)); } } | 896,947 |
1 | public static void cpdir(File src, File dest) throws BrutException { dest.mkdirs(); File[] files = src.listFiles(); for (int i = 0; i < files.length; i++) { File file = files[i]; File destFile = new File(dest.getPath() + File.separatorChar + file.getName()); if (file.isDirectory()) { cpdir(file, destFile); continue; } try { InputStream in = new FileInputStream(file); OutputStream out = new FileOutputStream(destFile); IOUtils.copy(in, out); in.close(); out.close(); } catch (IOException ex) { throw new BrutException("Could not copy file: " + file, ex); } } } | public void execute() { File sourceFile = new File(oarfilePath); File destinationFile = new File(deploymentDirectory + File.separator + sourceFile.getName()); try { FileInputStream fis = new FileInputStream(sourceFile); FileOutputStream fos = new FileOutputStream(destinationFile); byte[] readArray = new byte[2048]; while (fis.read(readArray) != -1) { fos.write(readArray); } fis.close(); fos.flush(); fos.close(); } catch (IOException ioe) { logger.severe("failed to copy the file:" + ioe); } } | 896,948 |
0 | public boolean executeUpdate(String strSql) throws SQLException { getConnection(); boolean flag = false; stmt = con.createStatement(); logger.info("###############::执行SQL语句操作(更新数据 无参数):" + strSql); try { if (0 < stmt.executeUpdate(strSql)) { close_DB_Object(); flag = true; con.commit(); } } catch (SQLException ex) { logger.info("###############Error DBManager Line126::执行SQL语句操作(更新数据 无参数):" + strSql + "失败!"); flag = false; con.rollback(); throw ex; } return flag; } | public String getMatches() { StringBuilder builder = new StringBuilder(""); try { URL url = new URL(LIVE_SCORE_URL); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String inputLine; while ((inputLine = in.readLine()) != null) { builder.append(inputLine); } in.close(); } catch (IOException e) { e.printStackTrace(); } return builder.toString(); } | 896,949 |
0 | public static String contents(URL url) throws IOException { InputStream is = url.openStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); byte[] buf = new byte[1024]; while (true) { int len = is.read(buf); if (len < 0) { break; } baos.write(buf, 0, len); } is.close(); String contents = new String(baos.toByteArray(), "iso8859_1"); baos.close(); return contents; } | public boolean run() { Connection conn = null; Statement stmt = null; try { conn = getDataSource().getConnection(); conn.setAutoCommit(false); conn.rollback(); stmt = conn.createStatement(); for (String task : tasks) { if (task.length() == 0) continue; LOGGER.info("Executing SQL migration: " + task); stmt.executeUpdate(task); } conn.commit(); } catch (SQLException ex) { try { conn.rollback(); } catch (Throwable th) { } throw new SystemException("Cannot execute SQL migration", ex); } finally { try { if (stmt != null) stmt.close(); } catch (Throwable th) { LOGGER.error(th); } try { if (stmt != null) conn.close(); } catch (Throwable th) { LOGGER.error(th); } } return true; } | 896,950 |
1 | private static File copyFileTo(File file, File directory) throws IOException { File newFile = new File(directory, file.getName()); FileInputStream fis = null; FileOutputStream fos = null; try { fis = new FileInputStream(file); fos = new FileOutputStream(newFile); byte buff[] = new byte[1024]; int val; while ((val = fis.read(buff)) > 0) fos.write(buff, 0, val); } finally { if (fis != null) fis.close(); if (fos != null) fos.close(); } return newFile; } | 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); } } | 896,951 |
0 | public static String cryptSha(String target) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(target.getBytes("UTF-16")); BigInteger res = new BigInteger(1, md.digest(key.getBytes())); return res.toString(16); } | public static void main(String[] args) { String inFile = "test_data/blobs.png"; String outFile = "ReadWriteTest.png"; itkImageFileReaderUC2_Pointer reader = itkImageFileReaderUC2.itkImageFileReaderUC2_New(); itkImageFileWriterUC2_Pointer writer = itkImageFileWriterUC2.itkImageFileWriterUC2_New(); reader.SetFileName(inFile); writer.SetFileName(outFile); writer.SetInput(reader.GetOutput()); writer.Update(); } | 896,952 |
0 | public void run() { URL url; InputSource i; Message m = ThemeListActivity.FeaturedThemesProgressHandler.obtainMessage(); try { url = new URL(mUrl); i = new InputSource(url.openStream()); SAXParserFactory spf = SAXParserFactory.newInstance(); SAXParser sp = spf.newSAXParser(); XMLReader xr = sp.getXMLReader(); FeaturedThemesHandler fth = new FeaturedThemesHandler(); xr.setContentHandler(fth); xr.parse(i); m.obj = fth.getParsedData(); } catch (MalformedURLException e) { m.obj = e.toString(); Log.e(TAG, "Malformed URL!", e); } catch (IOException e) { m.obj = e.toString(); Log.e(TAG, "Exception on opening Input Stream", e); } catch (ParserConfigurationException e) { m.obj = e.toString(); Log.e(TAG, "Exception on parsing XML File", e); } catch (SAXException e) { m.obj = e.toString(); Log.e(TAG, "Exception while creating SAXParser", e); } ThemeListActivity.FeaturedThemesProgressHandler.sendMessage(m); } | private static String getUnsaltedHash(String algorithm, String input) throws NoSuchAlgorithmException { MessageDigest messageDigest = MessageDigest.getInstance(algorithm); messageDigest.reset(); messageDigest.update(input.getBytes(Main.DEFAULT_CHARSET)); byte[] digest = messageDigest.digest(); return String.format(Main.DEFAULT_LOCALE, "%0" + (digest.length << 1) + "x", new BigInteger(1, digest)); } | 896,953 |
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(); } } | private void copyTemplate(String resource, OutputStream outputStream) throws IOException { URL url = Tools.getResource(resource); if (url == null) { throw new IOException("could not find resource"); } BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(outputStream, Charset.forName("UTF-8"))); String line = null; do { line = reader.readLine(); if (line != null) { writer.write(line); writer.newLine(); } } while (line != null); reader.close(); writer.close(); } | 896,954 |
0 | public CandleSeries fetchSeries(final String symbol) throws Exception { Calendar cal = Calendar.getInstance(TimeZone.getTimeZone("UTC")); cal.setTime(begin); String beginYear = String.valueOf(cal.get(Calendar.YEAR)); String beginMonth = String.valueOf(cal.get(Calendar.MONTH)); String beginDay = String.valueOf(cal.get(Calendar.DAY_OF_MONTH)); if (end == null) { GregorianCalendar gCal = new GregorianCalendar(); gCal.add(Calendar.DATE, -1); end = gCal.getTime(); } cal.setTime(end); String day = String.valueOf(cal.get(Calendar.DAY_OF_MONTH)); String month = String.valueOf(cal.get(Calendar.MONTH)); String year = String.valueOf(cal.get(Calendar.YEAR)); String resolution = "d"; String urlStr = MessageFormat.format(YAHOO_URL, symbol, beginMonth, beginDay, beginYear, month, day, year, resolution); BufferedReader reader; String line; List<String> lineList = new ArrayList<String>(); log.info("URL [" + urlStr + "]"); URL url = new URL(urlStr); reader = new BufferedReader(new InputStreamReader(url.openStream())); line = reader.readLine(); log.debug(line); while ((line = reader.readLine()) != null) { lineList.add(0, line); } List<Candle> candles = new ArrayList<Candle>(); for (String currentLine : lineList) { log.debug(currentLine); StringTokenizer str = new StringTokenizer(currentLine, ","); String datestring = str.nextToken(); double open = round(Double.parseDouble(str.nextToken()), 2); double high = Double.parseDouble(str.nextToken()); double low = Double.parseDouble(str.nextToken()); double close = Double.parseDouble(str.nextToken()); long volume = 0; double adjclose = 0; if (str.hasMoreTokens()) { volume = Long.parseLong(str.nextToken()); if (splitAdjust) { adjclose = Double.parseDouble(str.nextToken()); } } Date date = sdf.parse(datestring); Candle candle = null; if (splitAdjust) { double adjustmentFactor = adjclose / close; candle = new Candle(symbol, date, round(open * adjustmentFactor, 2), round(high * adjustmentFactor, 2), round(low * adjustmentFactor, 2), adjclose, volume); } else { candle = new Candle(symbol, date, open, high, low, close, volume); } candles.add(candle); } return new CandleSeries(candles); } | private Properties getProperties(URL url) throws java.io.IOException { Properties cdrList = new Properties(); java.io.InputStream stream = url.openStream(); cdrList.load(stream); stream.close(); return cdrList; } | 896,955 |
0 | public static String md5Hash(String inString) throws TopicSpacesException { try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(inString.getBytes()); byte[] array = md5.digest(); StringBuffer buf = new StringBuffer(); int len = array.length; for (int i = 0; i < len; i++) { int b = array[i] & 0xFF; buf.append(Integer.toHexString(b)); } return buf.toString(); } catch (Exception x) { throw new TopicSpacesException(x); } } | public static void find(String pckgname, Class tosubclass) { String name = new String(pckgname); if (!name.startsWith("/")) { name = "/" + name; } name = name.replace('.', '/'); URL url = RTSI.class.getResource(name); System.out.println(name + "->" + url); if (url == null) return; File directory = new File(url.getFile()); if (directory.exists()) { String[] files = directory.list(); for (int i = 0; i < files.length; i++) { if (files[i].endsWith(".class")) { String classname = files[i].substring(0, files[i].length() - 6); try { Object o = Class.forName(pckgname + "." + classname).newInstance(); if (tosubclass.isInstance(o)) { System.out.println(classname); } } catch (ClassNotFoundException cnfex) { System.err.println(cnfex); } catch (InstantiationException iex) { } catch (IllegalAccessException iaex) { } } } } else { try { JarURLConnection conn = (JarURLConnection) url.openConnection(); String starts = conn.getEntryName(); JarFile jfile = conn.getJarFile(); Enumeration e = jfile.entries(); while (e.hasMoreElements()) { ZipEntry entry = (ZipEntry) e.nextElement(); String entryname = entry.getName(); if (entryname.startsWith(starts) && (entryname.lastIndexOf('/') <= starts.length()) && entryname.endsWith(".class")) { String classname = entryname.substring(0, entryname.length() - 6); if (classname.startsWith("/")) classname = classname.substring(1); classname = classname.replace('/', '.'); try { Object o = Class.forName(classname).newInstance(); if (tosubclass.isInstance(o)) { System.out.println(classname.substring(classname.lastIndexOf('.') + 1)); } } catch (ClassNotFoundException cnfex) { System.err.println(cnfex); } catch (InstantiationException iex) { } catch (IllegalAccessException iaex) { } } } } catch (IOException ioex) { System.err.println(ioex); } } } | 896,956 |
0 | public static void doVersionCheck(View view) { view.showWaitCursor(); try { URL url = new URL(jEdit.getProperty("version-check.url")); InputStream in = url.openStream(); BufferedReader bin = new BufferedReader(new InputStreamReader(in)); String line; String develBuild = null; String stableBuild = null; while ((line = bin.readLine()) != null) { if (line.startsWith(".build")) develBuild = line.substring(6).trim(); else if (line.startsWith(".stablebuild")) stableBuild = line.substring(12).trim(); } bin.close(); if (develBuild != null && stableBuild != null) { doVersionCheck(view, stableBuild, develBuild); } } catch (IOException e) { String[] args = { jEdit.getProperty("version-check.url"), e.toString() }; GUIUtilities.error(view, "read-error", args); } view.hideWaitCursor(); } | public static void main(String[] args) { System.out.println(args.length); FTPClient ftp = new FTPClient(); ftp.addProtocolCommandListener(new PrintCommandListener(new PrintWriter(System.out))); try { ftp.connect("localhost"); ftp.login("ethan", "ethan"); ftp.setFileType(FTP.BINARY_FILE_TYPE); ftp.enterLocalPassiveMode(); InputStream input; input = new FileInputStream("d:/tech/webwork-2.2.7.zip"); boolean is = ftp.storeFile("backup/webwork-2.2.7.zip", input); input.close(); System.out.println(is); FTPFile[] files = ftp.listFiles("backup"); for (FTPFile ftpFile : files) { long time = ftpFile.getTimestamp().getTimeInMillis(); long days = (System.currentTimeMillis() - time) / (1000 * 60 * 60 * 24); if (days > 30) { System.out.println(ftpFile.getName() + "is a old file"); ftp.deleteFile("backup/" + ftpFile.getName()); } else { System.out.println(ftpFile.getName() + "is a new file"); } } } catch (SocketException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } finally { try { ftp.logout(); } catch (IOException e1) { e1.printStackTrace(); } if (ftp.isConnected()) { try { ftp.disconnect(); } catch (IOException e) { e.printStackTrace(); } } } } | 896,957 |
