label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
|---|---|---|---|
1 | public static void copyFile(String from, String to, boolean append) throws IOException { FileChannel in = new FileInputStream(from).getChannel(); FileChannel out = new FileOutputStream(to, append).getChannel(); ByteBuffer buffer = ByteBuffer.allocate(BSIZE); while (in.read(buffer) != -1) { buffer.flip(); out.write(buffer); buffer.clear(); } } | private static void convertToOnline(final String filePath, final DocuBean docuBean) throws Exception { File source = new File(filePath + File.separator + docuBean.getFileName()); File dir = new File(filePath + File.separator + docuBean.getId()); if (!dir.exists()) { dir.mkdir(); } File in = source; boolean isSpace = false; if (source.getName().indexOf(" ") != -1) { in = new File(StringUtils.replace(source.getName(), " ", "")); try { IOUtils.copyFile(source, in); } catch (IOException e) { e.printStackTrace(); } isSpace = true; } File finalPdf = null; try { String outPath = dir.getAbsolutePath(); final File pdf = DocViewerConverter.toPDF(in, outPath); convertToSwf(pdf, outPath, docuBean); finalPdf = new File(outPath + File.separator + FileUtils.getFilePrefix(StringUtils.replace(source.getName(), " ", "")) + "_decrypted.pdf"); if (!finalPdf.exists()) { finalPdf = pdf; } pdfByFirstPageToJpeg(finalPdf, outPath, docuBean); if (docuBean.getSuccess() == 2 && dir.listFiles().length < 2) { docuBean.setSuccess(3); } } catch (Exception e) { throw e; } finally { if (isSpace) { IOUtils.delete(in); } } } | 884,900 |
1 | public String[][] getProjectTreeData() { String[][] treeData = null; String filename = dms_home + FS + "temp" + FS + username + "projects.xml"; String urlString = dms_url + "/servlet/com.ufnasoft.dms.server.ServerGetProjects"; try { String urldata = urlString + "?username=" + URLEncoder.encode(username, "UTF-8") + "&key=" + URLEncoder.encode(key, "UTF-8") + "&filename=" + URLEncoder.encode(username, "UTF-8") + "projects.xml"; System.out.println(urldata); DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); 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("j"); int num = nodelist.getLength(); treeData = new String[num][5]; for (int i = 0; i < num; i++) { treeData[i][0] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "i")); treeData[i][1] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "pi")); treeData[i][2] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "p")); treeData[i][3] = ""; treeData[i][4] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "f")); } } catch (MalformedURLException ex) { System.out.println(ex); } catch (ParserConfigurationException ex) { System.out.println(ex); } catch (NullPointerException e) { } catch (Exception ex) { System.out.println(ex); } return treeData; } | private void appendArchive(File instClass) throws IOException { FileOutputStream out = new FileOutputStream(instClass.getName(), true); FileInputStream zipStream = new FileInputStream("install.jar"); byte[] buf = new byte[2048]; int read = zipStream.read(buf); while (read > 0) { out.write(buf, 0, read); read = zipStream.read(buf); } zipStream.close(); out.close(); } | 884,901 |
1 | public static void copyFile(final String inFile, final String outFile) { FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(inFile).getChannel(); out = new FileOutputStream(outFile).getChannel(); in.transferTo(0, in.size(), out); } catch (final Exception e) { } finally { if (in != null) { try { in.close(); } catch (final Exception e) { } } if (out != null) { try { out.close(); } catch (final Exception e) { } } } } | public void copyFile(File in, File out) throws Exception { FileChannel ic = new FileInputStream(in).getChannel(); FileChannel oc = new FileOutputStream(out).getChannel(); ic.transferTo(0, ic.size(), oc); ic.close(); oc.close(); } | 884,902 |
1 | public static String CreateHash(String s) { String str = s.toString(); if (str == null || str.length() == 0) { throw new IllegalArgumentException("String cannot be null or empty"); } StringBuffer hexString = new StringBuffer(); try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(str.getBytes()); byte[] hash = md.digest(); for (int i = 0; i < hash.length; i++) { if ((0xff & hash[i]) < 0x10) { hexString.append("0" + Integer.toHexString((0xFF & hash[i]))); } else { hexString.append(Integer.toHexString(0xFF & hash[i])); } } } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return (hexString.toString()); } | public String encrypt(String password) { String encrypted_pass = ""; ByteArrayOutputStream output = null; MessageDigest md = null; try { md = MessageDigest.getInstance("SHA"); md.update(password.getBytes("UTF-8")); byte byte_array[] = md.digest(); output = new ByteArrayOutputStream(byte_array.length); output.write(byte_array); encrypted_pass = output.toString("UTF-8"); System.out.println("password: " + encrypted_pass); } catch (Exception e) { System.out.println("Exception thrown: " + e.getMessage()); } return encrypted_pass; } | 884,903 |
1 | public static File copyFile(File srcFile, File destFolder, FileCopyListener copyListener) { File dest = new File(destFolder, srcFile.getName()); try { FileInputStream in = new FileInputStream(srcFile); FileOutputStream out = new FileOutputStream(dest); byte[] readBuf = new byte[1024 * 512]; int readLength; long totalCopiedSize = 0; long totalSize = srcFile.length(); boolean canceled = false; if (copyListener == null) { while ((readLength = in.read(readBuf)) != -1) { out.write(readBuf, 0, readLength); } } else { while ((readLength = in.read(readBuf)) != -1) { out.write(readBuf, 0, readLength); if (!copyListener.updateCheck(readLength, totalSize)) { canceled = true; break; } } } in.close(); out.close(); if (canceled) { dest.delete(); } } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return dest; } | 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(); } } | 884,904 |
0 | private void documentFileChooserActionPerformed(java.awt.event.ActionEvent evt) { if (evt.getActionCommand().equals(JFileChooser.APPROVE_SELECTION)) { File selectedFile = documentFileChooser.getSelectedFile(); File collectionCopyFile; String newDocumentName = selectedFile.getName(); Document newDocument = new Document(newDocumentName); if (activeCollection.containsDocument(newDocument)) { int matchingFilenameDistinguisher = 1; StringBuilder distinguisherReplacer = new StringBuilder(); newDocumentName = newDocumentName.concat("(" + matchingFilenameDistinguisher + ")"); newDocument.setDocumentName(newDocumentName); while (activeCollection.containsDocument(newDocument)) { matchingFilenameDistinguisher++; newDocumentName = distinguisherReplacer.replace(newDocumentName.length() - 2, newDocumentName.length() - 1, new Integer(matchingFilenameDistinguisher).toString()).toString(); newDocument.setDocumentName(newDocumentName); } } Scanner tokenizer = null; FileChannel fileSource = null; FileChannel collectionDestination = null; HashMap<String, Integer> termHashMap = new HashMap<String, Integer>(); Index collectionIndex = activeCollection.getIndex(); int documentTermMaxFrequency = 0; int currentTermFrequency; try { tokenizer = new Scanner(new BufferedReader(new FileReader(selectedFile))); tokenizer.useDelimiter(Pattern.compile("\\p{Space}|\\p{Punct}|\\p{Cntrl}")); String nextToken; while (tokenizer.hasNext()) { nextToken = tokenizer.next().toLowerCase(); if (!nextToken.isEmpty()) if (termHashMap.containsKey(nextToken)) termHashMap.put(nextToken, termHashMap.get(nextToken) + 1); else termHashMap.put(nextToken, 1); } Term newTerm; for (String term : termHashMap.keySet()) { newTerm = new Term(term); if (!collectionIndex.termExists(newTerm)) collectionIndex.addTerm(newTerm); currentTermFrequency = termHashMap.get(term); if (currentTermFrequency > documentTermMaxFrequency) documentTermMaxFrequency = currentTermFrequency; collectionIndex.addOccurence(newTerm, newDocument, currentTermFrequency); } activeCollection.addDocument(newDocument); String userHome = System.getProperty("user.home"); String fileSeparator = System.getProperty("file.separator"); collectionCopyFile = new File(userHome + fileSeparator + "Infrared" + fileSeparator + activeCollection.getDocumentCollectionName() + fileSeparator + newDocumentName); collectionCopyFile.createNewFile(); fileSource = new FileInputStream(selectedFile).getChannel(); collectionDestination = new FileOutputStream(collectionCopyFile).getChannel(); collectionDestination.transferFrom(fileSource, 0, fileSource.size()); } catch (FileNotFoundException e) { System.err.println(e.getMessage() + " This error should never occur! The file was just selected!"); return; } catch (IOException e) { JOptionPane.showMessageDialog(this, "An I/O error occured during file transfer!", "File transfer I/O error", JOptionPane.WARNING_MESSAGE); return; } finally { try { if (tokenizer != null) tokenizer.close(); if (fileSource != null) fileSource.close(); if (collectionDestination != null) collectionDestination.close(); } catch (IOException e) { System.err.println(e.getMessage()); } } processWindowEvent(new WindowEvent(this, WindowEvent.WINDOW_CLOSING)); } else if (evt.getActionCommand().equalsIgnoreCase(JFileChooser.CANCEL_SELECTION)) processWindowEvent(new WindowEvent(this, WindowEvent.WINDOW_CLOSING)); } | private static String getDocumentAt(String urlString) { StringBuffer html_text = new StringBuffer(); try { URL url = new URL(urlString); URLConnection conn = url.openConnection(); BufferedReader reader = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line = null; while ((line = reader.readLine()) != null) html_text.append(line + "\n"); reader.close(); } catch (MalformedURLException e) { System.out.println("����URL: " + urlString); } catch (IOException e) { e.printStackTrace(); } return html_text.toString(); } | 884,905 |
1 | public static void copyFile(String sourceName, String destName) throws IOException { FileChannel sourceChannel = null; FileChannel destChannel = null; try { sourceChannel = new FileInputStream(sourceName).getChannel(); destChannel = new FileOutputStream(destName).getChannel(); destChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); } catch (IOException exception) { throw exception; } finally { if (sourceChannel != null) { try { sourceChannel.close(); } catch (IOException ex) { } } if (destChannel != null) { try { destChannel.close(); } catch (IOException ex) { } } } } | private 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!"); } | 884,906 |
1 | public static boolean start(RootDoc root) { Logger log = Logger.getLogger("DocletGenerator"); if (destination == null) { try { ruleListenerDef = IOUtils.toString(GeneratorOfXmlSchemaForConvertersDoclet.class.getResourceAsStream("/RuleListenersFragment.xsd"), "UTF-8"); String fn = System.getenv("annocultor.xconverter.destination.file.name"); fn = (fn == null) ? "./../../../src/site/resources/schema/XConverterInclude.xsd" : fn; destination = new File(fn); if (destination.exists()) { destination.delete(); } FileOutputStream os; os = new FileOutputStream(new File(destination.getParentFile(), "XConverter.xsd")); IOUtils.copy(new AutoCloseInputStream(GeneratorOfXmlSchemaForConvertersDoclet.class.getResourceAsStream("/XConverterTemplate.xsd")), os); os.close(); os = new FileOutputStream(destination); IOUtils.copy(new AutoCloseInputStream(GeneratorOfXmlSchemaForConvertersDoclet.class.getResourceAsStream("/XConverterInclude.xsd")), os); os.close(); } catch (Exception e) { try { throw new RuntimeException("On destination " + destination.getCanonicalPath(), e); } catch (IOException e1) { throw new RuntimeException(e1); } } } try { String s = Utils.loadFileToString(destination.getCanonicalPath(), "\n"); int breakPoint = s.indexOf(XSD_TEXT_TO_REPLACED_WITH_GENERATED_XML_SIGNATURES); if (breakPoint < 0) { throw new Exception("Signature not found in XSD: " + XSD_TEXT_TO_REPLACED_WITH_GENERATED_XML_SIGNATURES); } String preambula = s.substring(0, breakPoint); String appendix = s.substring(breakPoint); destination.delete(); PrintWriter schemaWriter = new PrintWriter(destination); schemaWriter.print(preambula); ClassDoc[] classes = root.classes(); for (int i = 0; i < classes.length; ++i) { ClassDoc cd = classes[i]; PrintWriter documentationWriter = null; if (getSuperClasses(cd).contains(Rule.class.getName())) { for (ConstructorDoc constructorDoc : cd.constructors()) { if (constructorDoc.isPublic()) { if (isMeantForXMLAccess(constructorDoc)) { if (documentationWriter == null) { File file = new File("./../../../src/site/xdoc/rules." + cd.name() + ".xml"); documentationWriter = new PrintWriter(file); log.info("Generating doc for rule " + file.getCanonicalPath()); printRuleDocStart(cd, documentationWriter); } boolean initFound = false; for (MethodDoc methodDoc : cd.methods()) { if ("init".equals(methodDoc.name())) { if (methodDoc.parameters().length == 0) { initFound = true; break; } } } if (!initFound) { } printConstructorSchema(constructorDoc, schemaWriter); if (documentationWriter != null) { printConstructorDoc(constructorDoc, documentationWriter); } } } } } if (documentationWriter != null) { printRuleDocEnd(documentationWriter); } } schemaWriter.print(appendix); schemaWriter.close(); log.info("Saved to " + destination.getCanonicalPath()); } catch (Exception e) { throw new RuntimeException(e); } return true; } | protected void copyDependents() { for (File source : dependentFiles.keySet()) { try { if (!dependentFiles.get(source).exists()) { if (dependentFiles.get(source).isDirectory()) dependentFiles.get(source).mkdirs(); else dependentFiles.get(source).getParentFile().mkdirs(); } IOUtils.copyEverything(source, dependentFiles.get(source)); } catch (IOException e) { e.printStackTrace(); } } } | 884,907 |
0 | public Configuration(URL url) { InputStream in = null; try { load(in = url.openStream()); } catch (Exception e) { throw new RuntimeException("Could not load configuration from " + url, e); } finally { if (in != null) { try { in.close(); } catch (IOException ignore) { } } } } | public static String digest(String algorithm, String text) { MessageDigest mDigest = null; try { mDigest = MessageDigest.getInstance(algorithm); mDigest.update(text.getBytes(ENCODING)); } catch (Exception e) { e.printStackTrace(); mDigest = null; } if (mDigest == null) return null; byte[] raw = mDigest.digest(); BASE64Encoder encoder = new BASE64Encoder(); return encoder.encode(raw); } | 884,908 |
0 | public static String md5(String input) throws NoSuchAlgorithmException, UnsupportedEncodingException { StringBuffer result = new StringBuffer(); MessageDigest md = MessageDigest.getInstance("MD5"); md.update(input.getBytes("utf-8")); byte[] digest = md.digest(); for (byte b : digest) { result.append(String.format("%02X ", b & 0xff)); } return result.toString(); } | @Override protected void copyContent(String filename) throws IOException { InputStream in = null; try { String resourceDir = System.getProperty("resourceDir"); File resource = new File(resourceDir, filename); ByteArrayOutputStream out = new ByteArrayOutputStream(); if (resource.exists()) { in = new FileInputStream(resource); } else { in = LOADER.getResourceAsStream(RES_PKG + filename); } IOUtils.copy(in, out); setResponseData(out.toByteArray()); } finally { if (in != null) { in.close(); } } } | 884,909 |
1 | public void copyContent(long mailId1, long mailId2) throws Exception { File file1 = new File(this.getMailDir(mailId1) + "/"); File file2 = new File(this.getMailDir(mailId2) + "/"); this.recursiveDir(file2); if (file1.isDirectory()) { File[] files = file1.listFiles(); if (files != null) { for (int i = 0; i < files.length; i++) { if (files[i].isFile()) { File file2s = new File(file2.getAbsolutePath() + "/" + files[i].getName()); if (!file2s.exists()) { file2s.createNewFile(); BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(file2s)); BufferedInputStream in = new BufferedInputStream(new FileInputStream(files[i])); int read; while ((read = in.read()) != -1) { out.write(read); } out.flush(); if (in != null) { try { in.close(); } catch (IOException ex1) { ex1.printStackTrace(); } } if (out != null) { try { out.close(); } catch (IOException ex) { ex.printStackTrace(); } } } } } } } } | public void unzip(String zipFileName, String outputDirectory) throws Exception { ZipInputStream in = new ZipInputStream(new FileInputStream(zipFileName)); ZipEntry z; while ((z = in.getNextEntry()) != null) { System.out.println("unziping " + z.getName()); if (z.isDirectory()) { String name = z.getName(); name = name.substring(0, name.length() - 1); File f = new File(outputDirectory + File.separator + name); f.mkdir(); System.out.println("mkdir " + outputDirectory + File.separator + name); } else { File f = new File(outputDirectory + File.separator + z.getName()); f.createNewFile(); FileOutputStream out = new FileOutputStream(f); int b; while ((b = in.read()) != -1) out.write(b); out.close(); } } in.close(); } | 884,910 |
1 | public static String stringToHash(String text) { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA-1"); md.update(text.getBytes("iso-8859-1"), 0, text.length()); } catch (NoSuchAlgorithmException e) { throw new IllegalStateException("Should not happened: SHA-1 algorithm is missing."); } catch (UnsupportedEncodingException e) { throw new IllegalStateException("Should not happened: Could not encode text bytes '" + text + "' to iso-8859-1."); } return new String(Base64.encodeBase64(md.digest())); } | public static String SHA1(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } | 884,911 |
1 | public static void main(String[] args) throws Exception { if (args.length != 2) { PrintUtil.prt("arguments: sourcefile, destfile"); System.exit(1); } FileChannel in = new FileInputStream(args[0]).getChannel(), out = new FileOutputStream(args[1]).getChannel(); in.transferTo(0, in.size(), out); } | private void buildBundle() { if (targetProject == null) { MessageDialog.openError(getShell(), "Error", "No target SPAB project selected!"); return; } if (projectProcessDirSelector.getText().trim().length() == 0) { MessageDialog.openError(getShell(), "Error", "No process directory selected for project " + targetProject.getName() + "!"); return; } deleteBundleFile(); try { File projectDir = targetProject.getLocation().toFile(); File projectProcessesDir = new File(projectDir, projectProcessDirSelector.getText()); boolean bpmoCopied = IOUtils.copyProcessFilesSecure(getBPMOFile(), projectProcessesDir); boolean sbpelCopied = IOUtils.copyProcessFilesSecure(getSBPELFile(), projectProcessesDir); boolean xmlCopied = IOUtils.copyProcessFilesSecure(getBPEL4SWSFile(), projectProcessesDir); bundleFile = IOUtils.archiveBundle(projectDir, Activator.getDefault().getStateLocation().toFile()); if (bpmoCopied) { new File(projectProcessesDir, getBPMOFile().getName()).delete(); } if (sbpelCopied) { new File(projectProcessesDir, getSBPELFile().getName()).delete(); } if (xmlCopied) { new File(projectProcessesDir, getBPEL4SWSFile().getName()).delete(); } } catch (Throwable anyError) { LogManager.logError(anyError); MessageDialog.openError(getShell(), "Error", "Error building SPAB :\n" + anyError.getMessage()); updateBundleUI(); return; } bpmoFile = getBPMOFile(); sbpelFile = getSBPELFile(); xmlFile = getBPEL4SWSFile(); updateBundleUI(); getWizard().getContainer().updateButtons(); } | 884,912 |
0 | public String installCode(String serviceName, String location) throws DeploymentException { FileOutputStream out = null; mLog.debug("overwriteWarFile = " + overwriteWarFile); String fileData = null; String filepath = location; String[] splitString = filepath.split("/"); String filename = splitString[splitString.length - 1]; int fileNameLength = filename.length(); warname = filename.substring(0, fileNameLength - 4); mLog.debug("WAR file name = " + warname); String filepath2 = warDesination + File.separator + filename; ret = "http://" + containerAddress + "/" + warname + "/services/" + serviceName; mLog.debug("filepath2 = " + filepath2); mLog.debug("ret = " + ret); mLog.debug("filepath = " + filepath); boolean warExists = new File(filepath2).exists(); boolean webAppExists = true; try { String webAppName = filepath2.substring(0, (filepath2.length() - 4)); mLog.debug("Web Application Name = " + webAppName); webAppExists = new File(webAppName).isDirectory(); if (!webAppExists) { URL url = new URL(filepath); File targetFile = new File(filepath2); if (!targetFile.exists()) { targetFile.createNewFile(); } InputStream in = null; try { in = url.openStream(); out = new FileOutputStream(targetFile); } catch (Exception e) { e.printStackTrace(); throw new DeploymentException("couldn't open stream due to: " + e.getMessage()); } URLConnection con = url.openConnection(); int fileLength = con.getContentLength(); ReadableByteChannel channelIn = Channels.newChannel(in); FileChannel channelOut = out.getChannel(); channelOut.transferFrom(channelIn, 0, fileLength); channelIn.close(); channelOut.close(); out.flush(); out.close(); in.close(); long time = System.currentTimeMillis(); check(ret, time, STARTCONTROL); } } catch (Exception e) { webAppExists = false; } mLog.debug("webAppExists = " + webAppExists); return (ret); } | public static String getSSHADigest(String password, String salt) { String digest = null; MessageDigest sha = null; try { sha = MessageDigest.getInstance("SHA-1"); sha.reset(); sha.update(password.getBytes()); sha.update(salt.getBytes()); byte[] pwhash = sha.digest(); digest = "{SSHA}" + new String(Base64.encode(concatenate(pwhash, salt.getBytes()))); } catch (NoSuchAlgorithmException nsae) { CofaxToolsUtil.log("Algorithme SHA-1 non supporte a la creation du hashage" + nsae + id); } return digest; } | 884,913 |