0 | public static String getContents(String urlStr) throws Exception { String contents = ""; URL url = new URL(urlStr); URLConnection openConnection = url.openConnection(); final char[] buffer = new char[1024 * 1024]; StringBuilder out = new StringBuilder(); Reader in = new InputStreamReader(openConnection.getInputStream(), "UTF-8"); int read; do { read = in.read(buffer, 0, buffer.length); if (read > 0) { out.append(buffer, 0, read); } } while (read >= 0); contents = out.toString(); return contents; } | public boolean verify(final char[] password, final String encryptedPassword) { MessageDigest digest = null; int size = 0; String base64 = null; if (encryptedPassword.regionMatches(true, 0, "{SHA}", 0, 5)) { size = 20; base64 = encryptedPassword.substring(5); try { digest = MessageDigest.getInstance("SHA-1"); } catch (final NoSuchAlgorithmException e) { throw new IllegalStateException("Invalid algorithm"); } } else if (encryptedPassword.regionMatches(true, 0, "{SSHA}", 0, 6)) { size = 20; base64 = encryptedPassword.substring(6); try { digest = MessageDigest.getInstance("SHA-1"); } catch (final NoSuchAlgorithmException e) { throw new IllegalStateException("Invalid algorithm"); } } else if (encryptedPassword.regionMatches(true, 0, "{MD5}", 0, 5)) { size = 16; base64 = encryptedPassword.substring(5); try { digest = MessageDigest.getInstance("MD5"); } catch (final NoSuchAlgorithmException e) { throw new IllegalStateException("Invalid algorithm"); } } else if (encryptedPassword.regionMatches(true, 0, "{SMD5}", 0, 6)) { size = 16; base64 = encryptedPassword.substring(6); try { digest = MessageDigest.getInstance("MD5"); } catch (final NoSuchAlgorithmException e) { throw new IllegalStateException("Invalid algorithm"); } } else { return false; } try { final byte[] data = Base64.decodeBase64(base64.getBytes("UTF-8")); final byte[] orig = new byte[size]; System.arraycopy(data, 0, orig, 0, size); digest.reset(); digest.update(new String(password).getBytes("UTF-8")); if (data.length > size) { digest.update(data, size, data.length - size); } return MessageDigest.isEqual(digest.digest(), orig); } catch (UnsupportedEncodingException e) { throw new IllegalStateException("UTF-8 Unsupported"); } } | 896,958 |
1 | public CertificateID(String hashAlgorithm, X509Certificate issuerCert, BigInteger number, String provider) throws OCSPException { try { MessageDigest digest = MessageDigest.getInstance(hashAlgorithm, provider); AlgorithmIdentifier hashAlg = new AlgorithmIdentifier(new DERObjectIdentifier(hashAlgorithm), new DERNull()); X509Principal issuerName = PrincipalUtil.getSubjectX509Principal(issuerCert); digest.update(issuerName.getEncoded()); ASN1OctetString issuerNameHash = new DEROctetString(digest.digest()); PublicKey issuerKey = issuerCert.getPublicKey(); ASN1InputStream aIn = new ASN1InputStream(issuerKey.getEncoded()); SubjectPublicKeyInfo info = SubjectPublicKeyInfo.getInstance(aIn.readObject()); digest.update(info.getPublicKeyData().getBytes()); ASN1OctetString issuerKeyHash = new DEROctetString(digest.digest()); DERInteger serialNumber = new DERInteger(number); this.id = new CertID(hashAlg, issuerNameHash, issuerKeyHash, serialNumber); } catch (Exception e) { throw new OCSPException("problem creating ID: " + e, e); } } | public String plainStringToMD5(String input) { MessageDigest md = null; byte[] byteHash = null; StringBuffer resultString = new StringBuffer(); try { md = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { System.exit(-1); } md.reset(); md.update(input.getBytes()); byteHash = md.digest(); for (int i = 0; i < byteHash.length; i++) { resultString.append(Integer.toHexString(0xFF & byteHash[i])); } return (resultString.toString()); } | 896,959 |
0 | public boolean receiveFile(FileDescriptor fileDescriptor) { try { byte[] block = new byte[1024]; int sizeRead = 0; int totalRead = 0; File dir = new File(Constants.DOWNLOAD_DIR + fileDescriptor.getLocation()); if (!dir.exists()) { dir.mkdirs(); } File file = new File(Constants.DOWNLOAD_DIR + fileDescriptor.getLocation() + fileDescriptor.getName()); if (!file.exists()) { file.createNewFile(); } SSLSocket sslsocket = getFileTransferConectionConnectMode(ServerAdress.getServerAdress()); OutputStream fileOut = new FileOutputStream(file); InputStream dataIn = sslsocket.getInputStream(); while ((sizeRead = dataIn.read(block)) >= 0) { totalRead += sizeRead; fileOut.write(block, 0, sizeRead); propertyChangeSupport.firePropertyChange("fileByte", 0, totalRead); } fileOut.close(); dataIn.close(); sslsocket.close(); if (fileDescriptor.getName().contains(".snapshot")) { try { File fileData = new File(Constants.DOWNLOAD_DIR + fileDescriptor.getLocation() + fileDescriptor.getName()); File dirData = new File(Constants.PREVAYLER_DATA_DIRETORY + Constants.FILE_SEPARATOR); File destino = new File(dirData, fileData.getName()); boolean success = fileData.renameTo(destino); if (!success) { deleteDir(Constants.DOWNLOAD_DIR); return false; } deleteDir(Constants.DOWNLOAD_DIR); } catch (Exception e) { e.printStackTrace(); } } else { if (Server.isServerOpen()) { FileChannel inFileChannel = new FileInputStream(file).getChannel(); File dirServer = new File(Constants.DOWNLOAD_DIR + fileDescriptor.getLocation()); if (!dirServer.exists()) { dirServer.mkdirs(); } File fileServer = new File(Constants.DOWNLOAD_DIR + fileDescriptor.getName()); if (!fileServer.exists()) { fileServer.createNewFile(); } inFileChannel.transferTo(0, inFileChannel.size(), new FileOutputStream(fileServer).getChannel()); inFileChannel.close(); } } if (totalRead == fileDescriptor.getSize()) { return true; } } catch (Exception e) { logger.error("Receive File:", e); } return false; } | public static void assertEquals(String xmlpath, Object actualObject) throws Exception { InputStreamReader isr; try { isr = new FileReader(xmlpath); } catch (FileNotFoundException e) { URL url = AssertHelper.class.getClassLoader().getResource(xmlpath); if (null != url) { try { isr = new InputStreamReader(url.openStream()); } catch (Exception e1) { throw new AssertionFailedError("Unable to find output xml : " + xmlpath); } } else { throw new AssertionFailedError("Could not read output xml : " + xmlpath); } } DOMParser parser = new DOMParser(); parser.parse(new InputSource(isr)); Document document = parser.getDocument(); try { assertEqual(document.getDocumentElement(), actualObject); } catch (AssertionFailedError e) { String message = null; if (null != e.getCause()) { message = e.getCause().getMessage(); } else { message = e.getMessage(); } StringBuffer sbf = new StringBuffer(message + " \n " + xmlpath); Iterator iter = nodestack.iterator(); while (iter.hasNext()) { sbf.append(" -> " + ((Object[]) iter.next())[0]); iter.remove(); } AssertionFailedError a = new AssertionFailedError(sbf.toString()); a.setStackTrace(e.getStackTrace()); throw a; } catch (Exception e) { String message = null; if (null != e.getCause()) { message = e.getCause().getMessage(); } else { message = e.getMessage(); } StringBuffer sbf = new StringBuffer(message + " \n " + xmlpath); Iterator iter = nodestack.iterator(); while (iter.hasNext()) { sbf.append(" -> " + ((Object[]) iter.next())[0]); iter.remove(); } Exception ex = new Exception(sbf.toString()); ex.setStackTrace(e.getStackTrace()); throw ex; } } | 896,960 |
1 | protected void copy(File source, File destination) throws IOException { final FileChannel inChannel = new FileInputStream(source).getChannel(); final FileChannel outChannel = new FileOutputStream(destination).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } finally { if (inChannel != null) { inChannel.close(); } if (outChannel != null) { outChannel.close(); } } } | public static void copyTo(File src, File dest) throws IOException { if (src.equals(dest)) throw new IOException("copyTo src==dest file"); FileOutputStream fout = new FileOutputStream(dest); InputStream in = new FileInputStream(src); IOUtils.copyTo(in, fout); fout.flush(); fout.close(); in.close(); } | 896,961 |
1 | public static void encryptFile(String infile, String outfile, String keyFile) throws Exception { javax.crypto.Cipher cipher = javax.crypto.Cipher.getInstance("DES/ECB/PKCS5Padding"); cipher.init(javax.crypto.Cipher.ENCRYPT_MODE, getKey()); java.io.FileInputStream in = new java.io.FileInputStream(infile); java.io.FileOutputStream fileOut = new java.io.FileOutputStream(outfile); javax.crypto.CipherOutputStream out = new javax.crypto.CipherOutputStream(fileOut, cipher); byte[] buffer = new byte[kBufferSize]; int length; while ((length = in.read(buffer)) != -1) out.write(buffer, 0, length); in.close(); out.close(); } | private static void prepare() { System.err.println("PREPARING-----------------------------------------"); deleteHome(); InputStream configStream = null; FileOutputStream tempStream = null; try { configStream = AllTests.class.getClassLoader().getResourceAsStream("net/sf/archimede/test/resources/repository.xml"); new File("temp").mkdir(); tempStream = new FileOutputStream(new File("temp/repository.xml")); IOUtils.copy(configStream, tempStream); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } finally { try { if (configStream != null) { configStream.close(); } } catch (IOException e) { e.printStackTrace(); } finally { if (tempStream != null) { try { tempStream.close(); } catch (IOException e) { e.printStackTrace(); } } } } String repositoryName = "jackrabbit.repository"; Properties jndiProperties = new Properties(); jndiProperties.put("java.naming.provider.url", "http://sf.net/projects/archimede#1"); jndiProperties.put("java.naming.factory.initial", "org.apache.jackrabbit.core.jndi.provider.DummyInitialContextFactory"); startupUtil = new StartupJcrUtil(REPOSITORY_HOME, "temp/repository.xml", repositoryName, jndiProperties); startupUtil.init(); } | 896,962 |
1 | void copyFile(File inputFile, File outputFile) { try { FileReader in; in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } | private static void copyFile(String fromFile, String toFile) throws Exception { FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } | 896,963 |
1 | private String protectMarkup(String content, String markupRegex, String replaceSource, String replaceTarget) { Matcher matcher = Pattern.compile(markupRegex, Pattern.MULTILINE | Pattern.DOTALL).matcher(content); StringBuffer result = new StringBuffer(); while (matcher.find()) { String protectedMarkup = matcher.group(); protectedMarkup = protectedMarkup.replaceAll(replaceSource, replaceTarget); try { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.reset(); digest.update(protectedMarkup.getBytes("UTF-8")); String hash = bytesToHash(digest.digest()); matcher.appendReplacement(result, hash); c_protectionMap.put(hash, protectedMarkup); m_hashList.add(hash); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } } matcher.appendTail(result); return result.toString(); } | private byte[] _generate() throws NoSuchAlgorithmException { if (host == null) { try { seed = InetAddress.getLocalHost().toString(); } catch (UnknownHostException e) { seed = "localhost/127.0.0.1"; } catch (SecurityException e) { seed = "localhost/127.0.0.1"; } host = seed; } else { seed = host; } seed = seed + new Date().toString(); seed = seed + Long.toString(rnd.nextLong()); md = MessageDigest.getInstance(algorithm); md.update(seed.getBytes()); return md.digest(); } | 896,964 |