1 | public BufferedImage processUsingTemp(InputStream input, DjatokaDecodeParam params) throws DjatokaException { File in; try { in = File.createTempFile("tmp", ".jp2"); FileOutputStream fos = new FileOutputStream(in); in.deleteOnExit(); IOUtils.copyStream(input, fos); } catch (IOException e) { logger.error(e, e); throw new DjatokaException(e); } BufferedImage bi = process(in.getAbsolutePath(), params); if (in != null) in.delete(); return bi; } | public void copyFile(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | 884,914 |
0 | public String hash(String plainTextPassword) { try { MessageDigest digest = MessageDigest.getInstance(digestAlgorithm); digest.update(plainTextPassword.getBytes(charset)); byte[] rawHash = digest.digest(); return new String(org.jboss.seam.util.Hex.encodeHex(rawHash)); } catch (NoSuchAlgorithmException e) { log.error("Digest algorithm #0 to calculate the password hash will not be supported.", digestAlgorithm); throw new RuntimeException(e); } catch (UnsupportedEncodingException e) { log.error("The Character Encoding #0 is not supported", charset); throw new RuntimeException(e); } } | public static void copyFile(File src, File dest, int bufSize, boolean force) throws IOException { if (dest.exists()) { if (force) { dest.delete(); } else { throw new IOException("Cannot overwrite existing file: " + dest.getName()); } } byte[] buffer = new byte[bufSize]; int read = 0; InputStream in = null; OutputStream out = null; try { in = new FileInputStream(src); out = new FileOutputStream(dest); while (true) { read = in.read(buffer); if (read == -1) { break; } out.write(buffer, 0, read); } } finally { if (in != null) { try { in.close(); } finally { if (out != null) { out.close(); } } } } } | 884,915 |
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 static boolean copy(File from, File to) { if (from.isDirectory()) { for (String name : Arrays.asList(from.list())) { if (!copy(from, to, name)) { LogUtils.info("Failed to copy " + name + " from " + from + " to " + to, null); return false; } } } else { try { FileInputStream is = new FileInputStream(from); FileChannel ifc = is.getChannel(); FileOutputStream os = makeFile(to); if (USE_NIO) { FileChannel ofc = os.getChannel(); ofc.transferFrom(ifc, 0, from.length()); } else { pipe(is, os, false); } is.close(); os.close(); } catch (IOException ex) { LogUtils.warning("Failed to copy " + from + " to " + to, ex); return false; } } long time = from.lastModified(); setLastModified(to, time); long newtime = to.lastModified(); if (newtime != time) { LogUtils.info("Failed to set timestamp for file " + to + ": tried " + new Date(time) + ", have " + new Date(newtime), null); to.setLastModified(time); long morenewtime = to.lastModified(); return false; } return time == newtime; } | 884,916 |
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!"); } | private void openConnection() throws IOException { connection = (HttpURLConnection) url.openConnection(); connection.setDoInput(true); connection.setDoOutput(true); connection.setRequestMethod("POST"); connection.setRequestProperty("Content-Type", "text/xml"); } | 884,917 |
1 | public static void main(String[] args) { File container = new File(ArchiveFeature.class.getProtectionDomain().getCodeSource().getLocation().toURI()); if (container == null) { throw new RuntimeException("this use-case isn't being invoked from the executable jar"); } JarFile jarFile = new JarFile(container); String artifactName = PROJECT_DIST_ARCHIVE + ".tar.gz"; File artifactFile = new File(".", artifactName); ZipEntry artifactEntry = jarFile.getEntry(artifactName); InputStream source = jarFile.getInputStream(artifactEntry); try { FileOutputStream dest = new FileOutputStream(artifactFile); try { IOUtils.copy(source, dest); } finally { IOUtils.closeQuietly(dest); } } finally { IOUtils.closeQuietly(source); } Project project = new Project(); project.setName("project"); project.init(); Target target = new Target(); target.setName("target"); project.addTarget(target); project.addBuildListener(new Log4jListener()); Untar untar = new Untar(); untar.setTaskName("untar"); untar.setSrc(artifactFile); untar.setDest(new File(".")); Untar.UntarCompressionMethod method = new Untar.UntarCompressionMethod(); method.setValue("gzip"); untar.setCompression(method); untar.setProject(project); untar.setOwningTarget(target); target.addTask(untar); untar.execute(); } | public static void copyFile(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | 884,918 |
0 | static void copyFile(File file, File destDir) { File destFile = new File(destDir, file.getName()); if (destFile.exists() && (!destFile.canWrite())) { throw new SyncException("Cannot overwrite " + destFile + " because " + "it is read-only"); } try { FileInputStream in = new FileInputStream(file); try { FileOutputStream out = new FileOutputStream(destFile); try { byte[] buffer = new byte[BUFFER_SIZE]; int read; while ((read = in.read(buffer)) != -1) { out.write(buffer, 0, read); } } finally { out.close(); } } finally { in.close(); } } catch (IOException e) { throw new SyncException("I/O error copying " + file + " to " + destDir + " (message: " + e.getMessage() + ")", e); } if (!destFile.setLastModified(file.lastModified())) { throw new SyncException("Could not set last modified timestamp " + "of " + destFile); } } | public Psrxml getPsrxmlForCandidateList(CandidateList clist) throws BookKeeprCommunicationException { try { synchronized (httpClient) { long psrxmlid = clist.getPsrxmlId(); HttpGet req = new HttpGet(remoteHost.getUrl() + "/id/" + StringConvertable.ID.toString(psrxmlid)); HttpResponse resp = httpClient.execute(req); if (resp.getStatusLine().getStatusCode() == HttpStatus.SC_OK) { try { InputStream in = resp.getEntity().getContent(); XMLAble xmlable = XMLReader.read(in); in.close(); if (xmlable instanceof Psrxml) { Psrxml psrxml = (Psrxml) xmlable; return psrxml; } else { throw new BookKeeprCommunicationException("BookKeepr returned the wrong thing for psrxml id " + psrxmlid); } } catch (SAXException ex) { Logger.getLogger(BookKeeprConnection.class.getName()).log(Level.WARNING, "Got a malformed message from the bookkeepr", ex); throw new BookKeeprCommunicationException(ex); } } else { resp.getEntity().consumeContent(); throw new BookKeeprCommunicationException("Got a " + resp.getStatusLine().getStatusCode() + " from the BookKeepr (" + remoteHost.getUrl() + "/id/" + StringConvertable.ID + ")"); } } } catch (HttpException ex) { throw new BookKeeprCommunicationException(ex); } catch (IOException ex) { throw new BookKeeprCommunicationException(ex); } catch (URISyntaxException ex) { throw new BookKeeprCommunicationException(ex); } } | 884,919 |
0 | private File uploadFile(InputStream inputStream, File file) { FileOutputStream fileOutputStream = null; try { File dir = file.getParentFile(); if (!dir.exists()) { dir.mkdirs(); } FileUtils.touch(file); fileOutputStream = new FileOutputStream(file); IOUtils.copy(inputStream, fileOutputStream); } catch (IOException e) { throw new FileOperationException("Failed to save uploaded image", e); } finally { try { if (fileOutputStream != null) { fileOutputStream.close(); } } catch (IOException e) { LOGGER.warn("Failed to close resources on uploaded file", e); } } return file; } | public boolean saveVideoXMLOnWebserver() { String text = ""; boolean erg = false; try { URL url = new URL("http://localhost:8080/virtPresenterVerwalter/videofile.jsp?id=" + this.getId()); HttpURLConnection http = (HttpURLConnection) url.openConnection(); BufferedReader in = new BufferedReader(new InputStreamReader(http.getInputStream())); String zeile = ""; while ((zeile = in.readLine()) != null) { text += zeile + "\n"; } in.close(); http.disconnect(); erg = saveVideoXMLOnWebserver(text); System.err.println("Job " + this.getId() + " erfolgreich bearbeitet!"); } catch (MalformedURLException e) { System.err.println("Job " + this.getId() + ": Konnte video.xml nicht erstellen. Verbindung konnte nicht aufgebaut werden."); return false; } catch (IOException e) { System.err.println("Job " + this.getId() + ": Konnte video.xml nicht erstellen. Konnte Daten nicht lesen/schreiben."); return false; } return erg; } | 884,920 |
1 | 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(); } } | public static void main(String[] args) throws IOException, WrongFormatException, URISyntaxException { System.out.println(new URI("google.com.ua.css").toString()); Scanner scc = new Scanner(System.in); System.err.print(scc.nextLine().substring(1)); ServerSocket s = new ServerSocket(5354); while (true) { Socket client = s.accept(); InputStream iStream = client.getInputStream(); BufferedReader bf = new BufferedReader(new InputStreamReader(iStream)); String line = ""; while (!(line = bf.readLine()).equals("")) { System.out.println(line); } System.out.println("end of request"); new PrintWriter(client.getOutputStream()).println("hi"); bf.close(); } } | 884,921 |
0 | public String encodePassword(String password, byte[] salt) throws Exception { if (salt == null) { salt = new byte[12]; secureRandom.nextBytes(salt); } MessageDigest md = MessageDigest.getInstance("MD5"); md.update(salt); md.update(password.getBytes("UTF8")); byte[] digest = md.digest(); byte[] storedPassword = new byte[digest.length + 12]; System.arraycopy(salt, 0, storedPassword, 0, 12); System.arraycopy(digest, 0, storedPassword, 12, digest.length); return new String(Base64.encode(storedPassword)); } | public static void main(String[] args) throws Exception { String urlString = "http://php.tech.sina.com.cn/download/d_load.php?d_id=7877&down_id=151542"; urlString = EncodeUtils.encodeURL(urlString); URL url = new URL(urlString); System.out.println("第一次：" + url); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); HttpURLConnection.setFollowRedirects(true); Map req = conn.getRequestProperties(); System.out.println("第一次请求头："); printMap(req); conn.connect(); System.out.println("第一次响应："); System.out.println(conn.getResponseMessage()); int code = conn.getResponseCode(); System.out.println("第一次code:" + code); printMap(conn.getHeaderFields()); System.out.println(conn.getURL().getFile()); if (code == 404 && !(conn.getURL() + "").equals(urlString)) { System.out.println(conn.getURL()); String tmp = URLEncoder.encode(conn.getURL().toString(), "gbk"); System.out.println(URLEncoder.encode("在线音乐播放脚本", "GBK")); System.out.println(tmp); url = new URL(tmp); System.out.println("第二次：" + url); conn = (HttpURLConnection) url.openConnection(); System.out.println("第二次响应："); System.out.println("code:" + code); printMap(conn.getHeaderFields()); } } | 884,922 |
1 | private void documentFileChooserActionPerformed(java.awt.event.ActionEvent evt) { if (evt.getActionCommand().equals(JFileChooser.APPROVE_SELECTION)) { File selectedFile = documentFileChooser.getSelectedFile(); File collectionCopyFile; String newDocumentName = selectedFile.getName(); Document newDocument = new Document(newDocumentName); if (activeCollection.containsDocument(newDocument)) { int matchingFilenameDistinguisher = 1; StringBuilder distinguisherReplacer = new StringBuilder(); newDocumentName = newDocumentName.concat("(" + matchingFilenameDistinguisher + ")"); newDocument.setDocumentName(newDocumentName); while (activeCollection.containsDocument(newDocument)) { matchingFilenameDistinguisher++; newDocumentName = distinguisherReplacer.replace(newDocumentName.length() - 2, newDocumentName.length() - 1, new Integer(matchingFilenameDistinguisher).toString()).toString(); newDocument.setDocumentName(newDocumentName); } } Scanner tokenizer = null; FileChannel fileSource = null; FileChannel collectionDestination = null; HashMap<String, Integer> termHashMap = new HashMap<String, Integer>(); Index collectionIndex = activeCollection.getIndex(); int documentTermMaxFrequency = 0; int currentTermFrequency; try { tokenizer = new Scanner(new BufferedReader(new FileReader(selectedFile))); tokenizer.useDelimiter(Pattern.compile("\\p{Space}|\\p{Punct}|\\p{Cntrl}")); String nextToken; while (tokenizer.hasNext()) { nextToken = tokenizer.next().toLowerCase(); if (!nextToken.isEmpty()) if (termHashMap.containsKey(nextToken)) termHashMap.put(nextToken, termHashMap.get(nextToken) + 1); else termHashMap.put(nextToken, 1); } Term newTerm; for (String term : termHashMap.keySet()) { newTerm = new Term(term); if (!collectionIndex.termExists(newTerm)) collectionIndex.addTerm(newTerm); currentTermFrequency = termHashMap.get(term); if (currentTermFrequency > documentTermMaxFrequency) documentTermMaxFrequency = currentTermFrequency; collectionIndex.addOccurence(newTerm, newDocument, currentTermFrequency); } activeCollection.addDocument(newDocument); String userHome = System.getProperty("user.home"); String fileSeparator = System.getProperty("file.separator"); collectionCopyFile = new File(userHome + fileSeparator + "Infrared" + fileSeparator + activeCollection.getDocumentCollectionName() + fileSeparator + newDocumentName); collectionCopyFile.createNewFile(); fileSource = new FileInputStream(selectedFile).getChannel(); collectionDestination = new FileOutputStream(collectionCopyFile).getChannel(); collectionDestination.transferFrom(fileSource, 0, fileSource.size()); } catch (FileNotFoundException e) { System.err.println(e.getMessage() + " This error should never occur! The file was just selected!"); return; } catch (IOException e) { JOptionPane.showMessageDialog(this, "An I/O error occured during file transfer!", "File transfer I/O error", JOptionPane.WARNING_MESSAGE); return; } finally { try { if (tokenizer != null) tokenizer.close(); if (fileSource != null) fileSource.close(); if (collectionDestination != null) collectionDestination.close(); } catch (IOException e) { System.err.println(e.getMessage()); } } processWindowEvent(new WindowEvent(this, WindowEvent.WINDOW_CLOSING)); } else if (evt.getActionCommand().equalsIgnoreCase(JFileChooser.CANCEL_SELECTION)) processWindowEvent(new WindowEvent(this, WindowEvent.WINDOW_CLOSING)); } | private void serveCGI(TinyCGI script) throws IOException, TinyWebThreadException { parseHTTPHeaders(); OutputStream cgiOut = null; File tempFile = null; try { if (script == null) sendError(500, "Internal Error", "Couldn't load script."); if (script instanceof TinyCGIHighVolume) { tempFile = File.createTempFile("cgi", null); cgiOut = new FileOutputStream(tempFile); } else { cgiOut = new ByteArrayOutputStream(); } script.service(inputStream, cgiOut, env); } catch (Exception cgie) { this.exceptionEncountered = cgie; if (tempFile != null) tempFile.delete(); if (clientSocket == null) { return; } else if (cgie instanceof TinyCGIException) { TinyCGIException tce = (TinyCGIException) cgie; sendError(tce.getStatus(), tce.getTitle(), tce.getText(), tce.getOtherHeaders()); } else { StringWriter w = new StringWriter(); cgie.printStackTrace(new PrintWriter(w)); sendError(500, "CGI Error", "Error running script: " + "<PRE>" + w.toString() + "</PRE>"); } } finally { if (script != null) doneWithScript(script); } InputStream cgiResults = null; long totalSize = 0; if (tempFile == null) { byte[] results = ((ByteArrayOutputStream) cgiOut).toByteArray(); totalSize = results.length; cgiResults = new ByteArrayInputStream(results); } else { cgiOut.close(); totalSize = tempFile.length(); cgiResults = new FileInputStream(tempFile); } String contentType = null, statusString = "OK", line, header; StringBuffer otherHeaders = new StringBuffer(); StringBuffer text = new StringBuffer(); int status = 200; int headerLength = 0; while (true) { line = readLine(cgiResults, true); headerLength += line.length(); if (line.charAt(0) == '\r' || line.charAt(0) == '\n') break; header = parseHeader(line, text); if (header.toUpperCase().equals("STATUS")) { statusString = text.toString(); status = Integer.parseInt(statusString.substring(0, 3)); statusString = statusString.substring(4); } else if (header.toUpperCase().equals("CONTENT-TYPE")) contentType = text.toString(); else { if (header.toUpperCase().equals("LOCATION")) status = 302; otherHeaders.append(header).append(": ").append(text.toString()).append(CRLF); } } sendHeaders(status, statusString, contentType, totalSize - headerLength, -1, otherHeaders.toString()); byte[] buf = new byte[2048]; int bytesRead; while ((bytesRead = cgiResults.read(buf)) != -1) outputStream.write(buf, 0, bytesRead); outputStream.flush(); try { cgiResults.close(); if (tempFile != null) tempFile.delete(); } catch (IOException ioe) { } } | 884,923 |
0 | public String calcMD5(String sequence) { MessageDigest md5 = null; try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } md5.update(sequence.toString().toUpperCase().getBytes()); BigInteger md5hash = new BigInteger(1, md5.digest()); String sequence_md5 = md5hash.toString(16); while (sequence_md5.length() < 32) { sequence_md5 = "0" + sequence_md5; } return sequence_md5; } | public static void copy(FileInputStream in, File destination) throws IOException { FileChannel srcChannel = null; FileChannel dstChannel = null; try { srcChannel = in.getChannel(); dstChannel = new FileOutputStream(destination).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); } finally { if (srcChannel != null) { srcChannel.close(); } if (dstChannel != null) { dstChannel.close(); } } } | 884,924 |
1 | public static String hashValue(String password, String salt) throws TeqloException { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA"); md.update(password.getBytes("UTF-8")); md.update(salt.getBytes("UTF-8")); byte raw[] = md.digest(); char[] encoded = (new BASE64Encoder()).encode(raw).toCharArray(); int length = encoded.length; while (length > 0 && encoded[length - 1] == '=') length--; for (int i = 0; i < length; i++) { if (encoded[i] == '+') encoded[i] = '*'; else if (encoded[i] == '/') encoded[i] = '-'; } return new String(encoded, 0, length); } catch (Exception e) { throw new TeqloException("Security", "password", e, "Could not process password"); } } | 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(); } | 884,925 |
1 | public static void copyFile(File source, File destination) throws IOException { if (!source.isFile()) { throw new IOException(source + " is not a file."); } if (destination.exists()) { throw new IOException("Destination file " + destination + " is already exist."); } FileChannel inChannel = new FileInputStream(source).getChannel(); FileChannel outChannel = new FileOutputStream(destination).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } finally { inChannel.close(); outChannel.close(); } } | 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; } | 884,926 |
0 | public static Document getXHTMLDocument(URL _url) throws IOException { final Tidy tidy = new Tidy(); tidy.setQuiet(true); tidy.setShowWarnings(false); tidy.setXmlOut(true); final BufferedInputStream input_stream = new BufferedInputStream(_url.openStream()); return tidy.parseDOM(input_stream, null); } | static void xmlRpcCall(String method, String[] params) throws LastFMError { try { XmlPullParserFactory fac = XmlPullParserFactory.newInstance(); XmlSerializer serializer = fac.newSerializer(); URL url; url = new URL(XMLRPC_URL); URLConnection conn; conn = url.openConnection(); conn.setRequestProperty("Content-Type", "text/xml"); conn.setDoOutput(true); serializer.setOutput(conn.getOutputStream(), "UTF-8"); serializer.startDocument("UTF-8", true); serializer.startTag(null, "methodCall"); serializer.startTag(null, "methodName"); serializer.text(method); serializer.endTag(null, "methodName"); serializer.startTag(null, "params"); for (String s : params) { serializer.startTag(null, "param"); serializer.startTag(null, "value"); serializer.startTag(null, "string"); serializer.text(s); serializer.endTag(null, "string"); serializer.endTag(null, "value"); serializer.endTag(null, "param"); } serializer.endTag(null, "params"); serializer.endTag(null, "methodCall"); serializer.flush(); InputStream is = conn.getInputStream(); DocumentBuilderFactory dbFac = DocumentBuilderFactory.newInstance(); DocumentBuilder db = dbFac.newDocumentBuilder(); Document doc = db.parse(is); try { String res = Utils.getChildElement(doc.getDocumentElement(), new String[] { "params", "param", "value", "string" }); if (!res.equals("OK")) { Log.e(TAG, "while xmlrpc got " + res); throw new LastFMXmlRpcError("XMLRPC Call failed: " + res); } } catch (ParseException e) { String faultString = Utils.getChildElement(doc.getDocumentElement(), new String[] { "params", "param", "value", "struct", "member[1]", "value", "string" }); throw new LastFMXmlRpcError(faultString); } } catch (LastFMXmlRpcError e) { throw e; } catch (Exception e) { Log.e(TAG, "while xmlrpc", e); throw new LastFMError(e.toString()); } } | 884,927 |
0 | private static String doGetForSessionKey(String authCode) throws Exception { String sessionKey = ""; HttpClient hc = new DefaultHttpClient(); HttpGet hg = new HttpGet(Common.TEST_SESSION_HOST + Common.TEST_SESSION_PARAM + authCode); HttpResponse hr = hc.execute(hg); BufferedReader br = new BufferedReader(new InputStreamReader(hr.getEntity().getContent())); StringBuilder sb = new StringBuilder(); String line; while ((line = br.readLine()) != null) { sb.append(line); } String result = sb.toString(); Log.i("sessionKeyMessages", result); Map<String, String> map = Util.handleURLParameters(result); sessionKey = map.get(Common.TOP_SESSION); String topParameters = map.get(Common.TOP_PARAMETERS); String decTopParameters = Util.decodeBase64(topParameters); Log.i("base64", decTopParameters); map = Util.handleURLParameters(decTopParameters); Log.i("nick", map.get(Common.VISITOR_NICK)); CachePool.put(Common.VISITOR_NICK, map.get(Common.VISITOR_NICK)); return sessionKey; } | public int[] sort() { int i, tmp; int[] newIndex = new int[nrows]; for (i = 0; i < nrows; i++) { newIndex[i] = i; } boolean change = true; if (this.ascending) { if (data[0][column] instanceof Comparable) { while (change) { change = false; for (i = 0; i < nrows - 1; i++) { if (((Comparable) data[newIndex[i]][column]).compareTo((Comparable) data[newIndex[i + 1]][column]) > 0) { tmp = newIndex[i]; newIndex[i] = newIndex[i + 1]; newIndex[i + 1] = tmp; change = true; } } } return newIndex; } if (data[0][column] instanceof String || data[0][column] instanceof ClassLabel) { while (change) { change = false; for (i = 0; i < nrows - 1; i++) { if ((data[newIndex[i]][column].toString()).compareTo(data[newIndex[i + 1]][column].toString()) > 0) { tmp = newIndex[i]; newIndex[i] = newIndex[i + 1]; newIndex[i + 1] = tmp; change = true; } } } } return newIndex; } if (!this.ascending) { if (data[0][column] instanceof Comparable) { while (change) { change = false; for (i = 0; i < nrows - 1; i++) { if (((Comparable) data[newIndex[i]][column]).compareTo((Comparable) data[newIndex[i + 1]][column]) < 0) { tmp = newIndex[i]; newIndex[i] = newIndex[i + 1]; newIndex[i + 1] = tmp; change = true; } } } return newIndex; } if (data[0][column] instanceof String || data[0][column] instanceof ClassLabel) { while (change) { change = false; for (i = 0; i < nrows - 1; i++) { if ((data[newIndex[i]][column].toString()).compareTo(data[newIndex[i + 1]][column].toString()) < 0) { tmp = newIndex[i]; newIndex[i] = newIndex[i + 1]; newIndex[i + 1] = tmp; change = true; } } } } return newIndex; } else return newIndex; } | 884,928 |