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 saveFile(File destination) { InputStream in = null; OutputStream out = null; try { if (fileScheme) in = new BufferedInputStream(new FileInputStream(source.getPath())); else in = new BufferedInputStream(getContentResolver().openInputStream(source)); out = new BufferedOutputStream(new FileOutputStream(destination)); byte[] buffer = new byte[1024]; while (in.read(buffer) != -1) out.write(buffer); Toast.makeText(this, R.string.saveas_file_saved, Toast.LENGTH_SHORT).show(); } catch (FileNotFoundException e) { Toast.makeText(this, R.string.saveas_error, Toast.LENGTH_SHORT).show(); } catch (IOException e) { Toast.makeText(this, R.string.saveas_error, Toast.LENGTH_SHORT).show(); } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } if (out != null) { try { out.close(); } catch (IOException e) { } } } } | 896,965 |
1 | @Test public void testDocumentDownloadExcel() throws IOException { if (uploadedExcelDocumentID == null) { fail("Document Upload Test should run first"); } String downloadLink = GoogleDownloadLinkGenerator.generateXlDownloadLink(uploadedExcelDocumentID); URL url = new URL(downloadLink); URLConnection urlConnection = url.openConnection(); urlConnection.connect(); InputStream input = url.openStream(); FileWriter fw = new FileWriter("tmpOutput.kb"); Reader reader = new InputStreamReader(input); BufferedReader bufferedReader = new BufferedReader(reader); String strLine = ""; int count = 0; while (count < 10000) { strLine = bufferedReader.readLine(); if (strLine != null && strLine != "") { fw.write(strLine); } count++; } } | protected void registerClasses() throws PrintException { if (!init) { try { Enumeration<URL> somethingToRegister = this.getClass().getClassLoader().getResources("META-INF/" + getClass().getSimpleName() + ".properties"); while (somethingToRegister.hasMoreElements()) { URL url = (URL) somethingToRegister.nextElement(); InputStream in = url.openStream(); BufferedReader buff = new BufferedReader(new InputStreamReader(in)); String line = buff.readLine(); while (line != null) { log.debug(line); try { Class cls = Class.forName(line); cls.newInstance(); log.debug("class " + line + " registered " + url); } catch (ClassNotFoundException e) { log.error("class " + line + " not found " + url, e); } catch (InstantiationException e) { log.error("class " + line + " not found " + url, e); } catch (IllegalAccessException e) { log.error("class " + line + " not found " + url, e); } line = buff.readLine(); } buff.close(); in.close(); } } catch (IOException e) { throw new PrintException(e.getMessage(), e); } init = true; } } | 896,966 |
1 | public void createResource(String resourceUri, boolean publish, User user) throws IOException { PermissionAPI perAPI = APILocator.getPermissionAPI(); Logger.debug(this.getClass(), "createResource"); resourceUri = stripMapping(resourceUri); String hostName = getHostname(resourceUri); String path = getPath(resourceUri); String folderName = getFolderName(path); String fileName = getFileName(path); fileName = deleteSpecialCharacter(fileName); if (fileName.startsWith(".")) { return; } Host host = HostFactory.getHostByHostName(hostName); Folder folder = FolderFactory.getFolderByPath(folderName, host); boolean hasPermission = perAPI.doesUserHavePermission(folder, PERMISSION_WRITE, user, false); if (hasPermission) { if (!checkFolderFilter(folder, fileName)) { throw new IOException("The file doesn't comply the folder's filter"); } if (host.getInode() != 0 && folder.getInode() != 0) { File file = new File(); file.setTitle(fileName); file.setFileName(fileName); file.setShowOnMenu(false); file.setLive(publish); file.setWorking(true); file.setDeleted(false); file.setLocked(false); file.setModDate(new Date()); String mimeType = FileFactory.getMimeType(fileName); file.setMimeType(mimeType); String author = user.getFullName(); file.setAuthor(author); file.setModUser(author); file.setSortOrder(0); file.setShowOnMenu(false); try { Identifier identifier = null; if (!isResource(resourceUri)) { WebAssetFactory.createAsset(file, user.getUserId(), folder, publish); identifier = IdentifierCache.getIdentifierFromIdentifierCache(file); } else { File actualFile = FileFactory.getFileByURI(path, host, false); identifier = IdentifierCache.getIdentifierFromIdentifierCache(actualFile); WebAssetFactory.createAsset(file, user.getUserId(), folder, identifier, false, false); WebAssetFactory.publishAsset(file); String assetsPath = FileFactory.getRealAssetsRootPath(); new java.io.File(assetsPath).mkdir(); java.io.File workingIOFile = FileFactory.getAssetIOFile(file); DotResourceCache vc = CacheLocator.getVeloctyResourceCache(); vc.remove(ResourceManager.RESOURCE_TEMPLATE + workingIOFile.getPath()); if (file != null && file.getInode() > 0) { byte[] currentData = new byte[0]; FileInputStream is = new FileInputStream(workingIOFile); int size = is.available(); currentData = new byte[size]; is.read(currentData); java.io.File newVersionFile = FileFactory.getAssetIOFile(file); vc.remove(ResourceManager.RESOURCE_TEMPLATE + newVersionFile.getPath()); FileChannel channelTo = new FileOutputStream(newVersionFile).getChannel(); ByteBuffer currentDataBuffer = ByteBuffer.allocate(currentData.length); currentDataBuffer.put(currentData); currentDataBuffer.position(0); channelTo.write(currentDataBuffer); channelTo.force(false); channelTo.close(); } java.util.List<Tree> parentTrees = TreeFactory.getTreesByChild(file); for (Tree tree : parentTrees) { Tree newTree = TreeFactory.getTree(tree.getParent(), file.getInode()); if (newTree.getChild() == 0) { newTree.setParent(tree.getParent()); newTree.setChild(file.getInode()); newTree.setRelationType(tree.getRelationType()); newTree.setTreeOrder(0); TreeFactory.saveTree(newTree); } } } List<Permission> permissions = perAPI.getPermissions(folder); for (Permission permission : permissions) { Permission filePermission = new Permission(); filePermission.setPermission(permission.getPermission()); filePermission.setRoleId(permission.getRoleId()); filePermission.setInode(identifier.getInode()); perAPI.save(filePermission); } } catch (Exception ex) { Logger.debug(this, ex.toString()); } } } else { throw new IOException("You don't have access to add that folder/host"); } } | 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); } 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) { ; } } } | 896,967 |
0 | protected void truncate(File file) { LogLog.debug("Compression of file: " + file.getAbsolutePath() + " started."); if (FileUtils.isFileOlder(file, ManagementFactory.getRuntimeMXBean().getStartTime())) { File backupRoot = new File(getBackupDir()); if (!backupRoot.exists() && !backupRoot.mkdirs()) { throw new AppenderInitializationError("Can't create backup dir for backup storage"); } SimpleDateFormat df; try { df = new SimpleDateFormat(getBackupDateFormat()); } catch (Exception e) { throw new AppenderInitializationError("Invalid date formate for backup files: " + getBackupDateFormat(), e); } String date = df.format(new Date(file.lastModified())); File zipFile = new File(backupRoot, file.getName() + "." + date + ".zip"); ZipOutputStream zos = null; FileInputStream fis = null; try { zos = new ZipOutputStream(new FileOutputStream(zipFile)); ZipEntry entry = new ZipEntry(file.getName()); entry.setMethod(ZipEntry.DEFLATED); entry.setCrc(FileUtils.checksumCRC32(file)); zos.putNextEntry(entry); fis = FileUtils.openInputStream(file); byte[] buffer = new byte[1024]; int readed; while ((readed = fis.read(buffer)) != -1) { zos.write(buffer, 0, readed); } } catch (Exception e) { throw new AppenderInitializationError("Can't create zip file", e); } finally { if (zos != null) { try { zos.close(); } catch (IOException e) { LogLog.warn("Can't close zip file", e); } } if (fis != null) { try { fis.close(); } catch (IOException e) { LogLog.warn("Can't close zipped file", e); } } } if (!file.delete()) { throw new AppenderInitializationError("Can't delete old log file " + file.getAbsolutePath()); } } } | @Override protected RemoteInvocationResult doExecuteRequest(HttpInvokerClientConfiguration config, ByteArrayOutputStream baos) throws IOException, ClassNotFoundException { HttpPost postMethod = new HttpPost(config.getServiceUrl()); postMethod.setEntity(new ByteArrayEntity(baos.toByteArray())); HttpResponse rsp = httpClient.execute(postMethod); StatusLine sl = rsp.getStatusLine(); if (sl.getStatusCode() >= 300) { throw new IOException("Did not receive successful HTTP response: status code = " + sl.getStatusCode() + ", status message = [" + sl.getReasonPhrase() + "]"); } HttpEntity entity = rsp.getEntity(); InputStream responseBody = entity.getContent(); return readRemoteInvocationResult(responseBody, config.getCodebaseUrl()); } | 896,968 |
1 | public BufferedImage extract() throws DjatokaException { boolean useRegion = false; int left = 0; int top = 0; int width = 50; int height = 50; boolean useleftDouble = false; Double leftDouble = 0.0; boolean usetopDouble = false; Double topDouble = 0.0; boolean usewidthDouble = false; Double widthDouble = 0.0; boolean useheightDouble = false; Double heightDouble = 0.0; if (params.getRegion() != null) { StringTokenizer st = new StringTokenizer(params.getRegion(), "{},"); String token; if ((token = st.nextToken()).contains(".")) { topDouble = Double.parseDouble(token); usetopDouble = true; } else top = Integer.parseInt(token); if ((token = st.nextToken()).contains(".")) { leftDouble = Double.parseDouble(token); useleftDouble = true; } else left = Integer.parseInt(token); if ((token = st.nextToken()).contains(".")) { heightDouble = Double.parseDouble(token); useheightDouble = true; } else height = Integer.parseInt(token); if ((token = st.nextToken()).contains(".")) { widthDouble = Double.parseDouble(token); usewidthDouble = true; } else width = Integer.parseInt(token); useRegion = true; } try { if (is != null) { File f = File.createTempFile("tmp", ".jp2"); f.deleteOnExit(); FileOutputStream fos = new FileOutputStream(f); sourceFile = f.getAbsolutePath(); IOUtils.copyStream(is, fos); is.close(); fos.close(); } } catch (IOException e) { throw new DjatokaException(e); } try { Jp2_source inputSource = new Jp2_source(); Kdu_compressed_source input = null; Jp2_family_src jp2_family_in = new Jp2_family_src(); Jp2_locator loc = new Jp2_locator(); jp2_family_in.Open(sourceFile, true); inputSource.Open(jp2_family_in, loc); inputSource.Read_header(); input = inputSource; Kdu_codestream codestream = new Kdu_codestream(); codestream.Create(input); Kdu_channel_mapping channels = new Kdu_channel_mapping(); if (inputSource.Exists()) channels.Configure(inputSource, false); else channels.Configure(codestream); int ref_component = channels.Get_source_component(0); Kdu_coords ref_expansion = getReferenceExpansion(ref_component, channels, codestream); Kdu_dims image_dims = new Kdu_dims(); codestream.Get_dims(ref_component, image_dims); Kdu_coords imageSize = image_dims.Access_size(); Kdu_coords imagePosition = image_dims.Access_pos(); if (useleftDouble) left = imagePosition.Get_x() + (int) Math.round(leftDouble * imageSize.Get_x()); if (usetopDouble) top = imagePosition.Get_y() + (int) Math.round(topDouble * imageSize.Get_y()); if (useheightDouble) height = (int) Math.round(heightDouble * imageSize.Get_y()); if (usewidthDouble) width = (int) Math.round(widthDouble * imageSize.Get_x()); if (useRegion) { imageSize.Set_x(width); imageSize.Set_y(height); imagePosition.Set_x(left); imagePosition.Set_y(top); } int reduce = 1 << params.getLevelReductionFactor(); imageSize.Set_x(imageSize.Get_x() * ref_expansion.Get_x()); imageSize.Set_y(imageSize.Get_y() * ref_expansion.Get_y()); imagePosition.Set_x(imagePosition.Get_x() * ref_expansion.Get_x() / reduce - ((ref_expansion.Get_x() / reduce - 1) / 2)); imagePosition.Set_y(imagePosition.Get_y() * ref_expansion.Get_y() / reduce - ((ref_expansion.Get_y() / reduce - 1) / 2)); Kdu_dims view_dims = new Kdu_dims(); view_dims.Assign(image_dims); view_dims.Access_size().Set_x(imageSize.Get_x()); view_dims.Access_size().Set_y(imageSize.Get_y()); int region_buf_size = imageSize.Get_x() * imageSize.Get_y(); int[] region_buf = new int[region_buf_size]; Kdu_region_decompressor decompressor = new Kdu_region_decompressor(); decompressor.Start(codestream, channels, -1, params.getLevelReductionFactor(), 16384, image_dims, ref_expansion, new Kdu_coords(1, 1), false, Kdu_global.KDU_WANT_OUTPUT_COMPONENTS); Kdu_dims new_region = new Kdu_dims(); Kdu_dims incomplete_region = new Kdu_dims(); Kdu_coords viewSize = view_dims.Access_size(); incomplete_region.Assign(image_dims); int[] imgBuffer = new int[viewSize.Get_x() * viewSize.Get_y()]; int[] kduBuffer = null; while (decompressor.Process(region_buf, image_dims.Access_pos(), 0, 0, region_buf_size, incomplete_region, new_region)) { Kdu_coords newOffset = new_region.Access_pos(); Kdu_coords newSize = new_region.Access_size(); newOffset.Subtract(view_dims.Access_pos()); kduBuffer = region_buf; int imgBuffereIdx = newOffset.Get_x() + newOffset.Get_y() * viewSize.Get_x(); int kduBufferIdx = 0; int xDiff = viewSize.Get_x() - newSize.Get_x(); for (int j = 0; j < newSize.Get_y(); j++, imgBuffereIdx += xDiff) { for (int i = 0; i < newSize.Get_x(); i++) { imgBuffer[imgBuffereIdx++] = kduBuffer[kduBufferIdx++]; } } } BufferedImage image = new BufferedImage(imageSize.Get_x(), imageSize.Get_y(), BufferedImage.TYPE_INT_RGB); image.setRGB(0, 0, viewSize.Get_x(), viewSize.Get_y(), imgBuffer, 0, viewSize.Get_x()); if (params.getRotationDegree() > 0) { image = ImageProcessingUtils.rotate(image, params.getRotationDegree()); } decompressor.Native_destroy(); channels.Native_destroy(); if (codestream.Exists()) codestream.Destroy(); inputSource.Native_destroy(); input.Native_destroy(); jp2_family_in.Native_destroy(); return image; } catch (KduException e) { e.printStackTrace(); throw new DjatokaException(e); } catch (Exception e) { e.printStackTrace(); throw new DjatokaException(e); } } | public RepeatStatus execute(StepContribution contribution, ChunkContext chunkContext) throws Exception { ZipInputStream zis = new ZipInputStream(new BufferedInputStream(inputResource.getInputStream())); File targetDirectoryAsFile = new File(targetDirectory); if (!targetDirectoryAsFile.exists()) { FileUtils.forceMkdir(targetDirectoryAsFile); } File target = new File(targetDirectory, targetFile); BufferedOutputStream dest = null; while (zis.getNextEntry() != null) { if (!target.exists()) { target.createNewFile(); } FileOutputStream fos = new FileOutputStream(target); dest = new BufferedOutputStream(fos); IOUtils.copy(zis, dest); dest.flush(); dest.close(); } zis.close(); if (!target.exists()) { throw new IllegalStateException("Could not decompress anything from the archive!"); } return RepeatStatus.FINISHED; } | 896,969 |
1 | public static void main(String args[]) { int i, j, l; short NUMNUMBERS = 256; short numbers[] = new short[NUMNUMBERS]; Darjeeling.print("START"); for (l = 0; l < 100; l++) { for (i = 0; i < NUMNUMBERS; i++) numbers[i] = (short) (NUMNUMBERS - 1 - i); for (i = 0; i < NUMNUMBERS; i++) { for (j = 0; j < NUMNUMBERS - i - 1; j++) if (numbers[j] > numbers[j + 1]) { short temp = numbers[j]; numbers[j] = numbers[j + 1]; numbers[j + 1] = temp; } } } Darjeeling.print("END"); } | public static int[] bubbleSort(int[] source) { if (source != null && source.length > 0) { boolean flag = true; while (flag) { flag = false; for (int i = 0; i < source.length - 1; i++) { if (source[i] > source[i + 1]) { int temp = source[i]; source[i] = source[i + 1]; source[i + 1] = temp; flag = true; } } } } return source; } | 896,970 |
1 | private void copyFile(File file, File dir) throws IOException { BufferedReader in = new BufferedReader(new FileReader(file)); BufferedWriter out = new BufferedWriter(new FileWriter(new File(dir.getAbsolutePath() + File.separator + file.getName()))); char[] buffer = new char[512]; int read = -1; while ((read = in.read(buffer)) > 0) { out.write(buffer, 0, read); } in.close(); out.close(); } | public static void copyFromOffset(long offset, File exe, File cab) throws IOException { DataInputStream in = new DataInputStream(new FileInputStream(exe)); FileOutputStream out = new FileOutputStream(cab); byte[] buffer = new byte[4096]; int bytes_read; in.skipBytes((int) offset); while ((bytes_read = in.read(buffer)) != -1) out.write(buffer, 0, bytes_read); in.close(); out.close(); in = null; out = null; } | 896,971 |
1 | public void test() throws Exception { TranslationResponseStorage r = new TranslationResponseStorage(mockStorage, "UTF-8"); MockResponseStateObserver observer = new MockResponseStateObserver(); r.addStateObserver(observer); assertEquals("UTF-8", r.getCharacterEncoding()); assertEquals(-1L, r.getLastModified()); assertEquals(0, r.getTranslationCount()); r.setTranslationCount(10); assertEquals(10, r.getTranslationCount()); assertNotNull(r.getHeadersStorage()); assertNull(r.getHeaders()); r.setLastModified(100000L); assertEquals(100000L, r.getLastModified()); assertFalse(r.getHeaders().isEmpty()); { Set<ResponseHeader> set = new TreeSet<ResponseHeader>(); set.add(new ResponseHeaderImpl("Last-Modified", new String[] { DateUtil.formatDate(new Date(200000L)) })); r.addHeaders(set); } assertEquals(1, r.getHeaders().size()); assertEquals(200000L, r.getLastModified()); { Set<ResponseHeader> set = new TreeSet<ResponseHeader>(); set.add(new ResponseHeaderImpl("Last-Modified", new String[] { DateUtil.formatDate(new Date(310000L)) })); set.add(new ResponseHeaderImpl("User-Agent", new String[] { "Pinoccio" })); r.addHeaders(set); } assertEquals(2, r.getHeaders().size()); int ii = 0; for (ResponseHeader h : r.getHeaders()) { ii++; if (ii == 1) { assertEquals("Last-Modified", h.getName()); assertEquals(Arrays.toString(new String[] { DateUtil.formatDate(new Date(310000L)) }), Arrays.toString(h.getValues())); } else if (ii == 2) { assertEquals("User-Agent", h.getName()); assertEquals(Arrays.toString(new String[] { "Pinoccio" }), Arrays.toString(h.getValues())); } } r.addText("This is an example"); r.addText(" and another one."); assertEquals("This is an example and another one.", mockStorage.getText()); InputStream input = r.getInputStream(); StringWriter writer = new StringWriter(); try { IOUtils.copy(input, writer, "UTF-8"); } finally { input.close(); writer.close(); } assertEquals("This is an example and another one.", writer.toString()); { OutputStream output = r.getOutputStream(); output.write(" and another line".getBytes("UTF-8")); assertEquals("This is an example and another one. and another line", r.getText()); } { Writer output = r.getWriter(); output.write(" and write some more"); assertEquals("This is an example and another one. and another line and write some more", r.getText()); } assertFalse(r.hasEnded()); assertNull(r.getEndState()); assertEquals(0L, observer.getHits()); r.setEndState(ResponseStateOk.getInstance()); assertEquals(ResponseStateOk.getInstance(), r.getEndState()); assertTrue(r.hasEnded()); assertEquals(1L, observer.getHits()); try { r.getOutputStream(); fail("Previous line should throw IOException as result closed."); } catch (IOException e) { } try { r.getWriter(); fail("Previous line should throw IOException as result closed."); } catch (IOException e) { } } | public static void main(String[] args) { try { int encodeFlag = 0; if (args[0].equals("-e")) { encodeFlag = Base64.ENCODE; } else if (args[0].equals("-d")) { encodeFlag = Base64.DECODE; } String infile = args[1]; String outfile = args[2]; File fin = new File(infile); FileInputStream fis = new FileInputStream(fin); BufferedInputStream bis = new BufferedInputStream(fis); Base64.InputStream b64in = new Base64.InputStream(bis, encodeFlag | Base64.DO_BREAK_LINES); File fout = new File(outfile); FileOutputStream fos = new FileOutputStream(fout); BufferedOutputStream bos = new BufferedOutputStream(fos); byte[] buff = new byte[1024]; int read = -1; while ((read = b64in.read(buff)) >= 0) { bos.write(buff, 0, read); } bos.close(); b64in.close(); } catch (Exception e) { e.printStackTrace(); } } | 896,972 |
1 | public static Checksum checksum(File file, Checksum checksum) throws IOException { if (file.isDirectory()) { throw new IllegalArgumentException("Checksums can't be computed on directories"); } InputStream in = null; try { in = new CheckedInputStream(new FileInputStream(file), checksum); IOUtils.copy(in, new OutputStream() { @Override public void write(byte[] b, int off, int len) { } @Override public void write(int b) { } @Override public void write(byte[] b) throws IOException { } }); } finally { IOUtils.closeQuietly(in); } return checksum; } | @Override @RemoteMethod public boolean encrypt(int idAnexo) { try { Anexo anexo = anexoService.selectById(idAnexo); aes.init(Cipher.ENCRYPT_MODE, aeskeySpec); FileInputStream fis = new FileInputStream(config.baseDir + "/arquivos_upload_direto/" + anexo.getAnexoCaminho()); CipherOutputStream cos = new CipherOutputStream(new FileOutputStream(config.baseDir + "/arquivos_upload_direto/encrypt/" + anexo.getAnexoCaminho()), aes); IOUtils.copy(fis, cos); cos.close(); fis.close(); } catch (Exception e) { e.printStackTrace(); return false; } return true; } | 896,973 |
1 | public void encryptPassword() { MessageDigest digest = null; try { digest = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException e) { System.out.print(e); } try { digest.update(passwordIn.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { System.out.println("cannot find char set for getBytes"); } byte digestBytes[] = digest.digest(); passwordHash = (new BASE64Encoder()).encode(digestBytes); } | public static String generate(String source) { byte[] SHA = new byte[20]; try { MessageDigest digest = MessageDigest.getInstance("SHA-1"); digest.update(source.getBytes()); SHA = digest.digest(); } catch (NoSuchAlgorithmException e) { System.out.println("NO SUCH ALGORITHM EXCEPTION: " + e.getMessage()); } CommunicationLogger.warning("SHA1 DIGEST: " + SHA); return SHA.toString(); } | 896,974 |