1 | public void testStorageStringWriter() throws Exception { TranslationResponseInMemory r = new TranslationResponseInMemory(2048, "UTF-8"); { Writer w = r.getWriter(); w.write("This is an example"); w.write(" and another one."); w.flush(); assertEquals("This is an example and another one.", r.getText()); } { InputStream input = r.getInputStream(); StringWriter writer = new StringWriter(); try { IOUtils.copy(input, writer, "UTF-8"); } finally { input.close(); writer.close(); } assertEquals("This is an example and another one.", writer.toString()); } try { r.getOutputStream(); fail("Is not allowed as you already called getWriter()."); } catch (IOException e) { } { Writer output = r.getWriter(); output.write(" and another line"); output.write(" and write some more"); assertEquals("This is an example and another one. and another line and write some more", r.getText()); } { r.addText(" and some more."); assertEquals("This is an example and another one. and another line and write some more and some more.", r.getText()); } r.setEndState(ResponseStateOk.getInstance()); assertEquals(ResponseStateOk.getInstance(), r.getEndState()); try { r.getWriter(); fail("Previous line should throw IOException as result closed."); } catch (IOException e) { } } | public void doImport(File f, boolean checkHosp) throws Exception { connector.getConnection().setAutoCommit(false); File base = f.getParentFile(); ZipInputStream in = new ZipInputStream(new FileInputStream(f)); ZipEntry entry; while ((entry = in.getNextEntry()) != null) { String outFileName = entry.getName(); File outFile = new File(base, outFileName); OutputStream out = new FileOutputStream(outFile, false); byte[] buf = new byte[1024]; int len; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); out.close(); } in.close(); importDirectory(base, checkHosp); connector.getConnection().commit(); } | 884,929 |
1 | public BufferedWriter createOutputStream(String inFile, String outFile) throws IOException { int k_blockSize = 1024; int byteCount; char[] buf = new char[k_blockSize]; File ofp = new File(outFile); ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(ofp)); zos.setMethod(ZipOutputStream.DEFLATED); OutputStreamWriter osw = new OutputStreamWriter(zos, "ISO-8859-1"); BufferedWriter bw = new BufferedWriter(osw); ZipEntry zot = null; File ifp = new File(inFile); ZipInputStream zis = new ZipInputStream(new FileInputStream(ifp)); InputStreamReader isr = new InputStreamReader(zis, "ISO-8859-1"); BufferedReader br = new BufferedReader(isr); ZipEntry zit = null; while ((zit = zis.getNextEntry()) != null) { if (zit.getName().equals("content.xml")) { continue; } zot = new ZipEntry(zit.getName()); zos.putNextEntry(zot); while ((byteCount = br.read(buf, 0, k_blockSize)) >= 0) bw.write(buf, 0, byteCount); bw.flush(); zos.closeEntry(); } zos.putNextEntry(new ZipEntry("content.xml")); bw.flush(); osw = new OutputStreamWriter(zos, "UTF8"); bw = new BufferedWriter(osw); return bw; } | 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!"); } | 884,930 |
0 | @Override public void configure() { initResouce(); if (this.locale == null) { this.locale = Locale.getDefault(); } InputStream[] ins = new InputStream[getResourceList().size()]; try { int i = 0; for (URL url : getResourceList()) { ins[i++] = url.openStream(); } this.resources = new ValidatorResources(ins); } catch (IOException e) { e.printStackTrace(); throw new RuntimeException(e); } catch (SAXException e) { e.printStackTrace(); throw new RuntimeException(e); } } | public String getResourceAsString(String name) throws IOException { String content = null; InputStream stream = aClass.getResourceAsStream(name); if (stream != null) { ByteArrayOutputStream buffer = new ByteArrayOutputStream(); IOUtils.copyAndClose(stream, buffer); content = buffer.toString(); } else { Assert.fail("Resource not available: " + name); } return content; } | 884,931 |
0 | 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); } } | private int getRootNodeId(DataSource dataSource) throws SQLException { Connection conn = null; Statement st = null; ResultSet rs = null; String query = null; try { conn = dataSource.getConnection(); st = conn.createStatement(); query = "select " + col.id + " from " + DB.Tbl.tree + " where " + col.parentId + " is null"; rs = st.executeQuery(query); while (rs.next()) { return rs.getInt(col.id); } query = "insert into " + DB.Tbl.tree + "(" + col.lKey + ", " + col.rKey + ", " + col.level + ") values(1,2,0)"; st.executeUpdate(query, new String[] { col.id }); rs = st.getGeneratedKeys(); while (rs.next()) { int genId = rs.getInt(1); rs.close(); conn.commit(); return genId; } throw new SQLException("Не удается создать корневой элемент для дерева."); } finally { try { rs.close(); } catch (Exception e) { } try { st.close(); } catch (Exception e) { } try { conn.rollback(); } catch (Exception e) { } try { conn.close(); } catch (Exception e) { } } } | 884,932 |
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 void _resetLanguages(ActionRequest req, ActionResponse res, PortletConfig config, ActionForm form) throws Exception { List list = (List) req.getAttribute(WebKeys.LANGUAGE_MANAGER_LIST); for (int i = 0; i < list.size(); i++) { long langId = ((Language) list.get(i)).getId(); try { String filePath = getGlobalVariablesPath() + "cms_language_" + langId + ".properties"; File from = new java.io.File(filePath); from.createNewFile(); String tmpFilePath = getTemporyDirPath() + "cms_language_" + langId + "_properties.tmp"; File to = new java.io.File(tmpFilePath); to.createNewFile(); FileChannel srcChannel = new FileInputStream(from).getChannel(); FileChannel dstChannel = new FileOutputStream(to).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException e) { Logger.debug(this, "Property File copy Failed " + e, e); } } } | 884,933 |
0 | public static FTPClient getClient(String serverAddress, String login, String password, boolean PASV) throws SocketException, IOException { FTPClient client = new FTPClient(); client.connect(serverAddress); if (PASV) { client.enterLocalPassiveMode(); } client.login(login, password); return client; } | public static boolean copyFile(String fromfile, String tofile) { File from = new File(fromfile); File to = new File(tofile); if (!from.exists()) return false; if (to.exists()) { log.error(tofile + "exists already"); return false; } BufferedInputStream in = null; BufferedOutputStream out = null; FileInputStream fis = null; FileOutputStream ois = null; boolean flag = true; try { to.createNewFile(); fis = new FileInputStream(from); ois = new FileOutputStream(to); in = new BufferedInputStream(fis); out = new BufferedOutputStream(ois); byte[] buf = new byte[2048]; int readBytes = 0; while ((readBytes = in.read(buf, 0, buf.length)) != -1) { out.write(buf, 0, readBytes); } } catch (IOException e) { log.error(e); flag = false; } finally { try { if (in != null) in.close(); if (out != null) out.close(); } catch (IOException e) { log.error(e); flag = false; } } return flag; } | 884,934 |
0 | public void greatestIncrease(int maxIterations) { double[] increase = new double[numModels]; int[] id = new int[numModels]; Model md = new Model(); double oldPerf = 1; for (int i = 0; i < numModels; i++) { md.addModel(models[i], false); increase[i] = oldPerf - md.getLoss(); id[i] = i; oldPerf = md.getLoss(); } for (int i = 0; i < numModels; i++) { for (int j = 0; j < numModels - 1 - i; j++) { if (increase[j] < increase[j + 1]) { double increasetemp = increase[j]; int temp = id[j]; increase[j] = increase[j + 1]; id[j] = id[j + 1]; increase[j + 1] = increasetemp; id[j + 1] = temp; } } } for (int i = 0; i < maxIterations; i++) { addToEnsemble(models[id[i]]); if (report) ensemble.report(models[id[i]].getName(), allSets); updateBestModel(); } } | public void getDataFiles(String server, String username, String password, String folder, String destinationFolder) { try { FTPClient ftp = new FTPClient(); ftp.connect(server); ftp.login(username, password); System.out.println("Connected to " + server + "."); System.out.print(ftp.getReplyString()); ftp.enterLocalActiveMode(); ftp.changeWorkingDirectory(folder); System.out.println("Changed to " + folder); FTPFile[] files = ftp.listFiles(); System.out.println("Number of files in dir: " + files.length); for (int i = 0; i < files.length; i++) { getFiles(ftp, files[i], destinationFolder); } ftp.logout(); ftp.disconnect(); } catch (Exception e) { e.printStackTrace(); } } | 884,935 |
1 | private boolean copyFile(File file) throws Exception { destination = new File(ServiceLocator.getSqliteDir(), file.getName()); logger.debug("Writing to: " + destination); if (destination.exists()) { Frame.showMessage(ServiceLocator.getText("Error.file.exists") + file.getName(), null); logger.debug("File already exists: " + file); return false; } destination.createNewFile(); InputStream in = null; OutputStream out = null; try { in = new FileInputStream(file); out = new FileOutputStream(destination); int read = 0; byte[] buffer = new byte[2048]; while ((read = in.read(buffer)) > 0) { out.write(buffer, 0, read); } } finally { if (in != null) in.close(); if (out != null) out.close(); } return true; } | public void doInsertImage() { logger.debug(">>> Inserting image..."); logger.debug(" fullFileName : #0", uploadedFileName); String fileName = uploadedFileName.substring(uploadedFileName.lastIndexOf(File.separator) + 1); logger.debug(" fileName : #0", fileName); String newFileName = System.currentTimeMillis() + "_" + fileName; String filePath = ImageResource.getResourceDirectory() + File.separator + newFileName; logger.debug(" filePath : #0", filePath); try { File file = new File(filePath); file.createNewFile(); FileChannel srcChannel = null; FileChannel dstChannel = null; try { srcChannel = new FileInputStream(uploadedFile).getChannel(); dstChannel = new FileOutputStream(file).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); } finally { closeChannel(srcChannel); closeChannel(dstChannel); } StringBuilder imageTag = new StringBuilder(); imageTag.append("<img src=\""); imageTag.append(getRequest().getContextPath()); imageTag.append("/seam/resource"); imageTag.append(ImageResource.RESOURCE_PATH); imageTag.append("/"); imageTag.append(newFileName); imageTag.append("\"/>"); if (getQuestionDefinition().getDescription() == null) { getQuestionDefinition().setDescription(""); } getQuestionDefinition().setDescription(getQuestionDefinition().getDescription() + imageTag); } catch (IOException e) { logger.error("Error during saving image file", e); } uploadedFile = null; uploadedFileName = null; logger.debug("<<< Inserting image...Ok"); } | 884,936 |
1 | public static void copy(File source, File sink) throws IOException { if (source == null) throw new NullPointerException("Source file must not be null"); if (sink == null) throw new NullPointerException("Target file must not be null"); if (!source.exists()) throw new IOException("Source file " + source.getPath() + " does not exist"); if (!source.isFile()) throw new IOException("Source file " + source.getPath() + " is not a regular file"); if (!source.canRead()) throw new IOException("Source file " + source.getPath() + " can not be read (missing acces right)"); if (!sink.exists()) throw new IOException("Target file " + sink.getPath() + " does not exist"); if (!sink.isFile()) throw new IOException("Target file " + sink.getPath() + " is not a regular file"); if (!sink.canWrite()) throw new IOException("Target file " + sink.getPath() + " is write protected"); InputStream input = null; OutputStream output = null; try { input = new FileInputStream(source); output = new FileOutputStream(sink); byte[] buffer = new byte[1024]; while (input.available() > 0) { int bread = input.read(buffer); if (bread > 0) output.write(buffer, 0, bread); } } finally { if (input != null) try { input.close(); } catch (IOException x) { } if (output != null) try { output.close(); } catch (IOException x) { } } } | public static File createTempFile(InputStream contentStream, String ext) throws IOException { ExceptionUtils.throwIfNull(contentStream, "contentStream"); File file = File.createTempFile("test", ext); FileOutputStream fos = new FileOutputStream(file); try { IOUtils.copy(contentStream, fos, false); } finally { fos.close(); } return file; } | 884,937 |
0 | @Test public void test_lookupType_TooShortName() throws Exception { URL url = new URL(baseUrl + "/lookupType/A"); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.setRequestProperty("Accept", "application/json"); assertThat(connection.getResponseCode(), equalTo(400)); connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.setRequestProperty("Accept", "application/xml"); assertThat(connection.getResponseCode(), equalTo(400)); } | private BoardPattern[] getBoardPatterns() { Resource[] resources = boardManager.getResources("boards"); BoardPattern[] boardPatterns = new BoardPattern[resources.length]; for (int i = 0; i < resources.length; i++) boardPatterns[i] = (BoardPattern) resources[i]; for (int i = 0; i < resources.length; i++) { for (int j = 0; j < resources.length - (i + 1); j++) { String name1 = boardPatterns[j].getName(); String name2 = boardPatterns[j + 1].getName(); if (name1.compareTo(name2) > 0) { BoardPattern tmp = boardPatterns[j]; boardPatterns[j] = boardPatterns[j + 1]; boardPatterns[j + 1] = tmp; } } } return boardPatterns; } | 884,938 |
1 | public static void unzip(File sourceZipFile, File unzipDestinationDirectory, FileFilter filter) throws IOException { unzipDestinationDirectory.mkdirs(); if (!unzipDestinationDirectory.exists()) { throw new IOException("Unable to create destination directory: " + unzipDestinationDirectory); } ZipFile zipFile; zipFile = new ZipFile(sourceZipFile, ZipFile.OPEN_READ); Enumeration<? extends ZipEntry> zipFileEntries = zipFile.entries(); while (zipFileEntries.hasMoreElements()) { ZipEntry entry = (ZipEntry) zipFileEntries.nextElement(); if (!entry.isDirectory()) { String currentEntry = entry.getName(); File destFile = new File(unzipDestinationDirectory, currentEntry); if (filter == null || filter.accept(destFile)) { File destinationParent = destFile.getParentFile(); destinationParent.mkdirs(); BufferedInputStream is = new BufferedInputStream(zipFile.getInputStream(entry)); FileOutputStream fos = new FileOutputStream(destFile); IOUtils.copyLarge(is, fos); fos.flush(); IOUtils.closeQuietly(fos); } } } zipFile.close(); } | @Override protected int run(CmdLineParser parser) { final List<String> args = parser.getRemainingArgs(); if (args.isEmpty()) { System.err.println("summarysort :: WORKDIR not given."); return 3; } if (args.size() == 1) { System.err.println("summarysort :: INPATH not given."); return 3; } final String outS = (String) parser.getOptionValue(outputDirOpt); final Path wrkDir = new Path(args.get(0)), in = new Path(args.get(1)), out = outS == null ? null : new Path(outS); final boolean verbose = parser.getBoolean(verboseOpt); final Configuration conf = getConf(); final Timer t = new Timer(); try { @SuppressWarnings("deprecation") final int maxReduceTasks = new JobClient(new JobConf(conf)).getClusterStatus().getMaxReduceTasks(); conf.setInt("mapred.reduce.tasks", Math.max(1, maxReduceTasks * 9 / 10)); final Job job = sortOne(conf, in, wrkDir, "summarysort", ""); System.out.printf("summarysort :: Waiting for job completion...\n"); t.start(); if (!job.waitForCompletion(verbose)) { System.err.println("summarysort :: Job failed."); return 4; } System.out.printf("summarysort :: Job complete in %d.%03d s.\n", t.stopS(), t.fms()); } catch (IOException e) { System.err.printf("summarysort :: Hadoop error: %s\n", e); return 4; } catch (ClassNotFoundException e) { throw new RuntimeException(e); } catch (InterruptedException e) { throw new RuntimeException(e); } if (out != null) try { System.out.println("summarysort :: Merging output..."); t.start(); final FileSystem srcFS = wrkDir.getFileSystem(conf); final FileSystem dstFS = out.getFileSystem(conf); final OutputStream outs = dstFS.create(out); final FileStatus[] parts = srcFS.globStatus(new Path(wrkDir, in.getName() + "-[0-9][0-9][0-9][0-9][0-9][0-9]*")); { int i = 0; final Timer t2 = new Timer(); for (final FileStatus part : parts) { t2.start(); final InputStream ins = srcFS.open(part.getPath()); IOUtils.copyBytes(ins, outs, conf, false); ins.close(); System.out.printf("summarysort :: Merged part %d in %d.%03d s.\n", ++i, t2.stopS(), t2.fms()); } } for (final FileStatus part : parts) srcFS.delete(part.getPath(), false); outs.write(BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK); outs.close(); System.out.printf("summarysort :: Merging complete in %d.%03d s.\n", t.stopS(), t.fms()); } catch (IOException e) { System.err.printf("summarysort :: Output merging failed: %s\n", e); return 5; } return 0; } | 884,939 |
0 | private static MapEntry<String, Properties> loadFpmConf() throws ConfigurationReadException { MapEntry<String, Properties> ret = null; Scanner sc = new Scanner(CONF_PATHS).useDelimiter(SEP_P); String prev = ""; while (sc.hasNext() && !hasLoaded) { Properties fpmConf = null; boolean relative = false; String path = sc.next(); if (path.startsWith(PREV_P)) { path = path.replace(PREV_P, prev.substring(0, prev.length() - 1)); } else if (path.startsWith(REL_P)) { path = path.replace(REL_P + FS, ""); relative = true; } else if (path.contains(HOME_P)) { path = path.replace(HOME_P, USER_HOME); } prev = path; path = path.concat(MAIN_CONF_FILE); try { InputStream is = null; if (relative) { is = ClassLoader.getSystemResourceAsStream(path); path = getSystemConfDir(); Strings.getOne().createPath(path); path += MAIN_CONF_FILE; FileOutputStream os = new FileOutputStream(path); IOUtils.copy(is, os); os.flush(); os.close(); os = null; } else { is = new FileInputStream(path); } fpmConf = new Properties(); fpmConf.load(is); if (fpmConf.isEmpty()) { throw new ConfigurationReadException(); } ret = new MapEntry<String, Properties>(path, fpmConf); hasLoaded = true; } catch (FileNotFoundException e) { fpmConf = null; singleton = null; hasLoaded = false; } catch (IOException e) { throw new ConfigurationReadException(); } } return ret; } | public static boolean downloadFile(String url, String destination) { BufferedInputStream bi = null; BufferedOutputStream bo = null; File destfile; try { java.net.URL fileurl; try { fileurl = new java.net.URL(url); } catch (MalformedURLException e) { return false; } bi = new BufferedInputStream(fileurl.openStream()); destfile = new File(destination); if (!destfile.createNewFile()) { destfile.delete(); destfile.createNewFile(); } bo = new BufferedOutputStream(new FileOutputStream(destfile)); int readedbyte; while ((readedbyte = bi.read()) != -1) { bo.write(readedbyte); } bo.flush(); } catch (IOException ex) { return false; } finally { try { bi.close(); bo.close(); } catch (Exception ex) { } } return true; } | 884,940 |
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 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(); } } | 884,941 |
1 | public static void writeEntry(File file, File input) throws PersistenceException { try { File temporaryFile = File.createTempFile("pmMDA_zargo", ARGOUML_EXT); temporaryFile.deleteOnExit(); ZipOutputStream output = new ZipOutputStream(new FileOutputStream(temporaryFile)); FileInputStream inputStream = new FileInputStream(input); ZipEntry entry = new ZipEntry(file.getName().substring(0, file.getName().indexOf(ARGOUML_EXT)) + XMI_EXT); output.putNextEntry(new ZipEntry(entry)); IOUtils.copy(inputStream, output); output.closeEntry(); inputStream.close(); entry = new ZipEntry(file.getName().substring(0, file.getName().indexOf(ARGOUML_EXT)) + ".argo"); output.putNextEntry(new ZipEntry(entry)); output.write(ArgoWriter.getArgoContent(file.getName().substring(0, file.getName().indexOf(ARGOUML_EXT)) + XMI_EXT).getBytes()); output.closeEntry(); output.close(); temporaryFile.renameTo(file); } catch (IOException ioe) { throw new PersistenceException(ioe); } } | protected void copyFile(String from, String to, String workingDirectory) throws Exception { URL monitorCallShellScriptUrl = Thread.currentThread().getContextClassLoader().getResource(from); File f = new File(monitorCallShellScriptUrl.getFile()); String directoryPath = f.getAbsolutePath(); String fileName = from; InputStream in = null; if (directoryPath.indexOf(".jar!") > -1) { URL urlJar = new URL(directoryPath.substring(directoryPath.indexOf("file:"), directoryPath.indexOf('!'))); JarFile jf = new JarFile(urlJar.getFile()); JarEntry je = jf.getJarEntry(from); fileName = je.getName(); in = Thread.currentThread().getContextClassLoader().getResourceAsStream(fileName); } else { in = new FileInputStream(f); } File outScriptFile = new File(to); FileOutputStream fos = new FileOutputStream(outScriptFile); int nextChar; while ((nextChar = in.read()) != -1) fos.write(nextChar); fos.flush(); fos.close(); try { LinuxCommandExecutor cmdExecutor = new LinuxCommandExecutor(); cmdExecutor.setWorkingDirectory(workingDirectory); cmdExecutor.runCommand("chmod 777 " + to); } catch (Exception e) { throw e; } } | 884,942 |
1 | public void run() { StringBuffer xml; String tabName; Element guiElement; setBold(monitor.getReading()); setBold(monitor.getReadingStatus()); monitor.getReadingStatus().setText(" Working"); HttpMethod method = null; xml = new StringBuffer(); File tempfile = new File(url); if (tempfile.exists()) { try { InputStream in = new FileInputStream(tempfile); int temp; while ((temp = in.read()) != -1) { xml.append((char) temp); } in.close(); } catch (IOException e) { System.out.println("Loading Monitor Failed, error while reading XML file from local file"); e.printStackTrace(System.err); return; } } else { try { HttpClient client = new HttpClient(); method = new GetMethod(url); int response = client.executeMethod(method); if (response == 200) { InputStream in = method.getResponseBodyAsStream(); int temp; while ((temp = in.read()) != -1) { xml.append((char) temp); } in.close(); } else { if (method != null) { method.releaseConnection(); } System.out.println("Loading Monitor Failed. Incorrect response from HTTP Server " + response); return; } } catch (IOException e) { if (method != null) { method.releaseConnection(); } System.out.println("Loading Monitor Failed, error while reading XML file from HTTP Server"); e.printStackTrace(System.err); return; } } setPlain(monitor.getReading()); setPlain(monitor.getReadingStatus()); monitor.getReadingStatus().setText(" Done"); setBold(monitor.getValidating()); setBold(monitor.getValidatingStatus()); monitor.getValidatingStatus().setText(" Working"); DocumentBuilderFactoryImpl factory = new DocumentBuilderFactoryImpl(); try { DocumentBuilder parser = factory.newDocumentBuilder(); Document document = parser.parse(new ByteArrayInputStream(xml.toString().getBytes())); if (method != null) { method.releaseConnection(); } Element root = document.getDocumentElement(); NodeList temp = root.getElementsByTagName("resource"); for (int j = 0; j < temp.getLength(); j++) { Element resource = (Element) temp.item(j); resources.add(new URL(resource.getAttribute("url"))); } NodeList connections = root.getElementsByTagName("jmxserver"); for (int j = 0; j < connections.getLength(); j++) { Element connection = (Element) connections.item(j); String name = connection.getAttribute("name"); String tempUrl = connection.getAttribute("url"); String auth = connection.getAttribute("auth"); if (tempUrl.indexOf("${host}") != -1) { HostDialog dialog = new HostDialog(Config.getHosts()); String host = dialog.showDialog(); if (host == null) { System.out.println("Host can not be null, unable to create panel."); return; } tempUrl = tempUrl.replaceAll("\\$\\{host\\}", host); Config.addHost(host); } JMXServiceURL jmxUrl = new JMXServiceURL(tempUrl); JmxServerGraph server = new JmxServerGraph(name, jmxUrl, new JmxWorker(false)); if (auth != null && auth.equalsIgnoreCase("true")) { LoginTrueService loginService = new LoginTrueService(); JXLoginPanel.Status status = JXLoginPanel.showLoginDialog(null, loginService); if (status != JXLoginPanel.Status.SUCCEEDED) { return; } server.setUsername(loginService.getName()); server.setPassword(loginService.getPassword()); } servers.put(name, server); NodeList listeners = connection.getElementsByTagName("listener"); for (int i = 0; i < listeners.getLength(); i++) { Element attribute = (Element) listeners.item(i); String taskname = attribute.getAttribute("taskname"); MBean mbean = new MBean(attribute.getAttribute("mbean"), null); String filtertype = attribute.getAttribute("filterType"); TaskNotificationListener listener = new TaskNotificationListener(); NotificationFilterSupport filter = new NotificationFilterSupport(); if (filtertype == null || "".equals(filtertype)) { filter = null; } else { filter.enableType(filtertype); } Task task = new Task(-1, Task.LISTEN, server); task.setMbean(mbean); task.setListener(listener); task.setFilter(filter); server.getWorker().addTask(task); if (tasks.get(taskname) != null) { System.out.println("Task " + taskname + " already exists."); return; } List<Task> hashTempList = new ArrayList<Task>(); hashTempList.add(task); tasks.put(taskname, hashTempList); } NodeList attributes = connection.getElementsByTagName("attribute"); for (int i = 0; i < attributes.getLength(); i++) { Element attribute = (Element) attributes.item(i); String taskname = attribute.getAttribute("taskname"); MBean mbean = new MBean(attribute.getAttribute("mbean"), null); String attributename = attribute.getAttribute("attributename"); String frequency = attribute.getAttribute("frequency"); String onEvent = attribute.getAttribute("onEvent"); if (frequency.equalsIgnoreCase("onchange")) { TaskNotificationListener listener = new TaskNotificationListener(); AttributeChangeNotificationFilter filter = new AttributeChangeNotificationFilter(); filter.enableAttribute(attributename); Task task = new Task(-1, Task.LISTEN, server); MBeanAttribute att = new MBeanAttribute(mbean, attributename); task.setAttribute(att); task.setMbean(mbean); task.setListener(listener); task.setFilter(filter); server.getWorker().addTask(task); if (tasks.get(taskname) != null) { System.out.println("Task " + taskname + " already exists."); return; } Task task2 = new Task(-1, Task.GET_ATTRIBUTE, server); task2.setAttribute(att); task2.setMbean(mbean); server.getWorker().addTask(task2); List<Task> hashTempList = new ArrayList<Task>(); hashTempList.add(task); hashTempList.add(task2); tasks.put(taskname, hashTempList); } else { int frequency2 = Integer.parseInt(frequency); Task task = new Task(frequency2, Task.GET_ATTRIBUTE, server); MBeanAttribute att = new MBeanAttribute(mbean, attributename); task.setAttribute(att); task.setMbean(mbean); if (tasks.get(taskname) != null) { System.out.println("Task " + taskname + " already exists."); return; } List<Task> hashTempList = new ArrayList<Task>(); hashTempList.add(task); tasks.put(taskname, hashTempList); TaskNotificationListener listener = null; if (onEvent != null && !"".equals(onEvent)) { Task tempTask = tasks.get(onEvent).get(0); if (tempTask == null) { System.out.println(onEvent + " was not found."); return; } else { listener = (TaskNotificationListener) tempTask.getListener(); } } if (listener == null) { server.getWorker().addTask(task); } else { listener.addTask(task); } } } } NodeList guiTemp = root.getElementsByTagName("gui"); guiElement = (Element) guiTemp.item(0); tabName = guiElement.getAttribute("name"); if (MonitorServer.contains(tabName)) { JOptionPane.showMessageDialog(null, "This panel is already open, stoping creating of panel.", "Panel already exists", JOptionPane.ERROR_MESSAGE); return; } for (int i = 0; i < monitor.getTab().getTabCount(); i++) { if (monitor.getTab().getComponent(i).equals(monitor)) { monitor.getTab().setTitleAt(i, tabName); break; } } NodeList tempBindings = root.getElementsByTagName("binding"); for (int i = 0; i < tempBindings.getLength(); i++) { Element binding = (Element) tempBindings.item(i); String guiname = binding.getAttribute("guiname"); String tmethod = binding.getAttribute("method"); String taskname = binding.getAttribute("taskname"); String formater = binding.getAttribute("formater"); BindingContainer tempBinding; if (formater == null || (formater != null && formater.equals(""))) { tempBinding = new BindingContainer(guiname, tmethod, taskname); } else { tempBinding = new BindingContainer(guiname, tmethod, taskname, formater); } bindings.add(tempBinding); } } catch (Exception e) { System.err.println("Exception message: " + e.getMessage()); System.out.println("Loading Monitor Failed, couldnt parse XML file."); e.printStackTrace(System.err); return; } setPlain(monitor.getValidating()); setPlain(monitor.getValidatingStatus()); monitor.getValidatingStatus().setText(" Done"); setBold(monitor.getDownload()); setBold(monitor.getDownloadStatus()); monitor.getDownloadStatus().setText(" Working"); List<File> jarFiles = new ArrayList<File>(); File cacheDir = new File(Config.getCacheDir()); if (!cacheDir.exists()) { cacheDir.mkdir(); } for (URL resUrl : resources) { try { HttpClient client = new HttpClient(); HttpMethod methodRes = new GetMethod(resUrl.toString()); int response = client.executeMethod(methodRes); if (response == 200) { int index = resUrl.toString().lastIndexOf("/") + 1; File file = new File(Config.getCacheDir() + resUrl.toString().substring(index)); FileOutputStream out = new FileOutputStream(file); InputStream in = methodRes.getResponseBodyAsStream(); int readTemp = 0; while ((readTemp = in.read()) != -1) { out.write(readTemp); } System.out.println(file.getName() + " downloaded."); methodRes.releaseConnection(); if (file.getName().endsWith(".jar")) { jarFiles.add(file); } } else { methodRes.releaseConnection(); System.out.println("Loading Monitor Failed. Unable to get resource " + url); return; } } catch (IOException e) { System.out.println("Loading Monitor Failed, error while reading resource file " + "from HTTP Server"); e.printStackTrace(System.err); return; } } URL[] urls = new URL[jarFiles.size()]; try { for (int i = 0; i < jarFiles.size(); i++) { File file = jarFiles.get(i); File newFile = new File(Config.getCacheDir() + "/" + System.currentTimeMillis() + file.getName()); FileInputStream in = new FileInputStream(file); FileOutputStream out = new FileOutputStream(newFile); int n = 0; byte[] buf = new byte[1024]; while ((n = in.read(buf, 0, 1024)) > -1) { out.write(buf, 0, n); } out.close(); out.close(); in.close(); urls[i] = new URL("file:" + newFile.getAbsolutePath()); } } catch (Exception e1) { System.out.println("Unable to load jar files."); e1.printStackTrace(); } URLClassLoader loader = new URLClassLoader(urls); engine.setClassLoader(loader); setPlain(monitor.getDownload()); setPlain(monitor.getDownloadStatus()); monitor.getDownloadStatus().setText(" Done"); setBold(monitor.getGui()); setBold(monitor.getGuiStatus()); monitor.getGuiStatus().setText(" Working"); Container container; try { String tempXml = xml.toString(); int start = tempXml.indexOf("<gui"); start = tempXml.indexOf('>', start) + 1; int end = tempXml.indexOf("</gui>"); container = engine.render(new StringReader(tempXml.substring(start, end))); } catch (Exception e) { e.printStackTrace(System.err); System.err.println("Exception msg: " + e.getMessage()); System.out.println("Loading Monitor Failed, error creating gui."); return; } for (BindingContainer bcon : bindings) { List<Task> temp = tasks.get(bcon.getTask()); if (temp == null) { System.out.println("Task with name " + bcon.getTask() + " doesnt exist."); } else { for (Task task : temp) { if (task != null) { Object comp = engine.find(bcon.getComponent()); if (comp != null) { if (task.getTaskType() == Task.LISTEN && task.getFilter() instanceof AttributeChangeNotificationFilter) { TaskNotificationListener listener = (TaskNotificationListener) task.getListener(); if (bcon.getFormater() == null) { listener.addResultListener(new Binding(comp, bcon.getMethod())); } else { listener.addResultListener(new Binding(comp, bcon.getMethod(), bcon.getFormater(), loader)); } } else { if (bcon.getFormater() == null) { task.addResultListener(new Binding(comp, bcon.getMethod())); } else { task.addResultListener(new Binding(comp, bcon.getMethod(), bcon.getFormater(), loader)); } } } else { System.out.println("Refering to gui name, " + bcon.getComponent() + ", that doesnt exist. Unable to create monitor."); return; } } else { System.out.println("Refering to task name, " + bcon.getTask() + ", that doesnt exist. Unable to create monitor."); return; } } } } for (int i = 0; i < monitor.getTab().getTabCount(); i++) { if (monitor.getTab().getComponent(i).equals(monitor)) { monitor.getTab().setComponentAt(i, new MonitorContainerPanel(container, this)); break; } } System.out.println("Connecting to server(s)."); Enumeration e = servers.keys(); List<JmxWorker> list = new ArrayList<JmxWorker>(); while (e.hasMoreElements()) { JmxWorker worker = servers.get(e.nextElement()).getWorker(); worker.setRunning(true); worker.start(); list.add(worker); } MonitorServer.add(tabName, list); Config.addUrl(url); } | public void generate(FileObject outputDirectory, FileObject generatedOutputDirectory, List<Library> libraryModels, String tapdocXml) throws FileSystemException { if (!outputDirectory.exists()) { outputDirectory.createFolder(); } ZipUtils.extractZip(new ClasspathResource(classResolver, "/com/erinors/tapestry/tapdoc/standalone/resources.zip"), outputDirectory); for (Library library : libraryModels) { String libraryName = library.getName(); String libraryLocation = library.getLocation(); outputDirectory.resolveFile(fileNameGenerator.getLibraryDirectory(libraryLocation)).createFolder(); try { { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Library.xsl"), "libraryName", libraryName); FileObject index = outputDirectory.resolveFile(fileNameGenerator.getLibraryDirectory(libraryLocation)).resolveFile("index.html"); Writer out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("ComponentIndex.xsl"), "libraryName", libraryName); FileObject index = outputDirectory.resolveFile(fileNameGenerator.getLibraryDirectory(libraryLocation)).resolveFile("components.html"); Writer out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } } catch (Exception e) { throw new RuntimeException(e); } for (Component component : library.getComponents()) { String componentName = component.getName(); System.out.println("Generating " + libraryName + ":" + componentName + "..."); Map<String, String> parameters = new HashMap<String, String>(); parameters.put("libraryName", libraryName); parameters.put("componentName", componentName); String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Component.xsl"), parameters); Writer out = null; try { FileObject index = outputDirectory.resolveFile(fileNameGenerator.getComponentIndexFile(libraryLocation, componentName, true)); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); Resource specificationLocation = component.getSpecificationLocation(); if (specificationLocation.getRelativeResource(componentName + "_tapdoc/resource").getResourceURL() != null) { File srcResourcesDirectory = new File(specificationLocation.getRelativeResource(componentName + "_tapdoc/resource").getResourceURL().toURI()); FileObject dstResourcesFileObject = outputDirectory.resolveFile(fileNameGenerator.getComponentDirectory(libraryLocation, componentName)).resolveFile("resource"); if (srcResourcesDirectory.exists() && srcResourcesDirectory.isDirectory()) { File[] files = srcResourcesDirectory.listFiles(); if (files != null) { for (File resource : files) { if (resource.isFile() && !resource.isHidden()) { FileObject resourceFileObject = dstResourcesFileObject.resolveFile(resource.getName()); resourceFileObject.createFile(); InputStream inResource = null; OutputStream outResource = null; try { inResource = new FileInputStream(resource); outResource = resourceFileObject.getContent().getOutputStream(); IOUtils.copy(inResource, outResource); } finally { IOUtils.closeQuietly(inResource); IOUtils.closeQuietly(outResource); } } } } } } } catch (Exception e) { throw new RuntimeException(e); } finally { if (out != null) { try { out.close(); } catch (IOException e) { e.printStackTrace(); } } } } } { Writer out = null; try { { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("LibraryIndex.xsl")); FileObject index = outputDirectory.resolveFile("libraries.html"); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Overview.xsl")); FileObject index = outputDirectory.resolveFile("overview.html"); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("AllComponents.xsl")); FileObject index = outputDirectory.resolveFile("allcomponents.html"); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } } catch (Exception e) { throw new RuntimeException(e); } finally { IOUtils.closeQuietly(out); } } } | 884,943 |
0 | public static String rename_file(String sessionid, String key, String newFileName) { String jsonstring = ""; try { Log.d("current running function name:", "rename_file"); HttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost("https://mt0-app.cloud.cm/rpc/json"); List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(2); nameValuePairs.add(new BasicNameValuePair("c", "Storage")); nameValuePairs.add(new BasicNameValuePair("m", "rename_file")); nameValuePairs.add(new BasicNameValuePair("new_name", newFileName)); nameValuePairs.add(new BasicNameValuePair("key", key)); httppost.setEntity(new UrlEncodedFormEntity(nameValuePairs)); httppost.setHeader("Cookie", "PHPSESSID=" + sessionid); HttpResponse response = httpclient.execute(httppost); jsonstring = EntityUtils.toString(response.getEntity()); Log.d("jsonStringReturned:", jsonstring); return jsonstring; } catch (Exception e) { e.printStackTrace(); } return jsonstring; } | public static void copyFileStreams(File fromFile, File toFile) throws IOException { if (!fromFile.exists()) { return; } FileInputStream fis = new FileInputStream(fromFile); FileOutputStream fos = new FileOutputStream(toFile); int read = 0; byte[] buf = new byte[1024]; while (-1 != read) { read = fis.read(buf); if (read >= 0) { fos.write(buf, 0, read); } } fos.close(); fis.close(); } | 884,944 |
0 | private static String getRegistrationClasses() { CentralRegistrationClass c = new CentralRegistrationClass(); String name = c.getClass().getCanonicalName().replace('.', '/').concat(".class"); try { Enumeration<URL> urlEnum = c.getClass().getClassLoader().getResources("META-INF/MANIFEST.MF"); while (urlEnum.hasMoreElements()) { URL url = urlEnum.nextElement(); String file = url.getFile(); JarURLConnection jarConnection = (JarURLConnection) url.openConnection(); Manifest mf = jarConnection.getManifest(); Attributes attrs = (Attributes) mf.getAttributes(name); if (attrs != null) { String classes = attrs.getValue("RegistrationClasses"); return classes; } } } catch (IOException ex) { ex.printStackTrace(); } return ""; } | public static boolean copy(File src, File dest) { boolean result = true; String files[] = null; if (src.isDirectory()) { files = src.list(); result = dest.mkdir(); } else { files = new String[1]; files[0] = ""; } if (files == null) { files = new String[0]; } for (int i = 0; (i < files.length) && result; i++) { File fileSrc = new File(src, files[i]); File fileDest = new File(dest, files[i]); if (fileSrc.isDirectory()) { result = copy(fileSrc, fileDest); } else { FileChannel ic = null; FileChannel oc = null; try { ic = (new FileInputStream(fileSrc)).getChannel(); oc = (new FileOutputStream(fileDest)).getChannel(); ic.transferTo(0, ic.size(), oc); } catch (IOException e) { log.error(sm.getString("expandWar.copy", fileSrc, fileDest), e); result = false; } finally { if (ic != null) { try { ic.close(); } catch (IOException e) { } } if (oc != null) { try { oc.close(); } catch (IOException e) { } } } } } return result; } | 884,945 |
0 | void readData() { String[] nextLine; int line; double value; URL url = null; String FileToRead; try { for (int i = 0; i < names.length; i++) { FileToRead = "data/" + names[i] + ".csv"; url = new URL(ja.getCodeBase(), FileToRead); System.out.println(url.toString()); InputStream in = url.openStream(); CSVReader reader = new CSVReader(new InputStreamReader(in)); line = 0; while ((nextLine = reader.readNext()) != null) { allset.months[line] = Integer.parseInt(nextLine[0].substring(0, 2)); allset.years[line] = Integer.parseInt(nextLine[0].substring(6, 10)); value = Double.parseDouble(nextLine[1]); allset.values.getDataRef()[line][i] = value; line++; } } } catch (IOException e) { System.err.println("File Read Exception"); } } | private void readVersion() { URL url = ClassLoader.getSystemResource("version"); if (url == null) { return; } BufferedReader reader = null; String line = null; try { reader = new BufferedReader(new InputStreamReader(url.openStream())); while ((line = reader.readLine()) != null) { if (line.startsWith("Version=")) { version = (line.split("="))[1]; } if (line.startsWith("Revision=")) { revision = (line.split("="))[1]; } if (line.startsWith("Date=")) { String sSec = (line.split("="))[1]; Long lSec = Long.valueOf(sSec); compileDate = new Date(lSec); } } } catch (IOException e) { e.printStackTrace(); } finally { if (reader != null) { try { reader.close(); } catch (IOException e) { e.printStackTrace(); } } } return; } | 884,946 |
0 | public static String md5(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("MD5"); byte[] md5hash; md.update(text.getBytes("iso-8859-1"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } | public void testFidelity() throws ParserException, IOException { Lexer lexer; Node node; int position; StringBuffer buffer; String string; char[] ref; char[] test; URL url = new URL("http://sourceforge.net"); lexer = new Lexer(url.openConnection()); position = 0; buffer = new StringBuffer(80000); while (null != (node = lexer.nextNode())) { string = node.toHtml(); if (position != node.getStartPosition()) fail("non-contiguous" + string); buffer.append(string); position = node.getEndPosition(); if (buffer.length() != position) fail("text length differed after encountering node " + string); } ref = lexer.getPage().getText().toCharArray(); test = new char[buffer.length()]; buffer.getChars(0, buffer.length(), test, 0); assertEquals("different amounts of text", ref.length, test.length); for (int i = 0; i < ref.length; i++) if (ref[i] != test[i]) fail("character differs at position " + i + ", expected <" + ref[i] + "> but was <" + test[i] + ">"); } | 884,947 |