0 | public void createResource(String resourceUri, boolean publish, User user) throws IOException { PermissionAPI perAPI = APILocator.getPermissionAPI(); Logger.debug(this.getClass(), "createResource"); resourceUri = stripMapping(resourceUri); String hostName = getHostname(resourceUri); String path = getPath(resourceUri); String folderName = getFolderName(path); String fileName = getFileName(path); fileName = deleteSpecialCharacter(fileName); if (fileName.startsWith(".")) { return; } Host host = HostFactory.getHostByHostName(hostName); Folder folder = FolderFactory.getFolderByPath(folderName, host); boolean hasPermission = perAPI.doesUserHavePermission(folder, PERMISSION_WRITE, user, false); if (hasPermission) { if (!checkFolderFilter(folder, fileName)) { throw new IOException("The file doesn't comply the folder's filter"); } if (host.getInode() != 0 && folder.getInode() != 0) { File file = new File(); file.setTitle(fileName); file.setFileName(fileName); file.setShowOnMenu(false); file.setLive(publish); file.setWorking(true); file.setDeleted(false); file.setLocked(false); file.setModDate(new Date()); String mimeType = FileFactory.getMimeType(fileName); file.setMimeType(mimeType); String author = user.getFullName(); file.setAuthor(author); file.setModUser(author); file.setSortOrder(0); file.setShowOnMenu(false); try { Identifier identifier = null; if (!isResource(resourceUri)) { WebAssetFactory.createAsset(file, user.getUserId(), folder, publish); identifier = IdentifierCache.getIdentifierFromIdentifierCache(file); } else { File actualFile = FileFactory.getFileByURI(path, host, false); identifier = IdentifierCache.getIdentifierFromIdentifierCache(actualFile); WebAssetFactory.createAsset(file, user.getUserId(), folder, identifier, false, false); WebAssetFactory.publishAsset(file); String assetsPath = FileFactory.getRealAssetsRootPath(); new java.io.File(assetsPath).mkdir(); java.io.File workingIOFile = FileFactory.getAssetIOFile(file); DotResourceCache vc = CacheLocator.getVeloctyResourceCache(); vc.remove(ResourceManager.RESOURCE_TEMPLATE + workingIOFile.getPath()); if (file != null && file.getInode() > 0) { byte[] currentData = new byte[0]; FileInputStream is = new FileInputStream(workingIOFile); int size = is.available(); currentData = new byte[size]; is.read(currentData); java.io.File newVersionFile = FileFactory.getAssetIOFile(file); vc.remove(ResourceManager.RESOURCE_TEMPLATE + newVersionFile.getPath()); FileChannel channelTo = new FileOutputStream(newVersionFile).getChannel(); ByteBuffer currentDataBuffer = ByteBuffer.allocate(currentData.length); currentDataBuffer.put(currentData); currentDataBuffer.position(0); channelTo.write(currentDataBuffer); channelTo.force(false); channelTo.close(); } java.util.List<Tree> parentTrees = TreeFactory.getTreesByChild(file); for (Tree tree : parentTrees) { Tree newTree = TreeFactory.getTree(tree.getParent(), file.getInode()); if (newTree.getChild() == 0) { newTree.setParent(tree.getParent()); newTree.setChild(file.getInode()); newTree.setRelationType(tree.getRelationType()); newTree.setTreeOrder(0); TreeFactory.saveTree(newTree); } } } List<Permission> permissions = perAPI.getPermissions(folder); for (Permission permission : permissions) { Permission filePermission = new Permission(); filePermission.setPermission(permission.getPermission()); filePermission.setRoleId(permission.getRoleId()); filePermission.setInode(identifier.getInode()); perAPI.save(filePermission); } } catch (Exception ex) { Logger.debug(this, ex.toString()); } } } else { throw new IOException("You don't have access to add that folder/host"); } } | public static String MD5(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("MD5"); byte[] md5hash = new byte[32]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } | 896,975 |
1 | public static void kopirujSoubor(File vstup, File vystup) throws IOException { FileChannel sourceChannel = new FileInputStream(vstup).getChannel(); FileChannel destinationChannel = new FileOutputStream(vystup).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); } | public static void main(String[] args) throws Exception { String codecClassname = args[0]; Class<?> codecClass = Class.forName(codecClassname); Configuration conf = new Configuration(); CompressionCodec codec = (CompressionCodec) ReflectionUtils.newInstance(codecClass, conf); Compressor compressor = null; try { compressor = CodecPool.getCompressor(codec); CompressionOutputStream out = codec.createOutputStream(System.out, compressor); IOUtils.copyBytes(System.in, out, 4096, false); out.finish(); } finally { CodecPool.returnCompressor(compressor); } } | 896,976 |
0 | 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; } | public void read(Model model, String url) { try { URLConnection conn = new URL(url).openConnection(); String encoding = conn.getContentEncoding(); if (encoding == null) { read(model, conn.getInputStream(), url); } else { read(model, new InputStreamReader(conn.getInputStream(), encoding), url); } } catch (IOException e) { throw new JenaException(e); } } | 896,977 |
1 | private Object[] retrieveSecondURL(URL url, RSLink link) { link.setStatus(RSLink.STATUS_WAITING); Object[] result = new Object[2]; HttpURLConnection httpConn = null; BufferedReader inr = null; DataOutputStream outs = null; Pattern mirrorLinePattern = Pattern.compile("'<input.+checked.+type=\"radio\".+name=\"mirror\".+\\\\'.+\\\\'"); Pattern mirrorUrlPattern = Pattern.compile("\\\\'.+\\\\'"); Pattern counterPattern = Pattern.compile("var c=[0-9]+;"); Pattern counterIntPattern = Pattern.compile("[0-9]+"); try { String line = null; String urlLine = null; Integer counter = null; String postData = URLEncoder.encode("dl.start", "UTF-8") + "=" + URLEncoder.encode("Free", "UTF-8"); httpConn = (HttpURLConnection) url.openConnection(); httpConn.setRequestMethod("POST"); httpConn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); httpConn.setRequestProperty("Content-Length", "" + Integer.toString(postData.getBytes().length)); httpConn.setRequestProperty("Content-Language", "en-US"); httpConn.setDoOutput(true); httpConn.setDoInput(true); outs = new DataOutputStream(httpConn.getOutputStream()); outs.writeBytes(postData); outs.flush(); inr = new BufferedReader(new InputStreamReader(httpConn.getInputStream())); Matcher matcher = null; while ((line = inr.readLine()) != null) { matcher = mirrorLinePattern.matcher(line); if (matcher.find()) { matcher = mirrorUrlPattern.matcher(line); if (matcher.find()) { urlLine = matcher.group().substring(2, matcher.group().length() - 2); result[0] = new URL(urlLine); } } matcher = counterPattern.matcher(line); if (matcher.find()) { matcher = counterIntPattern.matcher(line); if (matcher.find()) { counter = new Integer(matcher.group()); result[1] = counter; } } } } catch (IOException ex) { log("I/O Exception!"); } finally { try { if (outs != null) outs.close(); if (inr != null) inr.close(); } catch (IOException ex) { JOptionPane.showMessageDialog(null, "Can not close some connections:\n" + ex.getMessage(), "ERROR", JOptionPane.ERROR_MESSAGE); } if (httpConn != null) httpConn.disconnect(); link.setStatus(RSLink.STATUS_NOTHING); return result; } } | public String sendRequest(java.lang.String servletName, java.lang.String request) { String reqxml = ""; org.jdom.Document retdoc = null; String myurl = java.util.prefs.Preferences.systemRoot().get("serverurl", ""); String myport = ""; myport = java.util.prefs.Preferences.systemRoot().get("portno", "8080"); if (myport == null || myport.trim().equals("")) { myport = "80"; } if (this.serverURL == null) { try { java.net.URL codebase = newgen.presentation.NewGenMain.getAppletInstance().getCodeBase(); if (codebase != null) serverURL = codebase.getHost(); else serverURL = "localhost"; } catch (Exception exp) { exp.printStackTrace(); serverURL = "localhost"; } newgen.presentation.component.IPAddressPortNoDialog ipdig = new newgen.presentation.component.IPAddressPortNoDialog(myurl, myport); ipdig.show(); serverURL = myurl = ipdig.getIPAddress(); myport = ipdig.getPortNo(); java.util.prefs.Preferences.systemRoot().put("serverurl", serverURL); java.util.prefs.Preferences.systemRoot().put("portno", myport); System.out.println(serverURL); } try { System.out.println("http://" + serverURL + ":" + myport + "/newgenlibctxt/" + servletName); java.net.URL url = new java.net.URL("http://" + serverURL + ":" + myport + "/newgenlibctxt/" + servletName); java.net.URLConnection urlconn = (java.net.URLConnection) url.openConnection(); urlconn.setDoOutput(true); urlconn.setRequestProperty("Content-type", "text/xml; charset=UTF-8"); java.io.OutputStream os = urlconn.getOutputStream(); String req1xml = request; java.util.zip.CheckedOutputStream cos = new java.util.zip.CheckedOutputStream(os, new java.util.zip.Adler32()); java.util.zip.GZIPOutputStream gop = new java.util.zip.GZIPOutputStream(cos); java.io.OutputStreamWriter dos = new java.io.OutputStreamWriter(gop, "UTF-8"); System.out.println("#########***********$$$$$$$$##########" + req1xml); dos.write(req1xml); dos.flush(); dos.close(); System.out.println("url conn: " + urlconn.getContentEncoding() + " " + urlconn.getContentType()); java.io.InputStream ios = urlconn.getInputStream(); java.util.zip.CheckedInputStream cis = new java.util.zip.CheckedInputStream(ios, new java.util.zip.Adler32()); java.util.zip.GZIPInputStream gip = new java.util.zip.GZIPInputStream(cis); java.io.InputStreamReader br = new java.io.InputStreamReader(gip, "UTF-8"); retdoc = (new org.jdom.input.SAXBuilder()).build(br); } catch (java.net.ConnectException conexp) { javax.swing.JOptionPane.showMessageDialog(null, newgen.presentation.NewGenMain.getAppletInstance().getMyResource().getString("ConnectExceptionMessage"), "Critical error", javax.swing.JOptionPane.ERROR_MESSAGE); } catch (Exception exp) { exp.printStackTrace(System.out); TroubleShootConnectivity troubleShoot = new TroubleShootConnectivity(); } System.out.println(reqxml); return (new org.jdom.output.XMLOutputter()).outputString(retdoc); } | 896,978 |
1 | public static void gunzip(File gzippedFile, File destinationFile) throws IOException { int buffer = 2048; FileInputStream in = new FileInputStream(gzippedFile); GZIPInputStream zipin = new GZIPInputStream(in); byte[] data = new byte[buffer]; FileOutputStream out = new FileOutputStream(destinationFile); int length; while ((length = zipin.read(data, 0, buffer)) != -1) out.write(data, 0, length); out.close(); zipin.close(); } | public static void decompress(final File file, final File folder, final boolean deleteZipAfter) throws IOException { final ZipInputStream zis = new ZipInputStream(new BufferedInputStream(new FileInputStream(file.getCanonicalFile()))); ZipEntry ze; try { while (null != (ze = zis.getNextEntry())) { final File f = new File(folder.getCanonicalPath(), ze.getName()); if (f.exists()) f.delete(); if (ze.isDirectory()) { f.mkdirs(); continue; } f.getParentFile().mkdirs(); final OutputStream fos = new BufferedOutputStream(new FileOutputStream(f)); try { try { final byte[] buf = new byte[8192]; int bytesRead; while (-1 != (bytesRead = zis.read(buf))) fos.write(buf, 0, bytesRead); } finally { fos.close(); } } catch (final IOException ioe) { f.delete(); throw ioe; } } } finally { zis.close(); } if (deleteZipAfter) file.delete(); } | 896,979 |