1 | public static final boolean zipUpdate(String zipfile, String name, String oldname, byte[] contents, boolean delete) { try { File temp = File.createTempFile("atf", ".zip"); InputStream in = new BufferedInputStream(new FileInputStream(zipfile)); OutputStream os = new BufferedOutputStream(new FileOutputStream(temp)); ZipInputStream zin = new ZipInputStream(in); ZipOutputStream zout = new ZipOutputStream(os); ZipEntry e; ZipEntry e2; byte buffer[] = new byte[TEMP_FILE_BUFFER_SIZE]; int bytesRead; boolean found = false; boolean rename = false; String oname = name; if (oldname != null) { name = oldname; rename = true; } while ((e = zin.getNextEntry()) != null) { if (!e.isDirectory()) { String ename = e.getName(); if (delete && ename.equals(name)) continue; e2 = new ZipEntry(rename ? oname : ename); zout.putNextEntry(e2); if (ename.equals(name)) { found = true; zout.write(contents); } else { while ((bytesRead = zin.read(buffer)) != -1) zout.write(buffer, 0, bytesRead); } zout.closeEntry(); } } if (!found && !delete) { e = new ZipEntry(name); zout.putNextEntry(e); zout.write(contents); zout.closeEntry(); } zin.close(); zout.close(); File fp = new File(zipfile); fp.delete(); MLUtil.copyFile(temp, fp); temp.delete(); return (true); } catch (FileNotFoundException e) { MLUtil.runtimeError(e, "updateZip " + zipfile + " " + name); } catch (IOException e) { MLUtil.runtimeError(e, "updateZip " + zipfile + " " + name); } return (false); } | public void extractPrincipalClasses(String[] info, int numFiles) { String methodName = ""; String finalClass = ""; String WA; String MC; String RA; int[] readCount = new int[numFiles]; int[] writeCount = new int[numFiles]; int[] methodCallCount = new int[numFiles]; int writeMax1; int writeMax2; int readMax; int methodCallMax; int readMaxIndex = 0; int writeMaxIndex1 = 0; int writeMaxIndex2; int methodCallMaxIndex = 0; try { MethodsDestClass = new BufferedWriter(new FileWriter("InfoFiles/MethodsDestclass.txt")); FileInputStream fstreamWriteAttr = new FileInputStream("InfoFiles/WriteAttributes.txt"); DataInputStream inWriteAttr = new DataInputStream(fstreamWriteAttr); BufferedReader writeAttr = new BufferedReader(new InputStreamReader(inWriteAttr)); FileInputStream fstreamMethodsCalled = new FileInputStream("InfoFiles/MethodsCalled.txt"); DataInputStream inMethodsCalled = new DataInputStream(fstreamMethodsCalled); BufferedReader methodsCalled = new BufferedReader(new InputStreamReader(inMethodsCalled)); FileInputStream fstreamReadAttr = new FileInputStream("InfoFiles/ReadAttributes.txt"); DataInputStream inReadAttr = new DataInputStream(fstreamReadAttr); BufferedReader readAttr = new BufferedReader(new InputStreamReader(inReadAttr)); while ((WA = writeAttr.readLine()) != null && (RA = readAttr.readLine()) != null && (MC = methodsCalled.readLine()) != null) { WA = writeAttr.readLine(); RA = readAttr.readLine(); MC = methodsCalled.readLine(); while (WA.compareTo("EndOfClass") != 0 && RA.compareTo("EndOfClass") != 0 && MC.compareTo("EndOfClass") != 0) { methodName = writeAttr.readLine(); readAttr.readLine(); methodsCalled.readLine(); WA = writeAttr.readLine(); MC = methodsCalled.readLine(); RA = readAttr.readLine(); while (true) { if (WA.compareTo("EndOfMethod") == 0 && RA.compareTo("EndOfMethod") == 0 && MC.compareTo("EndOfMethod") == 0) { break; } if (WA.compareTo("EndOfMethod") != 0) { if (WA.indexOf(".") > 0) { WA = WA.substring(0, WA.indexOf(".")); } } if (RA.compareTo("EndOfMethod") != 0) { if (RA.indexOf(".") > 0) { RA = RA.substring(0, RA.indexOf(".")); } } if (MC.compareTo("EndOfMethod") != 0) { if (MC.indexOf(".") > 0) { MC = MC.substring(0, MC.indexOf(".")); } } for (int i = 0; i < numFiles && info[i] != null; i++) { if (info[i].compareTo(WA) == 0) { writeCount[i]++; } if (info[i].compareTo(RA) == 0) { readCount[i]++; } if (info[i].compareTo(MC) == 0) { methodCallCount[i]++; } } if (WA.compareTo("EndOfMethod") != 0) { WA = writeAttr.readLine(); } if (MC.compareTo("EndOfMethod") != 0) { MC = methodsCalled.readLine(); } if (RA.compareTo("EndOfMethod") != 0) { RA = readAttr.readLine(); } } WA = writeAttr.readLine(); MC = methodsCalled.readLine(); RA = readAttr.readLine(); writeMax1 = writeCount[0]; writeMaxIndex1 = 0; for (int i = 1; i < numFiles; i++) { if (writeCount[i] > writeMax1) { writeMax1 = writeCount[i]; writeMaxIndex1 = i; } } writeCount[writeMaxIndex1] = 0; writeMax2 = writeCount[0]; writeMaxIndex2 = 0; for (int i = 1; i < numFiles; i++) { if (writeCount[i] > writeMax2) { writeMax2 = writeCount[i]; writeMaxIndex2 = i; } } readMax = readCount[0]; readMaxIndex = 0; for (int i = 1; i < numFiles; i++) { if (readCount[i] > readMax) { readMax = readCount[i]; readMaxIndex = i; } } methodCallMax = methodCallCount[0]; methodCallMaxIndex = 0; for (int i = 1; i < numFiles; i++) { if (methodCallCount[i] > methodCallMax) { methodCallMax = methodCallCount[i]; methodCallMaxIndex = i; } } boolean isNotEmpty = false; if (writeMax1 > 0 && writeMax2 == 0) { finalClass = info[writeMaxIndex1]; isNotEmpty = true; } else if (writeMax1 == 0) { if (readMax != 0) { finalClass = info[readMaxIndex]; isNotEmpty = true; } else if (methodCallMax != 0) { finalClass = info[methodCallMaxIndex]; isNotEmpty = true; } } if (isNotEmpty == true) { MethodsDestClass.write(methodName); MethodsDestClass.newLine(); MethodsDestClass.write(finalClass); MethodsDestClass.newLine(); isNotEmpty = false; } for (int j = 0; j < numFiles; j++) { readCount[j] = 0; writeCount[j] = 0; methodCallCount[j] = 0; } } } writeAttr.close(); methodsCalled.close(); readAttr.close(); MethodsDestClass.close(); int sizeInfoArray = 0; sizeInfoArray = infoArraySize(); boolean classWritten = false; principleClass = new String[100]; principleMethod = new String[100]; principleMethodsClass = new String[100]; String infoArray[] = new String[sizeInfoArray]; String field; int counter = 0; FileInputStream fstreamDestMethod = new FileInputStream("InfoFiles/MethodsDestclass.txt"); DataInputStream inDestMethod = new DataInputStream(fstreamDestMethod); BufferedReader destMethod = new BufferedReader(new InputStreamReader(inDestMethod)); PrincipleClassGroup = new BufferedWriter(new FileWriter("InfoFiles/PrincipleClassGroup.txt")); while ((field = destMethod.readLine()) != null) { infoArray[counter] = field; counter++; } for (int i = 0; i < numFiles; i++) { for (int j = 0; j < counter - 1 && info[i] != null; j++) { if (infoArray[j + 1].compareTo(info[i]) == 0) { if (classWritten == false) { PrincipleClassGroup.write(infoArray[j + 1]); PrincipleClassGroup.newLine(); principleClass[principleClassCount] = infoArray[j + 1]; principleClassCount++; classWritten = true; } PrincipleClassGroup.write(infoArray[j]); principleMethod[principleMethodCount] = infoArray[j]; principleMethodsClass[principleMethodCount] = infoArray[j + 1]; principleMethodCount++; PrincipleClassGroup.newLine(); } } if (classWritten == true) { PrincipleClassGroup.write("EndOfClass"); PrincipleClassGroup.newLine(); classWritten = false; } } destMethod.close(); PrincipleClassGroup.close(); readFileCount = readFileCount(); writeFileCount = writeFileCount(); methodCallFileCount = methodCallFileCount(); readArray = new String[readFileCount]; writeArray = new String[writeFileCount]; callArray = new String[methodCallFileCount]; initializeArrays(); constructFundamentalView(); constructInteractionView(); constructAssociationView(); } catch (IOException e) { e.printStackTrace(); } } | 884,948 |
1 | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public static boolean copy(File src, File dest) { boolean result = true; String files[] = null; if (src.isDirectory()) { files = src.list(); result = dest.mkdir(); } else { files = new String[1]; files[0] = ""; } if (files == null) { files = new String[0]; } for (int i = 0; (i < files.length) && result; i++) { File fileSrc = new File(src, files[i]); File fileDest = new File(dest, files[i]); if (fileSrc.isDirectory()) { result = copy(fileSrc, fileDest); } else { FileChannel ic = null; FileChannel oc = null; try { ic = (new FileInputStream(fileSrc)).getChannel(); oc = (new FileOutputStream(fileDest)).getChannel(); ic.transferTo(0, ic.size(), oc); } catch (IOException e) { log.error(sm.getString("expandWar.copy", fileSrc, fileDest), e); result = false; } finally { if (ic != null) { try { ic.close(); } catch (IOException e) { } } if (oc != null) { try { oc.close(); } catch (IOException e) { } } } } } return result; } | 884,949 |
0 | private void channelCopy(File source, File dest) throws IOException { FileChannel srcChannel = new FileInputStream(source).getChannel(); FileChannel dstChannel = new FileOutputStream(dest).getChannel(); try { dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); } finally { srcChannel.close(); dstChannel.close(); } } | public static String getMD5Str(String str) { MessageDigest messageDigest = null; try { messageDigest = MessageDigest.getInstance("MD5"); messageDigest.reset(); messageDigest.update(str.getBytes("UTF-8")); } catch (NoSuchAlgorithmException e) { System.out.println("NoSuchAlgorithmException caught!"); System.exit(-1); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } byte[] byteArray = messageDigest.digest(); StringBuffer md5StrBuff = new StringBuffer(); for (int i = 0; i < byteArray.length; i++) { if (Integer.toHexString(0xFF & byteArray[i]).length() == 1) md5StrBuff.append("0").append(Integer.toHexString(0xFF & byteArray[i])); else md5StrBuff.append(Integer.toHexString(0xFF & byteArray[i])); } return md5StrBuff.toString(); } | 884,950 |
0 | public String stringOfUrl(String addr) throws IOException { ByteArrayOutputStream output = new ByteArrayOutputStream(); URL url = new URL(addr); IOUtils.copy(url.openStream(), output); return output.toString(); } | public static boolean reportException(Throwable ex, HashMap<String, String> suppl) { if (Activator.getDefault().getPreferenceStore().getBoolean(PreferenceConstants.P_CRASH_REPORTING)) { logger.debug("Report exception to devs..."); String data = "reportType=exception&" + "message=" + ex.getMessage(); data += "&build=" + Platform.getBundle("de.uni_mannheim.swt.codeconjurer").getHeaders().get("Bundle-Version"); int ln = 0; for (StackTraceElement el : ex.getStackTrace()) { data += "&st_line_" + ++ln + "=" + el.getClassName() + "#" + el.getMethodName() + "<" + el.getLineNumber() + ">"; } data += "&lines=" + ln; data += "&Suppl-Description=" + ex.toString(); data += "&Suppl-Server=" + Activator.getDefault().getPreferenceStore().getString(PreferenceConstants.P_SERVER); data += "&Suppl-User=" + Activator.getDefault().getPreferenceStore().getString(PreferenceConstants.P_USERNAME); if (suppl != null) { for (String key : suppl.keySet()) { data += "&Suppl-" + key + "=" + suppl.get(key); } } try { URL url = new URL("http://www.merobase.com:7777/org.code_conjurer.udc/CrashReport"); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter writer = new OutputStreamWriter(conn.getOutputStream()); writer.write(data); writer.flush(); StringBuffer answer = new StringBuffer(); BufferedReader reader = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line; while ((line = reader.readLine()) != null) { answer.append(line + "\r\n"); } writer.close(); reader.close(); logger.debug(answer.toString()); } catch (Exception e) { logger.debug("Could not report exception"); return false; } return true; } else { logger.debug("Reporting not wished!"); return false; } } | 884,951 |
1 | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | @Override public void runTask(HashMap pjobParameters) throws Exception { if (hasRequiredResources(isSubTask())) { String lstrSource = getSourceFilename(); String lstrTarget = getTargetFilename(); if (getSourceDirectory() != null) { lstrSource = getSourceDirectory() + File.separator + getSourceFilename(); } if (getTargetDirectory() != null) { lstrTarget = getTargetDirectory() + File.separator + getTargetFilename(); } GZIPInputStream lgzipInput = new GZIPInputStream(new FileInputStream(lstrSource)); OutputStream lfosGUnzip = new FileOutputStream(lstrTarget); byte[] buf = new byte[1024]; int len; while ((len = lgzipInput.read(buf)) > 0) lfosGUnzip.write(buf, 0, len); lgzipInput.close(); lfosGUnzip.close(); } } | 884,952 |
0 | public static void storePolicy(DBBroker broker, XmldbURI docPath) throws EXistException, IOException { XmldbURI docName = docPath.lastSegment(); URL url = XACMLUtil.class.getResource(docPath.toString()); if (url == null) return; String content = toString(url.openStream()); if (content == null) return; Collection collection = getPolicyCollection(broker); if (collection == null) return; TransactionManager transact = broker.getBrokerPool().getTransactionManager(); Txn txn = transact.beginTransaction(); try { IndexInfo info = collection.validateXMLResource(txn, broker, docName, content); collection.store(txn, broker, info, content, false); transact.commit(txn); } catch (Exception e) { transact.abort(txn); if (e instanceof EXistException) throw (EXistException) e; throw new EXistException("Error storing policy '" + docPath + "'", e); } } | public static void postData(Reader data, URL endpoint, Writer output) throws Exception { HttpURLConnection urlc = null; try { urlc = (HttpURLConnection) endpoint.openConnection(); try { urlc.setRequestMethod("POST"); } catch (ProtocolException e) { throw new Exception("Shouldn't happen: HttpURLConnection doesn't support POST??", e); } urlc.setDoOutput(true); urlc.setDoInput(true); urlc.setUseCaches(false); urlc.setAllowUserInteraction(false); urlc.setRequestProperty("Content-type", "text/xml; charset=" + "UTF-8"); OutputStream out = urlc.getOutputStream(); try { Writer writer = new OutputStreamWriter(out, "UTF-8"); pipe(data, writer); writer.close(); } catch (IOException e) { throw new Exception("IOException while posting data", e); } finally { if (out != null) { out.close(); } } InputStream in = urlc.getInputStream(); try { Reader reader = new InputStreamReader(in); pipe(reader, output); reader.close(); } catch (IOException e) { throw new Exception("IOException while reading response", e); } finally { if (in != null) { in.close(); } } } catch (IOException e) { throw new Exception("Connection error (is server running at " + endpoint + " ?): " + e); } finally { if (urlc != null) { urlc.disconnect(); } } } | 884,953 |
1 | public static void zip(ZipOutputStream out, File f, String base) throws Exception { if (f.isDirectory()) { File[] fl = f.listFiles(); base = base.length() == 0 ? "" : base + File.separator; for (int i = 0; i < fl.length; i++) { zip(out, fl[i], base + fl[i].getName()); } } else { out.putNextEntry(new org.apache.tools.zip.ZipEntry(base)); FileInputStream in = new FileInputStream(f); IOUtils.copyStream(in, out); in.close(); } Thread.sleep(10); } | private static final void addFile(ZipArchiveOutputStream os, File file, String prefix) throws IOException { ArchiveEntry entry = os.createArchiveEntry(file, file.getAbsolutePath().substring(prefix.length() + 1)); os.putArchiveEntry(entry); FileInputStream fis = new FileInputStream(file); IOUtils.copy(fis, os); fis.close(); os.closeArchiveEntry(); } | 884,954 |
1 | private CharBuffer decodeToFile(ReplayInputStream inStream, String backingFilename, String encoding) throws IOException { CharBuffer charBuffer = null; BufferedReader reader = new BufferedReader(new InputStreamReader(inStream, encoding)); File backingFile = new File(backingFilename); this.decodedFile = File.createTempFile(backingFile.getName(), WRITE_ENCODING, backingFile.getParentFile()); FileOutputStream fos; fos = new FileOutputStream(this.decodedFile); IOUtils.copy(reader, fos, WRITE_ENCODING); fos.close(); charBuffer = getReadOnlyMemoryMappedBuffer(this.decodedFile).asCharBuffer(); return charBuffer; } | public void generate(FileObject outputDirectory, FileObject generatedOutputDirectory, List<Library> libraryModels, String tapdocXml) throws FileSystemException { if (!generatedOutputDirectory.exists()) { generatedOutputDirectory.createFolder(); } if (outputDirectory.exists()) { outputDirectory.createFolder(); } ZipUtils.extractZip(new ClasspathResource(classResolver, "/com/erinors/tapestry/tapdoc/service/xdoc/resources.zip"), outputDirectory); for (Library library : libraryModels) { String libraryName = library.getName(); String libraryLocation = library.getLocation(); generatedOutputDirectory.resolveFile(fileNameGenerator.getLibraryDirectory(libraryLocation)).createFolder(); try { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Library.xsl"), "libraryName", libraryName); FileObject index = generatedOutputDirectory.resolveFile(fileNameGenerator.getLibraryDirectory(libraryLocation)).resolveFile("index.xml"); Writer out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } catch (Exception e) { throw new RuntimeException(e); } for (Component component : library.getComponents()) { String componentName = component.getName(); System.out.println("Generating " + libraryName + ":" + componentName + "..."); Map<String, String> parameters = new HashMap<String, String>(); parameters.put("libraryName", libraryName); parameters.put("componentName", componentName); String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Component.xsl"), parameters); Writer out = null; try { FileObject index = generatedOutputDirectory.resolveFile(fileNameGenerator.getComponentIndexFile(libraryLocation, componentName, true)); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); Resource specificationLocation = component.getSpecificationLocation(); if (specificationLocation.getRelativeResource(componentName + "_tapdoc/resource").getResourceURL() != null) { File srcResourcesDirectory = new File(specificationLocation.getRelativeResource(componentName + "_tapdoc/resource").getResourceURL().toURI()); FileObject dstResourcesFileObject = outputDirectory.resolveFile(fileNameGenerator.getComponentDirectory(libraryLocation, componentName)).resolveFile("resource"); if (srcResourcesDirectory.exists() && srcResourcesDirectory.isDirectory()) { File[] files = srcResourcesDirectory.listFiles(); if (files != null) { for (File resource : files) { if (resource.isFile() && !resource.isHidden()) { FileObject resourceFileObject = dstResourcesFileObject.resolveFile(resource.getName()); resourceFileObject.createFile(); InputStream inResource = null; OutputStream outResource = null; try { inResource = new FileInputStream(resource); outResource = resourceFileObject.getContent().getOutputStream(); IOUtils.copy(inResource, outResource); } finally { IOUtils.closeQuietly(inResource); IOUtils.closeQuietly(outResource); } } } } } } } catch (Exception e) { throw new RuntimeException(e); } finally { IOUtils.closeQuietly(out); } } } { Writer out = null; try { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Overview.xsl")); FileObject index = generatedOutputDirectory.resolveFile("index.xml"); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } catch (Exception e) { throw new RuntimeException(e); } finally { IOUtils.closeQuietly(out); } } } | 884,955 |
0 | public static String generateSHA1Digest(String text) { try { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("UTF-8"), 0, text.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } return null; } | public void exe2(String[] args) { Connection con = null; Connection con2 = null; Statement stmt = null; PreparedStatement pstmt = null; ResultSet rs = null; ResultSetMetaData rsmd = null; try { Class.forName("oracle.jdbc.driver.OracleDriver"); con = getConnection("mis030dv"); con2 = getConnection("mis030db"); con2.setAutoCommit(false); stmt = con.createStatement(); rs = stmt.executeQuery("SELECT * FROM MIS.MAP_PUR0101 WHERE NOT EXISTS (SELECT 1 FROM MIS.RSCMGOOD@MIS030DB@DEVU01 WHERE GOODCD = PUM_CODE OR GOODCD = NEW_PUM_CODE)"); pstmt = con2.prepareStatement("INSERT INTO MIS.RSCMGOOD ( GOODCD,GOODFLAG,GOODNM,GOODHNGNM,GOODENGNM,GOODSPEC,GOODMODEL,ASETFLAG,LRGCD,MDLCD,SMLCD,EDICD,PRODCMPYCD,CMT,FSTRGSTRID,FSTRGSTDT,LASTUPDTRID,LASTUPDTDT,APPINSTDATA,MNGTFLAG) " + "VALUES ( ?,SUBSTR(?,1,1),?,?,?,?,NULL,'1',substr(?,2,2),substr(?,4,3),NULL,NULL,NULL,'OCS �����빰ǰ','MISASIS',TO_DATE('20111231','YYYYMMDD'),'MISASIS',TO_DATE('20111231','YYYYMMDD'),NULL,'N')"); int count = 0; String goodcd = null; String goodnm = null; while (rs.next()) { count++; goodcd = rs.getString("PUM_CODE").toUpperCase(); goodnm = rs.getString("PUM_HNAME"); StringUtils.trimWhitespace(goodnm); if (goodnm == null || goodnm.equals("")) goodnm = "-"; pstmt.setString(1, goodcd); pstmt.setString(2, goodcd); pstmt.setString(3, goodnm); pstmt.setString(4, goodnm); pstmt.setString(5, rs.getString("PUM_ENAME")); pstmt.setString(6, rs.getString("KYUKYEOK")); pstmt.setString(7, goodcd); pstmt.setString(8, goodcd); pstmt.executeUpdate(); if (count % 100 == 0) System.out.println("Copy Row : " + count); } System.out.println("Commit Copy Rows : " + count); con2.commit(); } catch (Exception e) { try { con2.rollback(); } catch (Exception ee) { ee.printStackTrace(); } e.printStackTrace(); } finally { try { if (rs != null) rs.close(); if (stmt != null) stmt.close(); if (con != null) con.close(); if (con2 != null) con2.close(); } catch (Exception e) { e.printStackTrace(); } } } | 884,956 |
1 | private static void readAndWriteFile(File source, File target) { try { FileInputStream in = new FileInputStream(source); FileOutputStream out = new FileOutputStream(target); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (Exception e) { } } | protected final void loadLogFile(String filename) throws IOException { cleanUp(true, false); InputStream is = null; OutputStream os = null; File f = File.createTempFile("log", null); try { is = getClass().getResourceAsStream(filename); Assert.isTrue(is != null, "File not found: " + filename); os = new FileOutputStream(f); IOUtils.copy(is, os); setLogFile(f); } finally { IOUtils.closeQuietly(is); IOUtils.closeQuietly(os); } } | 884,957 |
1 | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | public static void copyFile(File src, File dest, boolean notifyUserOnError) { if (src.exists()) { try { BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); BufferedInputStream in = new BufferedInputStream(new FileInputStream(src)); byte[] read = new byte[128]; int len = 128; while ((len = in.read(read)) > 0) out.write(read, 0, len); out.flush(); out.close(); in.close(); } catch (IOException e) { String message = "Error while copying " + src.getAbsolutePath() + " to " + dest.getAbsolutePath() + " : " + e.getMessage(); if (notifyUserOnError) { Log.getInstance(SystemUtils.class).warnWithUserNotification(message); } else { Log.getInstance(SystemUtils.class).warn(message); } } } else { String message = "Unable to copy file: source does not exists: " + src.getAbsolutePath(); if (notifyUserOnError) { Log.getInstance(SystemUtils.class).warnWithUserNotification(message); } else { Log.getInstance(SystemUtils.class).warn(message); } } } | 884,958 |
1 | public String get(String question) { try { System.out.println(url + question); URL urlonlineserver = new URL(url + question); BufferedReader in = new BufferedReader(new InputStreamReader(urlonlineserver.openStream())); String inputLine; String returnstring = ""; while ((inputLine = in.readLine()) != null) returnstring += inputLine; in.close(); return returnstring; } catch (IOException e) { return ""; } } | public static List<String> list() throws IOException { List<String> providers = new ArrayList<String>(); Enumeration<URL> urls = ClassLoader.getSystemResources("sentrick.classifiers"); while (urls.hasMoreElements()) { URL url = urls.nextElement(); String provider = null; BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); while ((provider = in.readLine()) != null) { provider = provider.trim(); if (provider.length() > 0) providers.add(provider); } in.close(); } return providers; } | 884,959 |
0 | public static void copyFiles(String strPath, String dstPath) throws IOException { File src = new File(strPath); File dest = new File(dstPath); if (src.isDirectory()) { dest.mkdirs(); String list[] = src.list(); for (int i = 0; i < list.length; i++) { String dest1 = dest.getAbsolutePath() + File.separatorChar + list[i]; String src1 = src.getAbsolutePath() + File.separatorChar + list[i]; copyFiles(src1, dest1); } } else { FileInputStream fin = new FileInputStream(src); FileOutputStream fout = new FileOutputStream(dest); int c; while ((c = fin.read()) >= 0) fout.write(c); fin.close(); fout.close(); } } | protected static void download(FtpSiteConnector connector, File localFile, String remotePath, final IProgressMonitor monitor) throws FtpException { if (!localFile.exists()) { FTPClient ftp = new FTPClient(); try { FTPClientConfig conf = new FTPClientConfig(FTPClientConfig.SYST_UNIX); ftp.configure(conf); String hostname = connector.getUrl().getHost(); ftp.connect(hostname); log.info("Connected to " + hostname); log.info(ftp.getReplyString()); boolean loggedIn = ftp.login(connector.getUsername(), connector.getPassword()); if (loggedIn) { log.info("downloading file: " + remotePath); ftp.setFileTransferMode(FTPClient.BINARY_FILE_TYPE); ftp.setFileType(FTPClient.BINARY_FILE_TYPE); ftp.enterLocalPassiveMode(); final long fileSize = getFileSize(ftp, remotePath); FileOutputStream dfile = new FileOutputStream(localFile); ftp.retrieveFile(remotePath, dfile, new CopyStreamListener() { public int worked = 0; public void bytesTransferred(long totalBytesTransferred, int bytesTransferred, long streamSize) { int percent = percent(fileSize, totalBytesTransferred); int delta = percent - worked; if (delta > 0) { if (monitor != null) { monitor.worked(delta); } worked = percent; } } public void bytesTransferred(CopyStreamEvent event) { } private int percent(long totalBytes, long totalBytesTransferred) { long percent = (totalBytesTransferred * 100) / totalBytes; return Long.valueOf(percent).intValue(); } }); dfile.flush(); dfile.close(); ftp.logout(); } else { throw new FtpException("Invalid login"); } ftp.disconnect(); } catch (SocketException e) { log.error("File download failed with message: " + e.getMessage()); throw new FtpException("File download failed with message: " + e.getMessage()); } catch (IOException e) { log.error("File download failed with message: " + e.getMessage()); throw new FtpException("File download failed with message: " + e.getMessage()); } finally { if (ftp.isConnected()) { try { ftp.disconnect(); } catch (IOException ioe) { throw new FtpException("File download failed with message: " + ioe.getMessage()); } } } } } | 884,960 |
0 | public static void downloadFile(String url, String filePath) throws IOException { BufferedInputStream inputStream = new BufferedInputStream(new URL(url).openStream()); BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(filePath)); try { int i = 0; while ((i = inputStream.read()) != -1) { bos.write(i); } } finally { if (inputStream != null) { inputStream.close(); } if (bos != null) { bos.close(); } } } | public static String getUserPass(String user) throws NoSuchAlgorithmException { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(user.getBytes()); byte[] hash = digest.digest(); System.out.println("Returning user pass:" + hash); return hash.toString(); } | 884,961 |
0 | public static void copy(String sourceName, String destName, StatusWindow status) throws IOException { File src = new File(sourceName); File dest = new File(destName); BufferedInputStream source = null; BufferedOutputStream destination = null; byte[] buffer; int bytes_read; long byteCount = 0; if (!src.exists()) throw new IOException("Source not found: " + src); if (!src.canRead()) throw new IOException("Source is unreadable: " + src); if (src.isFile()) { if (!dest.exists()) { File parentdir = Utils.parent(dest); if (!parentdir.exists()) parentdir.mkdir(); } else if (dest.isDirectory()) { if (src.isDirectory()) dest = new File(dest + File.separator + src); else dest = new File(dest + File.separator + src.getName()); } } else if (src.isDirectory()) { if (dest.isFile()) throw new IOException("Cannot copy directory " + src + " to file " + dest); if (!dest.exists()) dest.mkdir(); } if ((!dest.canWrite()) && (dest.exists())) throw new IOException("Destination is unwriteable: " + dest); if (src.isFile()) { try { if (status != null) { status.setMaximum(100); status.setMessage(Utils.trimFileName(src.toString(), 40), 50); } source = new BufferedInputStream(new FileInputStream(src)); destination = new BufferedOutputStream(new FileOutputStream(dest)); buffer = new byte[4096]; byteCount = 0; while (true) { bytes_read = source.read(buffer); if (bytes_read == -1) break; destination.write(buffer, 0, bytes_read); byteCount = byteCount + bytes_read; } } finally { if (status != null) { status.setMessage(Utils.trimFileName(src.toString(), 40), 100); } if (source != null) source.close(); if (destination != null) destination.close(); } } else if (src.isDirectory()) { String targetfile, target, targetdest; String[] files = src.list(); if (status != null) { status.setMaximum(files.length); } for (int i = 0; i < files.length; i++) { if (status != null) { status.setMessage(Utils.trimFileName(src.toString(), 40), i); } targetfile = files[i]; target = src + File.separator + targetfile; targetdest = dest + File.separator + targetfile; if ((new File(target)).isDirectory()) { copy(new File(target).getCanonicalPath(), new File(targetdest).getCanonicalPath(), status); } else { try { byteCount = 0; source = new BufferedInputStream(new FileInputStream(target)); destination = new BufferedOutputStream(new FileOutputStream(targetdest)); buffer = new byte[4096]; while (true) { bytes_read = source.read(buffer); if (bytes_read == -1) break; destination.write(buffer, 0, bytes_read); byteCount = byteCount + bytes_read; } } finally { if (source != null) source.close(); if (destination != null) destination.close(); } } } } } | private boolean verifyPassword(String password, byte[] hash) { boolean returnValue = false; try { MessageDigest msgDigest = MessageDigest.getInstance("SHA-1"); msgDigest.update(password.getBytes("UTF-8")); byte[] digest = msgDigest.digest(); returnValue = Arrays.equals(hash, digest); } catch (UnsupportedEncodingException ex) { Logger.getLogger(AuthentificationState.class.getName()).log(Level.SEVERE, null, ex); } catch (NoSuchAlgorithmException ex) { Logger.getLogger(AuthentificationState.class.getName()).log(Level.SEVERE, null, ex); } return returnValue; } | 884,962 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public static void compress(final File zip, final Map<InputStream, String> entries) throws IOException { if (zip == null || entries == null || CollectionUtils.isEmpty(entries.keySet())) throw new IllegalArgumentException("One ore more parameters are empty!"); if (zip.exists()) zip.delete(); else if (!zip.getParentFile().exists()) zip.getParentFile().mkdirs(); ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(zip))); out.setLevel(Deflater.BEST_COMPRESSION); InputStream in = null; try { for (InputStream inputStream : entries.keySet()) { in = inputStream; ZipEntry zipEntry = new ZipEntry(skipBeginningSlash(entries.get(in))); out.putNextEntry(zipEntry); IOUtils.copy(in, out); out.closeEntry(); in.close(); } } finally { IOUtils.closeQuietly(in); IOUtils.closeQuietly(out); } } | 884,963 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public static void copyFile(String fromPath, String toPath) { try { File inputFile = new File(fromPath); String dirImg = (new File(toPath)).getParent(); File tmp = new File(dirImg); if (!tmp.exists()) { tmp.mkdir(); } File outputFile = new File(toPath); if (!inputFile.getCanonicalPath().equals(outputFile.getCanonicalPath())) { FileInputStream in = new FileInputStream(inputFile); FileOutputStream out = new FileOutputStream(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } } catch (Exception ex) { ex.printStackTrace(); LogHandler.log(ex.getMessage(), Level.INFO, "LOG_MSG", isLoggingEnabled()); } } | 884,964 |
1 | public static int[] BubbleSortDEC(int[] values) { boolean change = true; int aux; int[] indexes = new int[values.length]; for (int i = 0; i < values.length; i++) { indexes[i] = i; } while (change) { change = false; for (int i = 0; i < values.length - 1; i++) { if (values[i] < values[i + 1]) { aux = values[i]; values[i] = values[i + 1]; values[i + 1] = aux; aux = indexes[i]; indexes[i] = indexes[i + 1]; indexes[i + 1] = aux; change = true; } } } return (indexes); } | public int[] bubbleSort(int[] data) { for (int i = 0; i < data.length; i++) { for (int j = 0; j < data.length - i - 1; j++) { if (data[j] > data[j + 1]) { int temp = data[j]; data[j] = data[j + 1]; data[j + 1] = temp; } } } return data; } | 884,965 |
0 | private void doIt() throws Throwable { GenericDAO<User> dao = DAOFactory.createDAO(User.class); try { final User user = dao.findUniqueByCriteria(Expression.eq("login", login)); if (user == null) throw new IllegalArgumentException("Specified user isn't exist"); if (srcDir.isDirectory() && srcDir.exists()) { final String[] fileList = srcDir.list(new XFilenameFilter() { public boolean accept(XFile dir, String file) { String[] fNArr = file.split("\\."); return (fNArr.length > 1 && (fNArr[fNArr.length - 1].equalsIgnoreCase("map") || fNArr[fNArr.length - 1].equalsIgnoreCase("plt") || fNArr[fNArr.length - 1].equalsIgnoreCase("wpt"))); } }); int pointsCounter = 0; int tracksCounter = 0; int mapsCounter = 0; for (final String fName : fileList) { try { TransactionManager.beginTransaction(); } catch (Throwable e) { logger.error(e); throw e; } final XFile file = new XFile(srcDir, fName); InputStream in = new XFileInputStream(file); try { ArrayList<UserMapOriginal> maps = new ArrayList<UserMapOriginal>(); ArrayList<MapTrackPointsScaleRequest> tracks = new ArrayList<MapTrackPointsScaleRequest>(); final byte[] headerBuf = new byte[1024]; if (in.read(headerBuf) <= 0) continue; final String fileHeader = new String(headerBuf); final boolean isOziWPT = (fileHeader.indexOf("OziExplorer Waypoint File") >= 0); final boolean isOziPLT = (fileHeader.indexOf("OziExplorer Track Point File") >= 0); final boolean isOziMAP = (fileHeader.indexOf("OziExplorer Map Data File") >= 0); final boolean isKML = (fileHeader.indexOf("<kml xmlns=") >= 0); if (isOziMAP || isOziPLT || isOziWPT || isKML) { in.close(); in = new XFileInputStream(file); } else continue; WPTPoint wp; if (isOziWPT) { try { wp = new WPTPointParser(in, "Cp1251").parse(); } catch (Throwable t) { wp = null; } if (wp != null) { Set<WayPointRow> rows = wp.getPoints(); for (WayPointRow row : rows) { final UserMapPoint p = BeanFactory.createUserPoint(row, user); logger.info("point:" + p.getGuid()); } pointsCounter += rows.size(); } } else if (isOziPLT) { PLTTrack plt; try { plt = new PLTTrackParser(in, "Cp1251").parse(); } catch (Throwable t) { plt = null; } if (plt != null) { final UserMapTrack t = BeanFactory.createUserTrack(plt, user); tracks.add(new MapTrackPointsScaleRequest(t)); tracksCounter++; logger.info("track:" + t.getGuid()); } } else if (isOziMAP) { MapProjection projection; MAPParser parser = new MAPParser(in, "Cp1251"); try { projection = parser.parse(); } catch (Throwable t) { projection = null; } if (projection != null && projection.getPoints() != null && projection.getPoints().size() >= 2) { GenericDAO<UserMapOriginal> mapDao = DAOFactory.createDAO(UserMapOriginal.class); final UserMapOriginal mapOriginal = new UserMapOriginal(); mapOriginal.setName(projection.getTitle()); mapOriginal.setUser(user); mapOriginal.setState(UserMapOriginal.State.UPLOAD); mapOriginal.setSubstate(UserMapOriginal.SubState.COMPLETE); MapManager.updateProjection(projection, mapOriginal); final XFile srcFile = new XFile(srcDir, projection.getPath()); if (!srcFile.exists() || !srcFile.isFile()) throw new IllegalArgumentException("file: " + srcFile.getPath() + " not found"); final XFile mapStorage = new XFile(new XFile(Configuration.getInstance().getPrivateMapStorage().toString()), mapOriginal.getGuid()); mapStorage.mkdir(); XFile dstFile = new XFile(mapStorage, mapOriginal.getGuid()); XFileOutputStream out = new XFileOutputStream(dstFile); XFileInputStream inImg = new XFileInputStream(srcFile); IOUtils.copy(inImg, out); out.flush(); out.close(); inImg.close(); mapDao.save(mapOriginal); maps.add(mapOriginal); srcFile.delete(); mapsCounter++; logger.info("map:" + mapOriginal.getGuid()); } } else logger.warn("unsupported file format: " + file.getName()); TransactionManager.commitTransaction(); for (MapTrackPointsScaleRequest track : tracks) { if (track != null) { try { PoolClientInterface pool = PoolFactory.getInstance().getClientPool(); if (pool == null) throw new IllegalStateException("pool not found"); pool.put(track, new StatesStack(new byte[] { 0x00, 0x11 }), GeneralCompleteStrategy.class); } catch (Throwable t) { logger.error(t); } } } } catch (Throwable e) { logger.error("Error importing", e); TransactionManager.rollbackTransaction(); } finally { in.close(); file.delete(); } } logger.info("waypoints: " + pointsCounter + "\ntracks: " + tracksCounter + "\nmaps: " + mapsCounter); } } catch (Throwable e) { logger.error("Error importing", e); } } | private static String getRegistrationClasses() { CentralRegistrationClass c = new CentralRegistrationClass(); String name = c.getClass().getCanonicalName().replace('.', '/').concat(".class"); try { Enumeration<URL> urlEnum = c.getClass().getClassLoader().getResources("META-INF/MANIFEST.MF"); while (urlEnum.hasMoreElements()) { URL url = urlEnum.nextElement(); String file = url.getFile(); JarURLConnection jarConnection = (JarURLConnection) url.openConnection(); Manifest mf = jarConnection.getManifest(); Attributes attrs = (Attributes) mf.getAttributes(name); if (attrs != null) { String classes = attrs.getValue("RegistrationClasses"); return classes; } } } catch (IOException ex) { ex.printStackTrace(); } return ""; } | 884,966 |
1 | public void testStorageByteArray() throws Exception { TranslationResponseInMemory r = new TranslationResponseInMemory(2048, "UTF-8"); { OutputStream output = r.getOutputStream(); output.write("This is an example".getBytes("UTF-8")); output.write(" and another one.".getBytes("UTF-8")); assertEquals("This is an example and another one.", r.getText()); } { InputStream input = r.getInputStream(); StringWriter writer = new StringWriter(); try { IOUtils.copy(input, writer, "UTF-8"); } finally { input.close(); writer.close(); } assertEquals("This is an example and another one.", writer.toString()); } { OutputStream output = r.getOutputStream(); output.write(" and another line".getBytes("UTF-8")); assertEquals("This is an example and another one. and another line", r.getText()); } { Writer output = r.getWriter(); output.write(" and write some more"); assertEquals("This is an example and another one. and another line and write some more", r.getText()); } { r.addText(" and even more."); assertEquals("This is an example and another one. and another line and write some more and even more.", r.getText()); } assertFalse(r.hasEnded()); r.setEndState(ResponseStateOk.getInstance()); assertTrue(r.hasEnded()); try { r.getOutputStream(); fail("Previous line should throw IOException as result closed."); } catch (IOException e) { } try { r.getWriter(); fail("Previous line should throw IOException as result closed."); } catch (IOException e) { } } | public static void main(String[] args) throws Exception { String localSrc = args[0]; String dst = args[1]; InputStream in = new BufferedInputStream(new FileInputStream(localSrc)); Configuration conf = new Configuration(); FileSystem fs = FileSystem.get(URI.create(dst), conf); OutputStream out = fs.create(new Path(dst), new Progressable() { public void progress() { System.out.print("."); } }); IOUtils.copyBytes(in, out, 4096, true); } | 884,967 |
1 | public BufferedWriter createOutputStream(String inFile, String outFile) throws IOException { int k_blockSize = 1024; int byteCount; char[] buf = new char[k_blockSize]; File ofp = new File(outFile); ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(ofp)); zos.setMethod(ZipOutputStream.DEFLATED); OutputStreamWriter osw = new OutputStreamWriter(zos, "ISO-8859-1"); BufferedWriter bw = new BufferedWriter(osw); ZipEntry zot = null; File ifp = new File(inFile); ZipInputStream zis = new ZipInputStream(new FileInputStream(ifp)); InputStreamReader isr = new InputStreamReader(zis, "ISO-8859-1"); BufferedReader br = new BufferedReader(isr); ZipEntry zit = null; while ((zit = zis.getNextEntry()) != null) { if (zit.getName().equals("content.xml")) { continue; } zot = new ZipEntry(zit.getName()); zos.putNextEntry(zot); while ((byteCount = br.read(buf, 0, k_blockSize)) >= 0) bw.write(buf, 0, byteCount); bw.flush(); zos.closeEntry(); } zos.putNextEntry(new ZipEntry("content.xml")); bw.flush(); osw = new OutputStreamWriter(zos, "UTF8"); bw = new BufferedWriter(osw); return bw; } | public 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(); } } | 884,968 |
0 | public static boolean update(Orgao orgao) { int result = 0; Connection c = DBConnection.getConnection(); PreparedStatement pst = null; if (c == null) { return false; } try { c.setAutoCommit(false); String sql = "update orgao set nome = (?) where id_orgao= ?"; pst = c.prepareStatement(sql); pst.setString(1, orgao.getNome()); pst.setInt(2, orgao.getCodigo()); result = pst.executeUpdate(); c.commit(); } catch (SQLException e) { try { c.rollback(); } catch (SQLException e1) { e1.printStackTrace(); } System.out.println("[OrgaoDAO.update] Erro ao atualizar -> " + e.getMessage()); } finally { DBConnection.closePreparedStatement(pst); DBConnection.closeConnection(c); } if (result > 0) { return true; } else { return false; } } | public static void copyResource(String args) { try { URL url = copyURL.class.getResource(args); InputStream is = url.openStream(); System.out.flush(); FileOutputStream fos = null; fos = new FileOutputStream(System.getProperty("user.home") + "/JavaCPC/" + args); int oneChar, count = 0; while ((oneChar = is.read()) != -1) { fos.write(oneChar); count++; } is.close(); fos.close(); } catch (MalformedURLException e) { System.err.println(e.toString()); } catch (IOException e) { System.err.println(e.toString()); } } | 884,969 |
0 | public void bubbleSort(int[] arr) { BasicProcessor.getInstance().getStartBlock(); BasicProcessor.getInstance().getVarDeclaration(); boolean swapped = true; BasicProcessor.getInstance().getVarDeclaration(); int j = 0; BasicProcessor.getInstance().getVarDeclaration(); int tmp; { BasicProcessor.getInstance().getWhileStatement(); while (swapped) { BasicProcessor.getInstance().getStartBlock(); swapped = false; j++; { BasicProcessor.getInstance().getForStatement(); for (int i = 0; i < arr.length - j; i++) { BasicProcessor.getInstance().getStartBlock(); { BasicProcessor.getInstance().getIfStatement(); if (arr[i] > arr[i + 1]) { BasicProcessor.getInstance().getStartBlock(); tmp = arr[i]; arr[i] = arr[i + 1]; arr[i + 1] = tmp; swapped = true; BasicProcessor.getInstance().getEndBlock(); } } BasicProcessor.getInstance().getEndBlock(); } } BasicProcessor.getInstance().getEndBlock(); } } BasicProcessor.getInstance().getEndBlock(); } | public boolean uploadFromServlet(InputStream is, String serverFileName, String serverPath, String serverUrl, int serverPort, String userName, String passWord) throws IOException { FTPClient ftp = new FTPClient(); FTPClientConfig conf = new FTPClientConfig(); conf.setServerLanguageCode("zh_CN"); conf.setServerTimeZoneId("Asia/Chongqing"); try { ftp.configure(conf); int reply; ftp.setDefaultPort(serverPort); ftp.connect(serverUrl); reply = ftp.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftp.disconnect(); throw new IOException("FTP server refused connection."); } } catch (IOException e) { disconnectFtp(ftp); } try { if (!ftp.login(userName, passWord)) { throw new IOException("Can not log in with given username and password."); } if (!ftp.changeWorkingDirectory(serverPath)) { throw new IOException("Can not change to working directory."); } ftp.setFileType(FTP.BINARY_FILE_TYPE); if (!ftp.storeFile(serverFileName, is)) { throw new IOException("Can not store file to FTP server."); } is.close(); } catch (SocketException e) { e.printStackTrace(); return false; } catch (IOException e) { e.printStackTrace(); return false; } finally { if (ftp != null && ftp.isConnected()) { try { ftp.logout(); ftp.disconnect(); } catch (IOException e) { e.printStackTrace(); return false; } } } return true; } | 884,970 |