0 | private void displayDiffResults() throws IOException { File outFile = File.createTempFile("diff", ".htm"); outFile.deleteOnExit(); FileOutputStream outStream = new FileOutputStream(outFile); BufferedWriter out = new BufferedWriter(new OutputStreamWriter(outStream)); out.write("<html><head><title>LOC Differences</title>\n" + SCRIPT + "</head>\n" + "<body bgcolor='#ffffff'>\n" + "<div onMouseOver=\"window.defaultStatus='Metrics'\">\n"); if (addedTable.length() > 0) { out.write("<table border><tr><th>Files Added:</th>" + "<th>Add</th><th>Type</th></tr>"); out.write(addedTable.toString()); out.write("</table><br><br>"); } if (modifiedTable.length() > 0) { out.write("<table border><tr><th>Files Modified:</th>" + "<th>Base</th><th>Del</th><th>Mod</th><th>Add</th>" + "<th>Total</th><th>Type</th></tr>"); out.write(modifiedTable.toString()); out.write("</table><br><br>"); } if (deletedTable.length() > 0) { out.write("<table border><tr><th>Files Deleted:</th>" + "<th>Del</th><th>Type</th></tr>"); out.write(deletedTable.toString()); out.write("</table><br><br>"); } out.write("<table name=METRICS BORDER>\n"); if (modifiedTable.length() > 0 || deletedTable.length() > 0) { out.write("<tr><td>Base: </td><td>"); out.write(Long.toString(base)); out.write("</td></tr>\n<tr><td>Deleted: </td><td>"); out.write(Long.toString(deleted)); out.write("</td></tr>\n<tr><td>Modified: </td><td>"); out.write(Long.toString(modified)); out.write("</td></tr>\n<tr><td>Added: </td><td>"); out.write(Long.toString(added)); out.write("</td></tr>\n<tr><td>New & Changed: </td><td>"); out.write(Long.toString(added + modified)); out.write("</td></tr>\n"); } out.write("<tr><td>Total: </td><td>"); out.write(Long.toString(total)); out.write("</td></tr>\n</table></div>"); redlinesOut.close(); out.flush(); InputStream redlines = new FileInputStream(redlinesTempFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = redlines.read(buffer)) != -1) outStream.write(buffer, 0, bytesRead); outStream.write("</BODY></HTML>".getBytes()); outStream.close(); Browser.launch(outFile.toURL().toString()); } | public RandomGUID() { MessageDigest md5 = null; try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e.getClass().getName() + ": " + e.getMessage()); } try { long time = System.currentTimeMillis(); long rand = 0; rand = myRand.nextLong(); StringBuffer sb = new StringBuffer(); sb.append(s_id); sb.append(":"); sb.append(Long.toString(time)); sb.append(":"); sb.append(Long.toString(rand)); md5.update(sb.toString().getBytes()); byte[] array = md5.digest(); sb.setLength(0); 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) { throw new RuntimeException(e.getClass().getName() + ": " + e.getMessage()); } } | 896,980 |
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(WebCastellumFilter.MODIFICATION_EXCLUDES_DEFAULT); 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); 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(WebCastellumFilter.RESPONSE_MODIFICATIONS_DEFAULT); final ResponseModificationDefinitionContainer container = new ResponseModificationDefinitionContainer(ruleFileLoaderResponseModifications); container.parseDefinitions(); final ResponseModificationDefinition[] responseModificationDefinitions = downCast(container.getAllEnabledRequestDefinitions()); final List tmpPatternsToExcludeCompleteTag = new ArrayList(responseModificationDefinitions.length); final List tmpPatternsToExcludeCompleteScript = new ArrayList(responseModificationDefinitions.length); final List tmpPatternsToExcludeLinksWithinScripts = new ArrayList(responseModificationDefinitions.length); final List tmpPatternsToExcludeLinksWithinTags = new ArrayList(responseModificationDefinitions.length); final List tmpPatternsToCaptureLinksWithinScripts = new ArrayList(responseModificationDefinitions.length); final List tmpPatternsToCaptureLinksWithinTags = new ArrayList(responseModificationDefinitions.length); final List tmpPrefiltersToExcludeCompleteTag = new ArrayList(responseModificationDefinitions.length); final List tmpPrefiltersToExcludeCompleteScript = new ArrayList(responseModificationDefinitions.length); final List tmpPrefiltersToExcludeLinksWithinScripts = new ArrayList(responseModificationDefinitions.length); final List tmpPrefiltersToExcludeLinksWithinTags = new ArrayList(responseModificationDefinitions.length); final List tmpPrefiltersToCaptureLinksWithinScripts = new ArrayList(responseModificationDefinitions.length); final List tmpPrefiltersToCaptureLinksWithinTags = new ArrayList(responseModificationDefinitions.length); final List tmpGroupNumbersToCaptureLinksWithinScripts = new ArrayList(responseModificationDefinitions.length); final List tmpGroupNumbersToCaptureLinksWithinTags = new ArrayList(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(); } | public boolean open(String mode) { if (source instanceof String) return false; else if (mode == null) mode = ""; else mode = mode.toLowerCase(); boolean toread = false, towrite = false; if (mode.indexOf("r") >= 0) toread = true; if (mode.indexOf("w") >= 0) towrite = true; if (!toread && !towrite) toread = towrite = true; try { if (toread && input == null) { if (isDirectory()) return true; else if (reader != null) return true; else if (source instanceof File) input = new FileInputStream((File) source); else if (source instanceof Socket) input = ((Socket) source).getInputStream(); else if (source instanceof URL) return getUrlInfo(toread, towrite); else return false; } if (towrite && output == null) { if (isDirectory()) return false; else if (writer != null) return true; else if (source instanceof File) output = new FileOutputStream((File) source); else if (source instanceof Socket) output = ((Socket) source).getOutputStream(); else if (source instanceof URL) return getUrlInfo(toread, towrite); else return false; } return true; } catch (Exception e) { return false; } } | 896,981 |
1 | private static BufferedInputStream getHTTPConnection(String sUrl) { URL url = null; BufferedInputStream bis = null; try { url = new URL(sUrl); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.setDoOutput(true); connection.setConnectTimeout(30000); connection.setReadTimeout(60000); connection.setRequestProperty("Accept-Encoding", "gzip, deflate"); connection.connect(); String encoding = connection.getContentEncoding(); if (!Utilities.isEmpty(encoding) && "gzip".equalsIgnoreCase(encoding)) { bis = new BufferedInputStream(new GZIPInputStream(connection.getInputStream()), IO_BUFFER_SIZE); } else if (!Utilities.isEmpty(encoding) && "deflate".equalsIgnoreCase(encoding)) { bis = new BufferedInputStream(new InflaterInputStream(connection.getInputStream(), new Inflater(true)), IO_BUFFER_SIZE); } else { bis = new BufferedInputStream(connection.getInputStream(), IO_BUFFER_SIZE); } } catch (Exception e) { LogUtil.e(Constants.TAG, e.getMessage()); } return bis; } | public static List importSymbol(Report report, Symbol symbol, TradingDate startDate, TradingDate endDate) throws IOException { List quotes = new ArrayList(); String URLString = constructURL(symbol, startDate, endDate); QuoteFilter filter = new YahooQuoteFilter(symbol); PreferencesManager.ProxyPreferences proxyPreferences = PreferencesManager.loadProxySettings(); try { URL url = new URL(URLString); InputStreamReader input = new InputStreamReader(url.openStream()); BufferedReader bufferedInput = new BufferedReader(input); String line = bufferedInput.readLine(); while (line != null) { line = bufferedInput.readLine(); if (line != null) { try { Quote quote = filter.toQuote(line); quotes.add(quote); verify(report, quote); } catch (QuoteFormatException e) { report.addError(Locale.getString("YAHOO") + ":" + symbol + ":" + Locale.getString("ERROR") + ": " + e.getMessage()); } } } bufferedInput.close(); } catch (BindException e) { DesktopManager.showErrorMessage(Locale.getString("UNABLE_TO_CONNECT_ERROR", e.getMessage())); throw new IOException(); } catch (ConnectException e) { DesktopManager.showErrorMessage(Locale.getString("UNABLE_TO_CONNECT_ERROR", e.getMessage())); throw new IOException(); } catch (UnknownHostException e) { DesktopManager.showErrorMessage(Locale.getString("UNKNOWN_HOST_ERROR", e.getMessage())); throw new IOException(); } catch (NoRouteToHostException e) { DesktopManager.showErrorMessage(Locale.getString("DESTINATION_UNREACHABLE_ERROR", e.getMessage())); throw new IOException(); } catch (MalformedURLException e) { DesktopManager.showErrorMessage(Locale.getString("INVALID_PROXY_ERROR", proxyPreferences.host, proxyPreferences.port)); throw new IOException(); } catch (FileNotFoundException e) { report.addError(Locale.getString("YAHOO") + ":" + symbol + ":" + Locale.getString("ERROR") + ": " + Locale.getString("NO_QUOTES_FOUND")); } catch (IOException e) { DesktopManager.showErrorMessage(Locale.getString("ERROR_DOWNLOADING_QUOTES")); throw new IOException(); } return quotes; } | 896,982 |
0 | public void execute() throws InstallerException { try { SQLCommand sqlCommand = new SQLCommand(connectionInfo); connection = sqlCommand.getConnection(); connection.setAutoCommit(false); sqlStatement = connection.createStatement(); double size = (double) statements.size(); for (String statement : statements) { sqlStatement.executeUpdate(statement); setCompletedPercentage(getCompletedPercentage() + (1 / size)); } connection.commit(); } catch (SQLException e) { try { connection.rollback(); } catch (SQLException e1) { throw new InstallerException(InstallerException.TRANSACTION_ROLLBACK_ERROR, new Object[] { e.getMessage() }, e); } throw new InstallerException(InstallerException.SQL_EXEC_EXCEPTION, new Object[] { e.getMessage() }, e); } catch (ClassNotFoundException e) { throw new InstallerException(InstallerException.DB_DRIVER_LOAD_ERROR, e); } finally { if (connection != null) { try { sqlStatement.close(); connection.close(); } catch (SQLException e) { } } } } | private HttpURLConnection makeGetRequest(String action, Object... parameters) throws IOException { StringBuffer request = new StringBuffer(remoteUrl); HTMLUtils.appendQuery(request, VERSION_PARAM, CLIENT_VERSION); HTMLUtils.appendQuery(request, ACTION_PARAM, action); for (int i = 0; i < parameters.length; i += 2) { HTMLUtils.appendQuery(request, String.valueOf(parameters[i]), String.valueOf(parameters[i + 1])); } String requestStr = request.toString(); URLConnection conn; if (requestStr.length() < MAX_URL_LENGTH) { URL url = new URL(requestStr); conn = url.openConnection(); } else { int queryPos = requestStr.indexOf('?'); byte[] query = requestStr.substring(queryPos + 1).getBytes(HTTPUtils.DEFAULT_CHARSET); URL url = new URL(requestStr.substring(0, queryPos)); conn = url.openConnection(); conn.setDoOutput(true); conn.setDoInput(true); conn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); conn.setRequestProperty("Content-Length", Integer.toString(query.length)); OutputStream outputStream = new BufferedOutputStream(conn.getOutputStream()); outputStream.write(query); outputStream.close(); } return (HttpURLConnection) conn; } | 896,983 |
0 | public DoSearch(String searchType, String searchString) { String urlString = dms_url + "/servlet/com.ufnasoft.dms.server.ServerDoSearch"; String rvalue = ""; String filename = dms_home + FS + "temp" + FS + username + "search.xml"; try { String urldata = urlString + "?username=" + URLEncoder.encode(username, "UTF-8") + "&key=" + key + "&search=" + URLEncoder.encode(searchString, "UTF-8") + "&searchtype=" + URLEncoder.encode(searchType, "UTF-8") + "&filename=" + URLEncoder.encode(username, "UTF-8") + "search.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("entry"); int num = nodelist.getLength(); searchDocs = new String[num][3]; searchDocImageName = new String[num]; searchDocsToolTip = new String[num]; for (int i = 0; i < num; i++) { searchDocs[i][0] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "filename"); searchDocs[i][1] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "project"); searchDocs[i][2] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "documentid"); searchDocImageName[i] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "imagename"); searchDocsToolTip[i] = DOMUtil.getSimpleElementText((Element) nodelist.item(i), "description"); } } catch (MalformedURLException ex) { System.out.println(ex); } catch (ParserConfigurationException ex) { System.out.println(ex); } catch (Exception ex) { System.out.println(ex); } System.out.println(rvalue); if (rvalue.equalsIgnoreCase("yes")) { } } | protected void handleUrl(URL url) throws Exception { BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String s; boolean moreResults = false; while ((s = in.readLine()) != null) { if (s.indexOf("<h1>Search Results</h1>") > -1) { System.err.println("found severals result"); moreResults = true; } else if (s.indexOf("Download <a href=") > -1) { if (s.indexOf("in JCAMP-DX format.") > -1) { System.err.println("download masspec"); super.handleUrl(new URL((url.getProtocol() + "://" + url.getHost() + s.substring(s.indexOf("\"") + 1, s.lastIndexOf("\""))).replaceAll("amp;", ""))); } moreResults = false; } if (moreResults == true) { if (s.indexOf("<li><a href=\"/cgi/cbook.cgi?ID") > -1) { System.err.println("\tdownloading new url " + new URL((url.getProtocol() + "://" + url.getHost() + s.substring(s.indexOf("\"") + 1, s.lastIndexOf("\""))).replaceAll("amp;", ""))); this.handleUrl(new URL((url.getProtocol() + "://" + url.getHost() + s.substring(s.indexOf("\"") + 1, s.lastIndexOf("\""))).replaceAll("amp;", ""))); } } } } | 896,984 |
1 | public String control(final String allOptions) throws SQLException { connect(); final Statement stmt = connection.createStatement(); final ResultSet rst1 = stmt.executeQuery("SELECT versionId FROM versions WHERE version='" + Concrete.version() + "'"); final long versionId; if (rst1.next()) { versionId = rst1.getInt(1); } else { disconnect(); return ""; } rst1.close(); final MessageDigest msgDigest; try { msgDigest = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e1) { logger.throwing(SQLExecutionController.class.getSimpleName(), "control", e1); disconnect(); return ""; } msgDigest.update(allOptions.getBytes()); final ResultSet rst2 = stmt.executeQuery("SELECT configId FROM configs WHERE md5='" + Concrete.md5(msgDigest.digest()) + "'"); final long configId; if (rst2.next()) { configId = rst2.getInt(1); } else { disconnect(); return ""; } rst2.close(); final ResultSet rst4 = stmt.executeQuery("SELECT problems.md5 FROM executions " + "LEFT JOIN problems ON executions.problemId = problems.problemId WHERE " + "configId=" + configId + " AND versionId=" + versionId); final StringBuilder stb = new StringBuilder(); while (rst4.next()) { stb.append(rst4.getString(1)).append('\n'); } rst4.close(); stmt.close(); return stb.toString(); } | protected final String H(String data) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(data.getBytes("UTF8")); byte[] bytes = digest.digest(); StringBuffer sb = new StringBuffer(); for (int i = 0; i < bytes.length; i++) { int aByte = bytes[i]; if (aByte < 0) aByte += 256; if (aByte < 16) sb.append('0'); sb.append(Integer.toHexString(aByte)); } return sb.toString(); } | 896,985 |
0 | public void gzipCompress(String file) { try { File inputFile = new File(file); FileInputStream fileinput = new FileInputStream(inputFile); File outputFile = new File(file.substring(0, file.length() - 1) + "z"); FileOutputStream stream = new FileOutputStream(outputFile); GZIPOutputStream gzipstream = new GZIPOutputStream(stream); BufferedInputStream bis = new BufferedInputStream(fileinput); int bytes_read = 0; byte[] buf = new byte[READ_BUFFER_SIZE]; while ((bytes_read = bis.read(buf, 0, BLOCK_SIZE)) != -1) { gzipstream.write(buf, 0, bytes_read); } bis.close(); inputFile.delete(); gzipstream.finish(); gzipstream.close(); } catch (FileNotFoundException fnfe) { System.out.println("Compressor: Cannot find file " + fnfe.getMessage()); } catch (SecurityException se) { System.out.println("Problem saving file " + se.getMessage()); } catch (IOException ioe) { System.out.println("Problem saving file " + ioe.getMessage()); } } | byte[] makeIDPFXORMask() { if (idpfMask == null) { try { MessageDigest sha = MessageDigest.getInstance("SHA-1"); String temp = strip(getPrimaryIdentifier()); sha.update(temp.getBytes("UTF-8"), 0, temp.length()); idpfMask = sha.digest(); } catch (NoSuchAlgorithmException e) { System.err.println("No such Algorithm (really, did I misspell SHA-1?"); System.err.println(e.toString()); return null; } catch (IOException e) { System.err.println("IO Exception. check out mask.write..."); System.err.println(e.toString()); return null; } } return idpfMask; } | 896,986 |
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 searchEntity(String login, String password, String searcheId, OutputStream os) throws SynchronizationException { HttpClient client = new SSLHttpClient(); try { StringBuilder builder = new StringBuilder(url).append("?" + CMD_PARAM + "=" + CMD_SEARCH).append("&" + LOGIN_PARAM + "=" + URLEncoder.encode(login, "UTF-8")).append("&" + PASSWD_PARAM + "=" + URLEncoder.encode(password, "UTF-8")).append("&" + SEARCH_PARAM + "=" + searcheId); HttpGet method = httpGetMethod(builder.toString()); HttpResponse response = client.execute(method); Header header = response.getFirstHeader(HEADER_NAME); if (header != null && HEADER_VALUE.equals(HEADER_VALUE)) { int code = response.getStatusLine().getStatusCode(); if (code == HttpStatus.SC_OK) { long expectedLength = response.getEntity().getContentLength(); InputStream is = response.getEntity().getContent(); FileUtils.writeInFile(is, os, expectedLength); return true; } else { throw new SynchronizationException("Command 'search' : HTTP error code returned." + code, SynchronizationException.ERROR_SEARCH); } } else { throw new SynchronizationException("HTTP header is invalid", SynchronizationException.ERROR_SEARCH); } } catch (Exception e) { throw new SynchronizationException("Command 'search' -> ", e, SynchronizationException.ERROR_SEARCH); } } | 896,987 |
1 | public static void main(String[] args) throws Exception { FileChannel fc = new FileOutputStream("data.txt").getChannel(); fc.write(ByteBuffer.wrap("Some text ".getBytes())); fc.close(); fc = new RandomAccessFile("data.txt", "rw").getChannel(); fc.position(fc.size()); fc.write(ByteBuffer.wrap("Some more".getBytes())); fc.close(); fc = new FileInputStream("data.txt").getChannel(); ByteBuffer buff = ByteBuffer.allocate(BSIZE); fc.read(buff); buff.flip(); while (buff.hasRemaining()) System.out.print((char) buff.get()); } | 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(); } | 896,988 |
0 | public HttpURLConnection getURLConnection() throws IOException { HttpURLConnection conn = null; try { conn = (HttpURLConnection) _url.openConnection(); conn.setUseCaches(false); conn.setRequestProperty("User-Agent", "WD-2.0"); if (_doConditionalGET) { ResourceInfo ri = (ResourceInfo) conditionalGetTable().get(_url.toString()); if (ri != null) { if (ri.lastModified != null) { conn.setRequestProperty("If-Modified-Since", ri.lastModified); } if (ri.etag != null) { conn.setRequestProperty("If-None-Match", ri.etag); } } } if (_username != null && _password != null) { String authenticationStr = _username + ":" + _password; String encodedAuthStr = Base64.encodeBytes(authenticationStr.getBytes()); conn.setRequestProperty("Authorization", "Basic " + encodedAuthStr); } _httpResponseCode = conn.getResponseCode(); if (_httpResponseCode == HttpURLConnection.HTTP_OK) { if (_doConditionalGET) { ResourceInfo ri = new ResourceInfo(); ri.lastModified = conn.getHeaderField("Last-Modified"); ri.etag = conn.getHeaderField("ETag"); Hashtable table = conditionalGetTable(); table.put(_url.toString(), ri); storeConditionalGetTable(table); } } else if (_httpResponseCode == HttpURLConnection.HTTP_NOT_MODIFIED) { _shouldGET = false; } else { Log.getInstance().write("Error getting url: " + _url + "\n" + "Error code: " + _httpResponseCode); _error = HTTP_NOT_OK; conn.disconnect(); conn = null; } } catch (SocketException ex) { conn.disconnect(); conn = null; _error = NETWORK_DOWN; } return conn; } | public static String loadSite(String spec) throws IOException { URL url = new URL(spec); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String output = ""; String str; while ((str = in.readLine()) != null) { output += str + "\n"; } in.close(); return output; } | 896,989 |
1 | @Override public void run() { long timeout = 10 * 1000L; long start = (new Date()).getTime(); try { InputStream is = socket.getInputStream(); boolean available = false; while (!available && !socket.isClosed()) { try { if (is.available() != 0) { available = true; } else { Thread.sleep(100); } } catch (Exception e) { LOG.error("Error checking socket", e); } long curr = (new Date()).getTime(); if ((curr - start) >= timeout) { break; } } if (socket.isClosed()) { } else { tmpFile = File.createTempFile("ftp", "dat", new File("./tmp")); BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(tmpFile)); IOUtils.copy(is, bos); bos.flush(); bos.close(); } String msg = FtpResponse.ReadComplete.asString() + ClientCommand.SP + "Read Complete" + ClientCommand.CRLF; List<String> list = new ArrayList<String>(); list.add(msg); ClientResponse response = new ClientResponse(list); ftpClient.notifyListeners(response); } catch (Exception e) { LOG.error("Error reading server response", e); } } | public java.io.File gzip(java.io.File file) throws Exception { java.io.File tmp = null; InputStream is = null; OutputStream os = null; try { tmp = java.io.File.createTempFile(file.getName(), ".gz"); tmp.deleteOnExit(); is = new BufferedInputStream(new FileInputStream(file)); os = new GZIPOutputStream(new BufferedOutputStream(new FileOutputStream(tmp))); byte[] buf = new byte[4096]; int nread = -1; while ((nread = is.read(buf)) != -1) { os.write(buf, 0, nread); } os.flush(); } finally { os.close(); is.close(); } return tmp; } | 896,990 |
0 | private void convertClasses(File source, File destination) throws PostProcessingException, CodeCheckException, IOException { Stack sourceStack = new Stack(); Stack destinationStack = new Stack(); sourceStack.push(source); destinationStack.push(destination); while (!sourceStack.isEmpty()) { source = (File) sourceStack.pop(); destination = (File) destinationStack.pop(); if (!destination.exists()) destination.mkdirs(); File[] files = source.listFiles(); for (int i = 0; i < files.length; i++) { File current = (File) files[i]; if (current.isDirectory()) { sourceStack.push(current); destinationStack.push(new File(destination, current.getName())); } else if (current.getName().endsWith(".class")) { ClassWriter writer = new ClassWriter(); InputStream is = new BufferedInputStream(new FileInputStream(current)); writer.readClass(is); is.close(); if ((getStatusFlags(writer.getClassName(writer.getCurrentClassIndex())) & PP_PROCESSED) != 0) { ClassWriter[] auxWriter = new ClassWriter[1]; transformClass(writer, auxWriter); File output = new File(destination, current.getName()); OutputStream os = new BufferedOutputStream(new FileOutputStream(output)); writer.writeClass(os); os.close(); if (auxWriter[0] != null) { String className = auxWriter[0].getClassName(auxWriter[0].getCurrentClassIndex()); className = className.substring(className.lastIndexOf('.') + 1, className.length()); output = new File(destination, className + ".class"); os = new BufferedOutputStream(new FileOutputStream(output)); auxWriter[0].writeClass(os); os.close(); } } } } } } | protected long getUrlSize(String location) { long returnValue = 0L; try { URL url = new URL(location); java.net.HttpURLConnection conn = (java.net.HttpURLConnection) url.openConnection(); conn.setRequestMethod("HEAD"); returnValue = conn.getContentLength(); } catch (IOException ioe) { logger.error("Failed to find proper size for entity at " + location, ioe); } return returnValue; } | 896,991 |
1 | 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); } } } } | public static void copyFile(File src, File dst) throws IOException { InputStream in = new FileInputStream(src); OutputStream out = new FileOutputStream(dst); byte[] buf = new byte[1024]; int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); in.close(); out.close(); } | 896,992 |