1 | public static byte[] expandPasswordToKey(String password, int keyLen, byte[] salt) { try { MessageDigest md5 = MessageDigest.getInstance("MD5"); int digLen = md5.getDigestLength(); byte[] mdBuf = new byte[digLen]; byte[] key = new byte[keyLen]; int cnt = 0; while (cnt < keyLen) { if (cnt > 0) { md5.update(mdBuf); } md5.update(password.getBytes()); md5.update(salt); md5.digest(mdBuf, 0, digLen); int n = ((digLen > (keyLen - cnt)) ? keyLen - cnt : digLen); System.arraycopy(mdBuf, 0, key, cnt, n); cnt += n; } return key; } catch (Exception e) { throw new Error("Error in SSH2KeyPairFile.expandPasswordToKey: " + e); } } | public static final String getHash(int iterationNb, String password, String salt) { try { MessageDigest digest = MessageDigest.getInstance("SHA-1"); digest.reset(); digest.update(salt.getBytes("UTF-8")); byte[] input = digest.digest(password.getBytes("UTF-8")); for (int i = 0; i < iterationNb; i++) { digest.reset(); input = digest.digest(input); } String hashedValue = encoder.encode(input); LOG.finer("Creating hash '" + hashedValue + "' with iterationNb '" + iterationNb + "' and password '" + password + "' and salt '" + salt + "'!!"); return hashedValue; } catch (Exception ex) { ex.printStackTrace(); throw new RuntimeException("Problem in the getHash method.", ex); } } | 884,971 |
1 | @Override public CasAssembly build() { try { prepareForBuild(); File casWorkingDirectory = casFile.getParentFile(); DefaultCasFileReadIndexToContigLookup read2contigMap = new DefaultCasFileReadIndexToContigLookup(); AbstractDefaultCasFileLookup readIdLookup = new DefaultReadCasFileLookup(casWorkingDirectory); CasParser.parseOnlyMetaData(casFile, MultipleWrapper.createMultipleWrapper(CasFileVisitor.class, read2contigMap, readIdLookup)); ReadWriteDirectoryFileServer consedOut = DirectoryFileServer.createReadWriteDirectoryFileServer(commandLine.getOptionValue("o")); long startTime = DateTimeUtils.currentTimeMillis(); int numberOfCasContigs = read2contigMap.getNumberOfContigs(); for (long i = 0; i < numberOfCasContigs; i++) { File outputDir = consedOut.createNewDir("" + i); Command aCommand = new Command(new File("fakeCommand")); aCommand.setOption("-casId", "" + i); aCommand.setOption("-cas", commandLine.getOptionValue("cas")); aCommand.setOption("-o", outputDir.getAbsolutePath()); aCommand.setOption("-tempDir", tempDir.getAbsolutePath()); aCommand.setOption("-prefix", "temp"); if (commandLine.hasOption("useIllumina")) { aCommand.addFlag("-useIllumina"); } if (commandLine.hasOption("useClosureTrimming")) { aCommand.addFlag("-useClosureTrimming"); } if (commandLine.hasOption("trim")) { aCommand.setOption("-trim", commandLine.getOptionValue("trim")); } if (commandLine.hasOption("trimMap")) { aCommand.setOption("-trimMap", commandLine.getOptionValue("trimMap")); } if (commandLine.hasOption("chromat_dir")) { aCommand.setOption("-chromat_dir", commandLine.getOptionValue("chromat_dir")); } submitSingleCasAssemblyConversion(aCommand); } waitForAllAssembliesToFinish(); int numContigs = 0; int numReads = 0; for (int i = 0; i < numberOfCasContigs; i++) { File countMap = consedOut.getFile(i + "/temp.counts"); Scanner scanner = new Scanner(countMap); if (!scanner.hasNextInt()) { throw new IllegalStateException("single assembly conversion # " + i + " did not complete"); } numContigs += scanner.nextInt(); numReads += scanner.nextInt(); scanner.close(); } System.out.println("num contigs =" + numContigs); System.out.println("num reads =" + numReads); consedOut.createNewDir("edit_dir"); consedOut.createNewDir("phd_dir"); String prefix = commandLine.hasOption("prefix") ? commandLine.getOptionValue("prefix") : DEFAULT_PREFIX; OutputStream masterAceOut = new FileOutputStream(consedOut.createNewFile("edit_dir/" + prefix + ".ace.1")); OutputStream masterPhdOut = new FileOutputStream(consedOut.createNewFile("phd_dir/" + prefix + ".phd.ball")); OutputStream masterConsensusOut = new FileOutputStream(consedOut.createNewFile(prefix + ".consensus.fasta")); OutputStream logOut = new FileOutputStream(consedOut.createNewFile(prefix + ".log")); try { masterAceOut.write(String.format("AS %d %d%n", numContigs, numReads).getBytes()); for (int i = 0; i < numberOfCasContigs; i++) { InputStream aceIn = consedOut.getFileAsStream(i + "/temp.ace"); IOUtils.copy(aceIn, masterAceOut); InputStream phdIn = consedOut.getFileAsStream(i + "/temp.phd"); IOUtils.copy(phdIn, masterPhdOut); InputStream consensusIn = consedOut.getFileAsStream(i + "/temp.consensus.fasta"); IOUtils.copy(consensusIn, masterConsensusOut); IOUtil.closeAndIgnoreErrors(aceIn, phdIn, consensusIn); File tempDir = consedOut.getFile(i + ""); IOUtil.recursiveDelete(tempDir); } consedOut.createNewSymLink("../phd_dir/" + prefix + ".phd.ball", "edit_dir/phd.ball"); if (commandLine.hasOption("chromat_dir")) { consedOut.createNewDir("chromat_dir"); File originalChromatDir = new File(commandLine.getOptionValue("chromat_dir")); for (File chromat : originalChromatDir.listFiles(new FilenameFilter() { @Override public boolean accept(File dir, String name) { return name.endsWith(".scf"); } })) { File newChromatFile = consedOut.createNewFile("chromat_dir/" + FilenameUtils.getBaseName(chromat.getName())); FileOutputStream newChromat = new FileOutputStream(newChromatFile); InputStream in = new FileInputStream(chromat); IOUtils.copy(in, newChromat); IOUtil.closeAndIgnoreErrors(in, newChromat); } } System.out.println("finished making casAssemblies"); for (File traceFile : readIdLookup.getFiles()) { final String name = traceFile.getName(); String extension = FilenameUtils.getExtension(name); if (name.contains("fastq")) { if (!consedOut.contains("solexa_dir")) { consedOut.createNewDir("solexa_dir"); } if (consedOut.contains("solexa_dir/" + name)) { IOUtil.delete(consedOut.getFile("solexa_dir/" + name)); } consedOut.createNewSymLink(traceFile.getAbsolutePath(), "solexa_dir/" + name); } else if ("sff".equals(extension)) { if (!consedOut.contains("sff_dir")) { consedOut.createNewDir("sff_dir"); } if (consedOut.contains("sff_dir/" + name)) { IOUtil.delete(consedOut.getFile("sff_dir/" + name)); } consedOut.createNewSymLink(traceFile.getAbsolutePath(), "sff_dir/" + name); } } long endTime = DateTimeUtils.currentTimeMillis(); logOut.write(String.format("took %s%n", new Period(endTime - startTime)).getBytes()); } finally { IOUtil.closeAndIgnoreErrors(masterAceOut, masterPhdOut, masterConsensusOut, logOut); } } catch (Exception e) { handleException(e); } finally { cleanup(); } return null; } | @Override protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException { String requestURI = req.getRequestURI(); logger.info("The requested URI: {}", requestURI); String parameter = requestURI.substring(requestURI.lastIndexOf(ARXIVID_ENTRY) + ARXIVID_ENTRY_LENGTH); int signIndex = parameter.indexOf(StringUtil.ARXIVID_SEGMENTID_DELIMITER); String arxivId = signIndex != -1 ? parameter.substring(0, signIndex) : parameter; String segmentId = signIndex != -1 ? parameter.substring(signIndex + 1) : null; if (arxivId == null) { logger.error("The request with an empty arxiv id parameter"); return; } String filePath = segmentId == null ? format("/opt/mocassin/aux-pdf/%s" + StringUtil.arxivid2filename(arxivId, "pdf")) : "/opt/mocassin/pdf/" + StringUtil.segmentid2filename(arxivId, Integer.parseInt(segmentId), "pdf"); if (!new File(filePath).exists()) { filePath = format("/opt/mocassin/aux-pdf/%s", StringUtil.arxivid2filename(arxivId, "pdf")); } try { FileInputStream fileInputStream = new FileInputStream(filePath); ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(); IOUtils.copy(fileInputStream, byteArrayOutputStream); resp.setContentType("application/pdf"); resp.setHeader("Content-disposition", String.format("attachment; filename=%s", StringUtil.arxivid2filename(arxivId, "pdf"))); ServletOutputStream outputStream = resp.getOutputStream(); outputStream.write(byteArrayOutputStream.toByteArray()); outputStream.close(); } catch (FileNotFoundException e) { logger.error("Error while downloading: PDF file= '{}' not found", filePath); } catch (IOException e) { logger.error("Error while downloading the PDF file", e); } } | 884,972 |
0 | public static String generateMD5(String clear) { byte hash[] = null; try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(clear.getBytes()); hash = md5.digest(); } catch (NoSuchAlgorithmException e) { } if (hash != null) { StringBuffer hexString = new StringBuffer(); for (int i = 0; i < hash.length; i++) { String tmp = Integer.toHexString(0xFF & hash[i]); if (tmp.length() == 1) { tmp = "0" + tmp; } hexString.append(tmp); } return hexString.toString(); } else { return null; } } | @Override public Object getImage(String key) { if (key.indexOf("exhibition/") != -1) { InputStream inputStream = null; try { URL url = new URL(getBaseURL() + "icons/" + key + ".png"); inputStream = url.openStream(); return url; } catch (Exception e) { } finally { if (inputStream != null) { try { inputStream.close(); } catch (IOException e) { ExceptionHandlingService.INSTANCE.handleException(e); } } } } return super.getImage(key); } | 884,973 |
0 | public static String getWhatsNew(String ver) { URL url = null; try { url = new URL("http://googlemeupdate.bravehost.com/History.htm"); } catch (MalformedURLException ex) { ex.printStackTrace(); } InputStream html = null; try { html = url.openStream(); int c = 0; String Buffer = ""; String Code = ""; while (c != -1) { try { c = html.read(); } catch (IOException ex) { } Buffer = Buffer + (char) c; } Buffer = Buffer.substring(Buffer.lastIndexOf(ver) + ver.length() + 2, Buffer.indexOf("end::")).replaceAll("||", ""); return "<html>" + Buffer.substring(Buffer.indexOf("Google.mE Version: ")); } catch (IOException ex) { ex.printStackTrace(); return ""; } } | public static String digest(String algorithm, String text) { MessageDigest mDigest = null; try { mDigest = MessageDigest.getInstance(algorithm); mDigest.update(text.getBytes(ENCODING)); } catch (NoSuchAlgorithmException nsae) { _log.error(nsae, nsae); } catch (UnsupportedEncodingException uee) { _log.error(uee, uee); } byte[] raw = mDigest.digest(); BASE64Encoder encoder = new BASE64Encoder(); return encoder.encode(raw); } | 884,974 |
0 | public boolean delwuliao(String pid) { boolean flag = false; Connection conn = null; PreparedStatement pm = null; try { conn = Pool.getConnection(); conn.setAutoCommit(false); pm = conn.prepareStatement("delete from addwuliao where pid=?"); pm.setString(1, pid); int x = pm.executeUpdate(); if (x == 0) { flag = false; } else { flag = true; } conn.commit(); Pool.close(pm); Pool.close(conn); } catch (Exception e) { e.printStackTrace(); flag = false; try { conn.rollback(); } catch (SQLException e1) { e1.printStackTrace(); } Pool.close(pm); Pool.close(conn); } finally { Pool.close(pm); Pool.close(conn); } return flag; } | public void updateCoordinates(Address address) { String mapURL = "http://maps.google.com/maps/geo?output=csv"; String mapKey = "ABQIAAAAi__aT6y6l86JjbootR-p9xQd1nlEHNeAVGWQhS84yIVN5yGO2RQQPg9QLzy82PFlCzXtMNe6ofKjnA"; String location = address.getStreet() + " " + address.getZip() + " " + address.getCity(); if (logger.isDebugEnabled()) { logger.debug(location); } double[] coordinates = { 0.0, 0.0 }; String content = ""; try { location = URLEncoder.encode(location, "UTF-8"); String request = mapURL + "&q=" + location + "&key=" + mapKey; URL url = new URL(request); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = reader.readLine()) != null) { content += line; } reader.close(); } catch (Exception e) { if (logger.isDebugEnabled()) { logger.debug("Error from google: " + e.getMessage()); } } if (logger.isDebugEnabled()) { logger.debug(content); } StringTokenizer tokenizer = new StringTokenizer(content, ","); int i = 0; while (tokenizer.hasMoreTokens()) { i++; String token = tokenizer.nextToken(); if (i == 3) { coordinates[0] = Double.parseDouble(token); } if (i == 4) { coordinates[1] = Double.parseDouble(token); } } if ((coordinates[0] != 0) || (coordinates[1] != 0)) { address.setLatitude(coordinates[0]); address.setLongitude(coordinates[1]); } else { if (logger.isDebugEnabled()) { logger.debug("Invalid coordinates for address " + address.getId()); } } } | 884,975 |
1 | public void run() { String s; s = ""; try { URL url = new URL("http://www.m-w.com/dictionary/" + word); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String str; while (((str = in.readLine()) != null) && (!stopped)) { s = s + str; } in.close(); } catch (MalformedURLException e) { } catch (IOException e) { } Pattern pattern = Pattern.compile("Main Entry:.+?<br>(.+?)</td>", Pattern.CASE_INSENSITIVE | Pattern.DOTALL); Matcher matcher = pattern.matcher(s); java.io.StringWriter wr = new java.io.StringWriter(); HTMLDocument doc = null; HTMLEditorKit kit = (HTMLEditorKit) editor.getEditorKit(); try { doc = (HTMLDocument) editor.getDocument(); } catch (Exception e) { } System.out.println(wr); editor.setContentType("text/html"); if (matcher.find()) try { kit.insertHTML(doc, editor.getCaretPosition(), "<HR>" + matcher.group(1) + "<HR>", 0, 0, null); } catch (Exception e) { System.out.println(e.getMessage()); } else try { kit.insertHTML(doc, editor.getCaretPosition(), "<HR><FONT COLOR='RED'>NOT FOUND!!</FONT><HR>", 0, 0, null); } catch (Exception e) { System.out.println(e.getMessage()); } button.setEnabled(true); } | String chooseHGVersion(String version) { String line = ""; try { URL connectURL = new URL("http://genome.ucsc.edu/cgi-bin/hgGateway?db=" + version); InputStream urlStream = connectURL.openStream(); BufferedReader reader = new BufferedReader(new InputStreamReader(urlStream)); while ((line = reader.readLine()) != null) { if (line.indexOf("hgsid") != -1) { line = line.substring(line.indexOf("hgsid")); line = line.substring(line.indexOf("VALUE=\"") + 7); line = line.substring(0, line.indexOf("\"")); return line; } } } catch (Exception e) { e.printStackTrace(); } return line; } | 884,976 |
1 | @Test public void testCopy() throws IOException { final byte[] input = { 0x00, 0x01, 0x7F, 0x03, 0x40 }; final byte[] verification = input.clone(); Assert.assertNotSame("Expecting verification to be a new array.", input, verification); final ByteArrayInputStream in = new ByteArrayInputStream(input); final ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copy(in, out); final byte[] output = out.toByteArray(); Assert.assertTrue("Expecting input to be unchanged.", Arrays.equals(verification, input)); Assert.assertTrue("Expecting output to be like input.", Arrays.equals(verification, output)); Assert.assertNotSame("Expecting output to be a new array.", input, output); Assert.assertNotSame("Expecting output to be a new array.", verification, output); } | private boolean performModuleInstallation(Model m) { String seldir = directoryHandler.getSelectedDirectory(); if (seldir == null) { MessageBox box = new MessageBox(shell, SWT.ICON_WARNING | SWT.OK); box.setText("Cannot install"); box.setMessage("A target directory must be selected."); box.open(); return false; } String sjar = pathText.getText(); File fjar = new File(sjar); if (!fjar.exists()) { MessageBox box = new MessageBox(shell, SWT.ICON_WARNING | SWT.OK); box.setText("Cannot install"); box.setMessage("A non-existing jar file has been selected."); box.open(); return false; } int count = 0; try { URLClassLoader loader = new URLClassLoader(new URL[] { fjar.toURI().toURL() }); JarInputStream jis = new JarInputStream(new FileInputStream(fjar)); JarEntry entry = jis.getNextJarEntry(); while (entry != null) { String name = entry.getName(); if (name.endsWith(".class")) { name = name.substring(0, name.length() - 6); name = name.replace('/', '.'); Class<?> cls = loader.loadClass(name); if (IAlgorithm.class.isAssignableFrom(cls) && !cls.isInterface() && (cls.getModifiers() & Modifier.ABSTRACT) == 0) { if (!testAlgorithm(cls, m)) return false; count++; } } entry = jis.getNextJarEntry(); } } catch (Exception e1) { Application.logexcept("Could not load classes from jar file.", e1); return false; } if (count == 0) { MessageBox box = new MessageBox(shell, SWT.ICON_WARNING | SWT.OK); box.setText("Cannot install"); box.setMessage("There don't seem to be any algorithms in the specified module."); box.open(); return false; } try { FileChannel ic = new FileInputStream(sjar).getChannel(); FileChannel oc = new FileOutputStream(seldir + File.separator + fjar.getName()).getChannel(); ic.transferTo(0, ic.size(), oc); ic.close(); oc.close(); } catch (Exception e) { Application.logexcept("Could not install module", e); return false; } result = new Object(); return true; } | 884,977 |
0 | public static void main(String[] argv) throws IOException { Session session = HibernateUtil.getSessionFactory().getCurrentSession(); ; try { session.beginTransaction(); Properties cfg = new Properties(); URL url = SVM.class.getClassLoader().getResource(CFG_FILE); cfg.load(url.openStream()); int runMode = Integer.valueOf(cfg.getProperty(KEY_RUN_MODE)); switch(runMode) { case RUN_OPT: new SVM().optimizeParameters(cfg); break; case RUN_PREDICT: new SVM().trainAndPredict(cfg); break; case RUN_OPT_AND_PREDICT: break; } session.getTransaction().commit(); } catch (HibernateException he) { session.getTransaction().rollback(); logger.error("Database error.", he); session.close(); } } | private static void reconfigureDebug() { useFile = false; logValue = 0; String methodString = NodeUtil.walkNodeTree(Server.getConfig(), "//configuration/object[@type='engine.debug']/property[@type='engine.method']/@value"); String levelString = NodeUtil.walkNodeTree(Server.getConfig(), "//configuration/object[@type='engine.debug']/property[@type='engine.level']/@value"); String quietString = NodeUtil.walkNodeTree(Server.getConfig(), "//configuration/object[@type='engine.debug']/property[@type='engine.quiet']/@value"); String fileString = NodeUtil.walkNodeTree(Server.getConfig(), "//configuration/object[@type='engine.debug']/property[@type='engine.file']/@value"); String filemodeString = NodeUtil.walkNodeTree(Server.getConfig(), "//configuration/object[@type='engine.debug']/property[@type='engine.filemode']/@value"); String calltraceString = NodeUtil.walkNodeTree(Server.getConfig(), "//configuration/object[@type='engine.debug']/property[@type='engine.calltrace']/@value"); String rotateTimeoutString = NodeUtil.walkNodeTree(Server.getConfig(), "//configuration/object[@type='engine.debug']/property[@type='engine.rotatetimeout']/@value"); String rotateDestString = NodeUtil.walkNodeTree(Server.getConfig(), "//configuration/object[@type='engine.debug']/property[@type='engine.rotatedest']/@value"); String rotateCompressString = NodeUtil.walkNodeTree(Server.getConfig(), "//configuration/object[@type='engine.debug']/property[@type='engine.rotatecompress']/@value"); String rotateDaysString = NodeUtil.walkNodeTree(Server.getConfig(), "//configuration/object[@type='engine.debug']/property[@type='engine.rotatedays']/@value"); String rotateArchiveString = NodeUtil.walkNodeTree(Server.getConfig(), "//configuration/object[@type='engine.debug']/property[@type='engine.rotatearchive']/@value"); String rotateDeleteString = NodeUtil.walkNodeTree(Server.getConfig(), "//configuration/object[@type='engine.debug']/property[@type='engine.rotatedelete']/@value"); String dirName = "."; if (rotateTimeoutString != null) { rotateTimeout = Integer.parseInt(rotateTimeoutString); } if (rotateDestString != null) { rotateDest = rotateDestString; } if (rotateCompressString != null && rotateCompressString.equalsIgnoreCase("true")) { rotateCompress = true; } if (rotateDaysString != null) { rotateDays = Integer.parseInt(rotateDaysString); } if (rotateArchiveString != null) { rotateArchive = rotateArchiveString; } if (rotateDeleteString != null && rotateDeleteString.equalsIgnoreCase("true")) { rotateDelete = true; } if (fileString != null && fileString.indexOf("/") != -1) { dirName = fileString.substring(0, fileString.lastIndexOf("/")); (new File(dirName)).mkdirs(); } if (methodString != null) { logMethod = methodString; } else { logMethod = "file"; } if (levelString != null) { logValue = Integer.parseInt(levelString); } else { logValue = 0; } if (calltraceString != null && calltraceString.equalsIgnoreCase("true")) { calltrace = true; } else { calltrace = false; } if (logMethod == null) { logMethod = "file"; } if (quietString != null) { if (quietString.equalsIgnoreCase("true")) { beQuiet = true; } } if (logMethod != null) { if (logMethod.equalsIgnoreCase("file")) { if (fileString != null) { logFile = fileString; } else { logFile = "log.txt"; } useFile = true; } } else { System.err.println("*** A debugging method (debug.method) is required in properties file!"); System.err.println("*** Please refer to configuration documentation."); System.exit(-1); } timesRepeated = 0; lastMessage = null; if (useFile) { logfile = new File(logFile); try { if (filemodeString != null && filemodeString.equalsIgnoreCase("append")) { ps = new PrintStream(new FileOutputStream(logfile, true)); } else { ps = new PrintStream(new FileOutputStream(logfile)); } isFile = true; Calendar calendar = new