0 | private String buildShaHashOf(String source) { try { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(source.getBytes()); return new BigInteger(1, md.digest()).toString(16); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); return ""; } } | public static ArrayList<Quote> fetchAllQuotes(String symbol, Date from, Date to) { try { GregorianCalendar calendar = new GregorianCalendar(); calendar.setTime(from); String monthFrom = (new Integer(calendar.get(GregorianCalendar.MONTH))).toString(); String dayFrom = (new Integer(calendar.get(GregorianCalendar.DAY_OF_MONTH))).toString(); String yearFrom = (new Integer(calendar.get(GregorianCalendar.YEAR))).toString(); calendar.setTime(to); String monthTo = (new Integer(calendar.get(GregorianCalendar.MONTH))).toString(); String dayTo = (new Integer(calendar.get(GregorianCalendar.DAY_OF_MONTH))).toString(); String yearTo = (new Integer(calendar.get(GregorianCalendar.YEAR))).toString(); URL url = new URL("http://ichart.finance.yahoo.com/table.csv?s=" + symbol + "&a=" + monthFrom + "&b=" + dayFrom + "&c=" + yearFrom + "&d=" + monthTo + "&e=" + dayTo + "&f=" + yearTo + "&g=d&ignore=.csv"); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line; ArrayList<Quote> result = new ArrayList<Quote>(); reader.readLine(); while ((line = reader.readLine()) != null) { String[] values = line.split(","); String date = values[0]; Date dateQuote = new SimpleDateFormat("yyyy-MM-dd").parse(date); double open = Double.valueOf(values[1]); double high = Double.valueOf(values[2]); double low = Double.valueOf(values[3]); double close = Double.valueOf(values[4]); long volume = Long.valueOf(values[5]); double adjClose = Double.valueOf(values[6]); Quote q = new Quote(dateQuote, open, high, low, close, volume, adjClose); result.add(q); } reader.close(); Collections.reverse(result); return result; } catch (MalformedURLException e) { System.out.println("URL malformee"); } catch (IOException e) { System.out.println("Donnees illisibles"); } catch (ParseException e) { e.printStackTrace(); } return null; } | 896,993 |
0 | private MapProperties readProperties(URL url) { @SuppressWarnings("unchecked") MapProperties properties = new MapProperties(new LinkedHashMap()); InputStream is = null; try { is = url.openStream(); properties.load(is); } catch (IOException ex) { throw new RuntimeException(ex); } finally { StreamUtils.close(is); } return properties; } | public String encryptLdapPassword(String algorithm) { String sEncrypted = _password; if ((_password != null) && (_password.length() > 0)) { algorithm = Val.chkStr(algorithm); boolean bMD5 = algorithm.equalsIgnoreCase("MD5"); boolean bSHA = algorithm.equalsIgnoreCase("SHA") || algorithm.equalsIgnoreCase("SHA1") || algorithm.equalsIgnoreCase("SHA-1"); if (bSHA || bMD5) { String sAlgorithm = "MD5"; if (bSHA) { sAlgorithm = "SHA"; } try { MessageDigest md = MessageDigest.getInstance(sAlgorithm); md.update(getPassword().getBytes("UTF-8")); sEncrypted = "{" + sAlgorithm + "}" + (new BASE64Encoder()).encode(md.digest()); } catch (NoSuchAlgorithmException e) { sEncrypted = null; e.printStackTrace(System.err); } catch (UnsupportedEncodingException e) { sEncrypted = null; e.printStackTrace(System.err); } } } return sEncrypted; } | 896,994 |
1 | public OutputStream getAsOutputStream() throws IOException { OutputStream out; if (contentStream != null) { File tmp = File.createTempFile(getId(), null); out = new FileOutputStream(tmp); IOUtils.copy(contentStream, out); } else { out = new ByteArrayOutputStream(); out.write(getContent()); } return out; } | public void postProcess() throws StopWriterVisitorException { shpWriter.postProcess(); try { FileChannel fcinShp = new FileInputStream(fTemp).getChannel(); FileChannel fcoutShp = new FileOutputStream(fileShp).getChannel(); DriverUtilities.copy(fcinShp, fcoutShp); File shxFile = SHP.getShxFile(fTemp); FileChannel fcinShx = new FileInputStream(shxFile).getChannel(); FileChannel fcoutShx = new FileOutputStream(SHP.getShxFile(fileShp)).getChannel(); DriverUtilities.copy(fcinShx, fcoutShx); File dbfFile = getDataFile(fTemp); short originalEncoding = DbfEncodings.getInstance().getDbfIdForCharset(shpWriter.getCharset()); RandomAccessFile fo = new RandomAccessFile(dbfFile, "rw"); fo.seek(29); fo.writeByte(originalEncoding); fo.close(); FileChannel fcinDbf = new FileInputStream(dbfFile).getChannel(); FileChannel fcoutDbf = new FileOutputStream(getDataFile(fileShp)).getChannel(); DriverUtilities.copy(fcinDbf, fcoutDbf); fTemp.delete(); shxFile.delete(); dbfFile.delete(); reload(); } catch (FileNotFoundException e) { throw new StopWriterVisitorException(getName(), e); } catch (IOException e) { throw new StopWriterVisitorException(getName(), e); } catch (ReloadDriverException e) { throw new StopWriterVisitorException(getName(), e); } } | 896,995 |
0 | void queryInactive() { try { XMLConfigParser.readUrlHost(); String url = XMLConfigParser.urlHost; Date currenttime = new Date(); String query; String param1 = "op=queryinactive"; String param2 = "time=" + currenttime.getTime(); query = String.format("%s&%s", param1, param2); openConnection(query, url); String line = br.readLine(); NetworkLog.logMsg(NetworkLog.LOG_DEBUG, this, "(Query inactive)Response of the server: " + line); br.close(); } catch (MalformedURLException e) { NetworkLog.logMsg(NetworkLog.LOG_ERROR, this, "Error" + e); } catch (IOException e) { NetworkLog.logMsg(NetworkLog.LOG_ERROR, this, e.getMessage()); } } | private void fileUpload() throws IOException { HttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost(postURL); MultipartEntity mpEntity = new MultipartEntity(HttpMultipartMode.BROWSER_COMPATIBLE); mpEntity.addPart("Filename", new StringBody(file.getName())); mpEntity.addPart("Filedata", new MonitoredFileBody(file, uploadProgress)); httppost.setEntity(mpEntity); NULogger.getLogger().log(Level.INFO, "executing request {0}", httppost.getRequestLine()); NULogger.getLogger().info("Now uploading your file into sharesend.com"); status = UploadStatus.UPLOADING; HttpResponse response = httpclient.execute(httppost); status = UploadStatus.GETTINGLINK; HttpEntity resEntity = response.getEntity(); NULogger.getLogger().info(response.getStatusLine().toString()); if (resEntity != null) { uploadresponse = EntityUtils.toString(resEntity); } NULogger.getLogger().log(Level.INFO, "Upload Response : {0}", uploadresponse); NULogger.getLogger().log(Level.INFO, "Download Link : http://sharesend.com/{0}", uploadresponse); downloadlink = "http://sharesend.com/" + uploadresponse; downURL = downloadlink; httpclient.getConnectionManager().shutdown(); uploadFinished(); } | 896,996 |
0 | @Override public DataTable generateDataTable(Query query, HttpServletRequest request) throws DataSourceException { String url = request.getParameter(URL_PARAM_NAME); if (StringUtils.isEmpty(url)) { log.error("url parameter not provided."); throw new DataSourceException(ReasonType.INVALID_REQUEST, "url parameter not provided"); } Reader reader; try { reader = new BufferedReader(new InputStreamReader(new URL(url).openStream())); } catch (MalformedURLException e) { log.error("url is malformed: " + url); throw new DataSourceException(ReasonType.INVALID_REQUEST, "url is malformed: " + url); } catch (IOException e) { log.error("Couldn't read from url: " + url, e); throw new DataSourceException(ReasonType.INVALID_REQUEST, "Couldn't read from url: " + url); } DataTable dataTable = null; ULocale requestLocale = DataSourceHelper.getLocaleFromRequest(request); try { dataTable = CsvDataSourceHelper.read(reader, null, true, requestLocale); } catch (IOException e) { log.error("Couldn't read from url: " + url, e); throw new DataSourceException(ReasonType.INVALID_REQUEST, "Couldn't read from url: " + url); } return dataTable; } | public SCFFile(URL url) throws IOException { URLConnection connection = url.openConnection(); byte[] content = new byte[connection.getContentLength()]; DataInputStream dis = new DataInputStream(connection.getInputStream()); dis.readFully(content); dis.close(); dis = new DataInputStream(new ByteArrayInputStream(content)); header = new SCFHeader(dis); if (!header.magicNumber.equals(".scf")) throw new RuntimeException(url + " is not an SCF file"); A = new int[header.samples]; C = new int[header.samples]; G = new int[header.samples]; T = new int[header.samples]; max = Integer.MIN_VALUE; dis.reset(); dis.skipBytes(header.samplesOffset); if (header.sampleSize == 1) { if (header.version < 3.00) { for (int i = 0; i < header.samples; ++i) { A[i] = dis.readUnsignedByte(); if (A[i] > max) max = A[i]; C[i] = dis.readUnsignedByte(); if (C[i] > max) max = C[i]; G[i] = dis.readUnsignedByte(); if (G[i] > max) max = G[i]; T[i] = dis.readUnsignedByte(); if (T[i] > max) max = T[i]; } } else { for (int i = 0; i < header.samples; ++i) { A[i] = dis.readUnsignedByte(); if (A[i] > max) max = A[i]; } for (int i = 0; i < header.samples; ++i) { C[i] = dis.readUnsignedByte(); if (C[i] > max) max = C[i]; } for (int i = 0; i < header.samples; ++i) { G[i] = dis.readUnsignedByte(); if (G[i] > max) max = G[i]; } for (int i = 0; i < header.samples; ++i) { T[i] = dis.readUnsignedByte(); if (T[i] > max) max = T[i]; } } } else if (header.sampleSize == 2) { if (header.version < 3.00) { for (int i = 0; i < header.samples; ++i) { A[i] = dis.readUnsignedShort(); if (A[i] > max) max = A[i]; C[i] = dis.readUnsignedShort(); if (C[i] > max) max = C[i]; G[i] = dis.readUnsignedShort(); if (G[i] > max) max = G[i]; T[i] = dis.readUnsignedShort(); if (T[i] > max) max = T[i]; } } else { for (int i = 0; i < header.samples; ++i) { A[i] = dis.readUnsignedShort(); if (A[i] > max) max = A[i]; } for (int i = 0; i < header.samples; ++i) { C[i] = dis.readUnsignedShort(); if (C[i] > max) max = C[i]; } for (int i = 0; i < header.samples; ++i) { G[i] = dis.readUnsignedShort(); if (G[i] > max) max = G[i]; } for (int i = 0; i < header.samples; ++i) { T[i] = dis.readUnsignedShort(); if (T[i] > max) max = T[i]; } } } centers = new int[header.bases]; byte[] buf = new byte[header.bases]; dis.reset(); dis.skipBytes(header.basesOffset); if (header.version < 3.00) { for (int i = 0; i < header.bases; ++i) { centers[i] = dis.readInt(); dis.skipBytes(4); buf[i] = dis.readByte(); dis.skipBytes(3); } } else { for (int i = 0; i < header.bases; ++i) centers[i] = dis.readInt(); dis.skipBytes(4 * header.bases); dis.readFully(buf); } sequence = new String(buf); dis.close(); } | 896,997 |
1 | private static File copyJarToPool(File file) { File outFile = new File(RizzToolConstants.TOOL_POOL_FOLDER.getAbsolutePath() + File.separator + file.getName()); if (file != null && file.exists() && file.canRead()) { try { FileChannel inChan = new FileInputStream(file).getChannel(); FileChannel outChan = new FileOutputStream(outFile).getChannel(); inChan.transferTo(0, inChan.size(), outChan); return outFile; } catch (Exception ex) { RizzToolConstants.DEFAULT_LOGGER.error("Exception while copying jar file to tool pool [inFile=" + file.getAbsolutePath() + "] [outFile=" + outFile.getAbsolutePath() + ": " + ex); } } else { RizzToolConstants.DEFAULT_LOGGER.error("Could not copy jar file. File does not exist or can't read file. [inFile=" + file.getAbsolutePath() + "]"); } return null; } | @Override protected svm_model loadModel(InputStream inputStream) throws IOException { File tmpFile = File.createTempFile("tmp", ".mdl"); FileOutputStream output = new FileOutputStream(tmpFile); try { IOUtils.copy(inputStream, output); return libsvm.svm.svm_load_model(tmpFile.getPath()); } finally { output.close(); tmpFile.delete(); } } | 896,998 |
0 | private void copyFile(File orig, File dest) { byte[] buffer = new byte[1024]; try { FileInputStream fis = new FileInputStream(orig); FileOutputStream fos = new FileOutputStream(dest, true); int readBytes = 0; do { readBytes = fis.read(buffer); if (readBytes > 0) fos.write(buffer, 0, readBytes); } while (readBytes > 0); fos.close(); fis.close(); } catch (Exception e) { e.printStackTrace(); } } | public static String encryptPassword(String password) { String hash = null; try { MessageDigest md = null; md = MessageDigest.getInstance("SHA"); md.update(password.getBytes("UTF-8")); byte raw[] = md.digest(); hash = Base64.encode(raw, false); } catch (Exception e) { } return hash; } | 896,999 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.