GregorianCalendar(); Date date = calendar.getTime(); DateFormat format1 = new SimpleDateFormat("yyyy-MM-dd 'at' HH:mm:ss z"); ps.println(); ps.println("--- Log file opened " + format1.format(date) + " ---"); } catch (FileNotFoundException e) { System.out.println("Debug: Unable to instantiate debugger: " + e.getMessage()); System.exit(-1); } catch (Exception e) { System.out.println("Debug: Unable to instantiate debugger - internal error: " + e.getMessage()); System.exit(-1); } } if (!registeredSchedule) { registeredSchedule = true; if (Server.getScheduler() != null) { Server.getScheduler().register("Log File Rotator for '" + logFile + "'", new SchedulerInterface() { public int getScheduleRate() { if (rotateTimeout != 0) { return rotateTimeout / 10; } return 0; } public void handle() { FileChannel srcChannel, destChannel; String destOutFile = logFile + "." + System.currentTimeMillis(); String destOutFileCompressed = logFile + "." + System.currentTimeMillis() + ".gz"; if (rotateDest != null) { (new File(rotateDest)).mkdirs(); if (destOutFile.indexOf("/") != -1) { destOutFile = rotateDest + "/" + destOutFile.substring(destOutFile.lastIndexOf("/") + 1); } if (destOutFileCompressed.indexOf("/") != -1) { destOutFileCompressed = rotateDest + "/" + destOutFileCompressed.substring(destOutFileCompressed.lastIndexOf("/") + 1); } } if (rotateCompress) { try { GZIPOutputStream out = new GZIPOutputStream(new FileOutputStream(destOutFileCompressed)); FileInputStream in = new FileInputStream(logFile); byte buf[] = new byte[1024]; int len; while ((len = in.read(buf)) > 0) { out.write(buf, 0, len); } in.close(); out.finish(); out.close(); buf = null; in = null; out = null; Debug.debug("Rotated log file '" + logFile + "' to '" + destOutFileCompressed + "'"); } catch (Exception e) { Debug.debug("Unable to rotate log file '" + logFile + "': " + e); } } else { try { srcChannel = new FileInputStream(logFile).getChannel(); } catch (IOException e) { Debug.debug("Unable to read log file '" + logFile + "': " + e.getMessage()); return; } try { destChannel = new FileOutputStream(destOutFile).getChannel(); } catch (IOException e) { Debug.debug("Unable to rotate log file to '" + destOutFile + "': " + e.getMessage()); return; } try { destChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); destChannel.close(); srcChannel = null; destChannel = null; } catch (IOException e) { Debug.debug("Unable to copy data for file rotation: " + e.getMessage()); return; } Debug.debug("Rotated log file '" + logFile + "' to '" + destOutFile + "'"); } if (rotateDelete && isFile) { try { ps.close(); } catch (Exception e) { } isFile = false; ps = null; (new File(logFile)).delete(); reconfigureDebug(); } if (rotateDest != null) { long comparisonTime = rotateDays * (60 * 60 * 24 * 1000); long currentTime = System.currentTimeMillis(); File fileList[] = (new File(rotateDest)).listFiles(); DateFormat format1 = new SimpleDateFormat("yyyy-MM-dd"); java.util.Date date = new java.util.Date(currentTime); String archiveFile = format1.format(date).toString() + ".zip"; if (rotateArchive != null) { archiveFile = rotateArchive + "/" + archiveFile; (new File(rotateArchive)).mkdirs(); } Archive archive = new Archive(archiveFile); for (int i = 0; i < fileList.length; i++) { String currentFilename = fileList[i].getName(); long timeDifference = (currentTime - fileList[i].lastModified()); if ((rotateCompress && currentFilename.endsWith(".gz")) || (!rotateCompress && currentFilename.indexOf(logFile + ".") != -1)) { if (rotateDest != null) { currentFilename = rotateDest + "/" + currentFilename; } if (timeDifference > comparisonTime) { archive.addFile(fileList[i].getName(), currentFilename); fileList[i].delete(); } } } archive = null; fileList = null; format1 = null; date = null; } } public String identString() { return "Debug Rotator for logs"; } }); } } } | 884,978 |
0 | public static void fileUpload() throws IOException { HttpClient httpclient = new DefaultHttpClient(); httpclient.getParams().setParameter(CoreProtocolPNames.PROTOCOL_VERSION, HttpVersion.HTTP_1_1); file = new File("H:\\FileServeUploader.java"); HttpPost httppost = new HttpPost(postURL); httppost.setHeader("Cookie", uprandcookie + ";" + autologincookie); MultipartEntity mpEntity = new MultipartEntity(); ContentBody cbFile = new FileBody(file); mpEntity.addPart("MAX_FILE_SIZE", new StringBody("2097152000")); mpEntity.addPart("UPLOAD_IDENTIFIER", new StringBody(uid)); mpEntity.addPart("go", new StringBody("1")); mpEntity.addPart("files", cbFile); httppost.setEntity(mpEntity); System.out.println("Now uploading your file into depositfiles..........................."); HttpResponse response = httpclient.execute(httppost); HttpEntity resEntity = response.getEntity(); System.out.println(response.getStatusLine()); if (resEntity != null) { uploadresponse = EntityUtils.toString(resEntity); downloadlink = parseResponse(uploadresponse, "ud_download_url = '", "'"); deletelink = parseResponse(uploadresponse, "ud_delete_url = '", "'"); System.out.println("download link : " + downloadlink); System.out.println("delete link : " + deletelink); } } | 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(); } } | 884,979 |
1 | public void copyFile(String oldPath, String newPath) { try { int bytesum = 0; int byteread = 0; File oldfile = new File(oldPath); if (oldfile.exists()) { InputStream inStream = new FileInputStream(oldPath); FileOutputStream fs = new FileOutputStream(newPath); byte[] buffer = new byte[1444]; while ((byteread = inStream.read(buffer)) != -1) { bytesum += byteread; fs.write(buffer, 0, byteread); } inStream.close(); fs.close(); } } catch (Exception e) { e.printStackTrace(); } } | public static void copyFile(File file, String pathExport) throws IOException { File out = new File(pathExport); FileChannel sourceChannel = new FileInputStream(file).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); } | 884,980 |
0 | private void transformFile(File input, File output, Cipher cipher, boolean compress, String progressMessage) throws IOException { FileInputStream fileInputStream = new FileInputStream(input); InputStream inputStream; if (progressMessage != null) { inputStream = new ProgressMonitorInputStream(null, progressMessage, fileInputStream); } else { inputStream = fileInputStream; } FilterInputStream is = new BufferedInputStream(inputStream); FilterOutputStream os = new BufferedOutputStream(new FileOutputStream(output)); FilterInputStream fis; FilterOutputStream fos; if (compress) { fis = is; fos = new GZIPOutputStream(new CipherOutputStream(os, cipher)); } else { fis = new GZIPInputStream(new CipherInputStream(is, cipher)); fos = os; } byte[] buffer = new byte[cipher.getBlockSize() * blocksInBuffer]; int readLength = fis.read(buffer); while (readLength != -1) { fos.write(buffer, 0, readLength); readLength = fis.read(buffer); } if (compress) { GZIPOutputStream gos = (GZIPOutputStream) fos; gos.finish(); } fos.close(); fis.close(); } | public void fillData() { try { URL urlhome = OpenerIF.class.getResource("Home.html"); URLConnection uc = urlhome.openConnection(); InputStreamReader input = new InputStreamReader(uc.getInputStream()); BufferedReader in = new BufferedReader(input); String inputLine; String htmlData = ""; while ((inputLine = in.readLine()) != null) { htmlData += inputLine; } in.close(); String[] str = new String[9]; str[0] = getLibName(); str[1] = getLoginId(); str[2] = getLoginName(); str[3] = getVerusSubscriptionIdHTML(); str[4] = getPendingJobsHTMLCode(); str[5] = getFrequentlyUsedScreensHTMLCode(); str[6] = getOpenCatalogHTMLCode(); str[7] = getNewsHTML(); str[8] = getOnlineInformationHTML(); MessageFormat mf = new MessageFormat(htmlData); String htmlContent = mf.format(htmlData, str); PrintWriter fw = new PrintWriter(System.getProperty("user.home") + "/homeNGL.html"); fw.println(htmlContent); fw.flush(); fw.close(); new LocalHtmlRendererContext(panel, new SimpleUserAgentContext(), this).navigate("file:" + System.getProperty("user.home") + "/homeNGL.html"); } catch (Exception exp) { exp.printStackTrace(); } } | 884,981 |
1 | public static String stringOfUrl(String addr) throws IOException { ByteArrayOutputStream output = new ByteArrayOutputStream(); URL url = new URL(addr); IOUtils.copy(url.openStream(), output); return output.toString(); } | 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()); } | 884,982 |
1 | private String[] verifyConnection(Socket clientConnection) throws Exception { List<String> requestLines = new ArrayList<String>(); InputStream is = clientConnection.getInputStream(); BufferedReader in = new BufferedReader(new InputStreamReader(is)); StringTokenizer st = new StringTokenizer(in.readLine()); if (!st.hasMoreTokens()) { throw new IllegalArgumentException("There's no method token in this connection"); } String method = st.nextToken(); if (!st.hasMoreTokens()) { throw new IllegalArgumentException("There's no URI token in this connection"); } String uri = decodePercent(st.nextToken()); if (!st.hasMoreTokens()) { throw new IllegalArgumentException("There's no version token in this connection"); } String version = st.nextToken(); Properties parms = new Properties(); int qmi = uri.indexOf('?'); if (qmi >= 0) { decodeParms(uri.substring(qmi + 1), parms); uri = decodePercent(uri.substring(0, qmi)); } String params = ""; if (parms.size() > 0) { params = "?"; for (Object key : parms.keySet()) { params = params + key + "=" + parms.getProperty(((String) key)) + "&"; } params = params.substring(0, params.length() - 1).replace(" ", "%20"); } logger.debug("HTTP Request: " + method + " " + uri + params + " " + version); requestLines.add(method + " " + uri + params + " " + version); Properties headerVars = new Properties(); String line; String currentBoundary = null; Stack<String> boundaryStack = new Stack<String>(); boolean readingBoundary = false; String additionalData = ""; while (in.ready() && (line = in.readLine()) != null) { if (line.equals("") && (headerVars.get("Content-Type") == null || headerVars.get("Content-Length") == null)) { break; } logger.debug("HTTP Request Header: " + line); if (line.contains(": ")) { String vals[] = line.split(": "); headerVars.put(vals[0].trim(), vals[1].trim()); } if (!readingBoundary && line.contains(": ")) { if (line.contains("boundary=")) { currentBoundary = line.split("boundary=")[1].trim(); boundaryStack.push("--" + currentBoundary); } continue; } else if (line.equals("") && boundaryStack.isEmpty()) { int val = Integer.parseInt((String) headerVars.get("Content-Length")); if (headerVars.getProperty("Content-Type").contains("x-www-form-urlencoded")) { char buf[] = new char[val]; int read = in.read(buf); line = String.valueOf(buf, 0, read); additionalData = line; logger.debug("HTTP Request Header Form Parameters: " + line); } } else if (line.equals(boundaryStack.peek()) && !readingBoundary) { readingBoundary = true; } else if (line.equals(boundaryStack.peek()) && readingBoundary) { readingBoundary = false; } else if (line.contains(": ") && readingBoundary) { if (method.equalsIgnoreCase("PUT")) { if (line.contains("form-data; ")) { String formValues = line.split("form-data; ")[1]; for (String varValue : formValues.replace("\"", "").split("; ")) { String[] vV = varValue.split("="); vV[0] = decodePercent(vV[0]); vV[1] = decodePercent(vV[1]); headerVars.put(vV[0], vV[1]); } } } } else if (line.contains("") && readingBoundary && !boundaryStack.isEmpty() && headerVars.get("filename") != null) { int length = Integer.parseInt(headerVars.getProperty("Content-Length")); if (headerVars.getProperty("Content-Transfer-Encoding").contains("binary")) { File uploadFilePath = new File(VOctopusConfigurationManager.WebServerProperties.HTTPD_CONF.getPropertyValue("TempDirectory")); if (!uploadFilePath.exists()) { logger.error("Temporaty dir does not exist: " + uploadFilePath.getCanonicalPath()); } if (!uploadFilePath.isDirectory()) { logger.error("Temporary dir is not a directory: " + uploadFilePath.getCanonicalPath()); } if (!uploadFilePath.canWrite()) { logger.error("VOctopus Webserver doesn't have permissions to write on temporary dir: " + uploadFilePath.getCanonicalPath()); } FileOutputStream out = null; try { String putUploadPath = uploadFilePath.getAbsolutePath() + "/" + headerVars.getProperty("filename"); out = new FileOutputStream(putUploadPath); OutputStream outf = new BufferedOutputStream(out); int c; while (in.ready() && (c = in.read()) != -1 && length-- > 0) { outf.write(c); } } finally { if (out != null) { out.close(); } } File copied = new File(VOctopusConfigurationManager.getInstance().getDocumentRootPath() + uri + headerVars.get("filename")); File tempFile = new File(VOctopusConfigurationManager.WebServerProperties.HTTPD_CONF.getPropertyValue("TempDirectory") + "/" + headerVars.get("filename")); FileChannel ic = new FileInputStream(tempFile.getAbsolutePath()).getChannel(); FileChannel oc = new FileOutputStream(copied.getAbsolutePath()).getChannel(); ic.transferTo(0, ic.size(), oc); ic.close(); oc.close(); } } } for (Object var : headerVars.keySet()) { requestLines.add(var + ": " + headerVars.get(var)); } if (!additionalData.equals("")) { requestLines.add("ADDITIONAL" + additionalData); } return requestLines.toArray(new String[requestLines.size()]); } | public static void copyFromFileToFileUsingNIO(File inputFile, File outputFile) throws FileNotFoundException, IOException { FileChannel inputChannel = new FileInputStream(inputFile).getChannel(); FileChannel outputChannel = new FileOutputStream(outputFile).getChannel(); try { inputChannel.transferTo(0, inputChannel.size(), outputChannel); } catch (IOException e) { throw e; } finally { if (inputChannel != null) inputChannel.close(); if (outputChannel != null) outputChannel.close(); } } | 884,983 |
1 | public static void s_copy(FileInputStream fis, FileOutputStream fos) throws Exception { FileChannel in = fis.getChannel(); FileChannel out = fos.getChannel(); in.transferTo(0, in.size(), out); if (in != null) in.close(); if (out != null) out.close(); } | 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; } | 884,984 |
1 | public void copyFile(String oldPath, String newPath) { try { int bytesum = 0; int byteread = 0; File oldfile = new File(oldPath); if (oldfile.exists()) { InputStream inStream = new FileInputStream(oldPath); FileOutputStream fs = new FileOutputStream(newPath); byte[] buffer = new byte[1444]; while ((byteread = inStream.read(buffer)) != -1) { bytesum += byteread; fs.write(buffer, 0, byteread); } inStream.close(); fs.close(); } } catch (Exception e) { e.printStackTrace(); } } | public static File insertFileInto(File zipFile, File toInsert, String targetPath) { Zip64File zip64File = null; try { boolean compress = false; zip64File = new Zip64File(zipFile); FileEntry testEntry = getFileEntry(zip64File, targetPath); if (testEntry != null && testEntry.getMethod() == FileEntry.iMETHOD_DEFLATED) { compress = true; } processAndCreateFolderEntries(zip64File, parseTargetPath(targetPath, toInsert), compress); if (testEntry != null) { log.info("[insertFileInto] Entry exists: " + testEntry.getName()); log.info("[insertFileInto] Will delete this entry before inserting: " + toInsert.getName()); if (!testEntry.isDirectory()) { zip64File.delete(testEntry.getName()); } else { log.info("[insertFileInto] Entry is a directory. " + "Will delete all files contained in this entry and insert " + toInsert.getName() + "and all nested files."); if (!targetPath.contains("/")) { targetPath = targetPath + "/"; } deleteFileEntry(zip64File, testEntry); log.info("[insertFileInto] Entry successfully deleted."); } log.info("[insertFileInto] Writing new Entry: " + targetPath); EntryOutputStream out = null; if (!compress) { out = zip64File.openEntryOutputStream(targetPath, FileEntry.iMETHOD_STORED, new Date(toInsert.lastModified())); } else { out = zip64File.openEntryOutputStream(targetPath, FileEntry.iMETHOD_DEFLATED, new Date(toInsert.lastModified())); } if (toInsert.isDirectory()) { out.flush(); out.close(); log.info("[insertFileInto] Finished writing entry: " + targetPath); List<String> containedPaths = normalizePaths(toInsert); List<File> containedFiles = listAllFilesAndFolders(toInsert, new ArrayList<File>()); log.info("[insertFileInto] Added entry is a folder."); log.info("[insertFileInto] Adding all nested files: "); for (int i = 0; i < containedPaths.size(); i++) { File currentFile = containedFiles.get(i); String currentPath = targetPath.replace("/", "") + File.separator + containedPaths.get(i); EntryOutputStream loop_out = null; if (!compress) { loop_out = zip64File.openEntryOutputStream(currentPath, FileEntry.iMETHOD_STORED, new Date(currentFile.lastModified())); } else { loop_out = zip64File.openEntryOutputStream(currentPath, FileEntry.iMETHOD_DEFLATED, new Date(currentFile.lastModified())); } if (currentFile.isFile()) { InputStream loop_in = new FileInputStream(currentFile); IOUtils.copyLarge(loop_in, loop_out); loop_in.close(); } log.info("[insertFileInto] Added: " + currentPath); loop_out.flush(); loop_out.close(); } } else { InputStream in = new FileInputStream(toInsert); IOUtils.copyLarge(in, out); in.close(); out.flush(); out.close(); } } else { EntryOutputStream out = null; if (!compress) { out = zip64File.openEntryOutputStream(targetPath, FileEntry.iMETHOD_STORED, new Date(toInsert.lastModified())); } else { out = zip64File.openEntryOutputStream(targetPath, FileEntry.iMETHOD_DEFLATED, new Date(toInsert.lastModified())); } if (toInsert.isDirectory()) { out.flush(); out.close(); log.info("[insertFileInto] Finished writing entry: " + targetPath); List<String> containedPaths = normalizePaths(toInsert); List<File> containedFiles = listAllFilesAndFolders(toInsert, new ArrayList<File>()); log.info("[insertFileInto] Added entry is a folder."); log.info("[insertFileInto] Adding all nested files: "); for (int i = 0; i < containedPaths.size(); i++) { File currentFile = containedFiles.get(i); String currentPath = targetPath.replace("/", "") + File.separator + containedPaths.get(i); EntryOutputStream loop_out = null; if (!compress) { loop_out = zip64File.openEntryOutputStream(currentPath, FileEntry.iMETHOD_STORED, new Date(currentFile.lastModified())); } else { loop_out = zip64File.openEntryOutputStream(currentPath, FileEntry.iMETHOD_DEFLATED, new Date(currentFile.lastModified())); } if (currentFile.isFile()) { InputStream loop_in = new FileInputStream(currentFile); IOUtils.copyLarge(loop_in, loop_out); loop_in.close(); } log.info("[insertFileInto] Added: " + currentPath); loop_out.flush(); loop_out.close(); } } else { InputStream in = new FileInputStream(toInsert); IOUtils.copyLarge(in, out); in.close(); out.flush(); out.close(); } } log.info("[insertFileInto] Done! Added " + toInsert.getName() + " to zip."); zip64File.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return new File(zip64File.getDiskFile().getFileName()); } | 884,985 |
1 | public static void main(String[] args) throws IOException { File fileIn = new File("D:\\zz_c\\study2\\src\\study\\io\\A.java"); InputStream fin = new FileInputStream(fileIn); PipedInputStream pin = new PipedInputStream(); PipedOutputStream pout = new PipedOutputStream(); pout.connect(pin); IoRead i = new IoRead(); i.setIn(pin); File fileOU1 = new File("D:\\zz_c\\study2\\src\\study\\io\\A1.java"); File fileOU2 = new File("D:\\zz_c\\study2\\src\\study\\io\\A2.java"); File fileOU3 = new File("D:\\zz_c\\study2\\src\\study\\io\\A3.java"); i.addOut(new BufferedOutputStream(new FileOutputStream(fileOU1))); i.addOut(new BufferedOutputStream(new FileOutputStream(fileOU2))); i.addOut(new BufferedOutputStream(new FileOutputStream(fileOU3))); PipedInputStream pin2 = new PipedInputStream(); PipedOutputStream pout2 = new PipedOutputStream(); i.addOut(pout2); pout2.connect(pin2); i.start(); int read; try { read = fin.read(); while (read != -1) { pout.write(read); read = fin.read(); } fin.close(); pout.close(); } catch (IOException e) { e.printStackTrace(); } int c = pin2.read(); while (c != -1) { System.out.print((char) c); c = pin2.read(); } pin2.close(); } | public static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } | 884,986 |
0 | public static String encriptaSenha(String string) throws ApplicationException { try { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(string.getBytes()); BASE64Encoder encoder = new BASE64Encoder(); return encoder.encode(digest.digest()); } catch (NoSuchAlgorithmException ns) { ns.printStackTrace(); throw new ApplicationException("Erro ao Encriptar Senha"); } } | 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; } | 884,987 |
1 | public void write(PDDocument doc) throws COSVisitorException { document = doc; SecurityHandler securityHandler = document.getSecurityHandler(); if (securityHandler != null) { try { securityHandler.prepareDocumentForEncryption(document); this.willEncrypt = true; } catch (IOException e) { throw new COSVisitorException(e); } catch (CryptographyException e) { throw new COSVisitorException(e); } } else { this.willEncrypt = false; } COSDocument cosDoc = document.getDocument(); COSDictionary trailer = cosDoc.getTrailer(); COSArray idArray = (COSArray) trailer.getDictionaryObject("ID"); if (idArray == null) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(Long.toString(System.currentTimeMillis()).getBytes()); COSDictionary info = (COSDictionary) trailer.getDictionaryObject("Info"); if (info != null) { Iterator values = info.getValues().iterator(); while (values.hasNext()) { md.update(values.next().toString().getBytes()); } } idArray = new COSArray(); COSString id = new COSString(md.digest()); idArray.add(id); idArray.add(id); trailer.setItem("ID", idArray); } catch (NoSuchAlgorithmException e) { throw new COSVisitorException(e); } } cosDoc.accept(this); } | public String hash(String password) { MessageDigest digest = null; try { digest = MessageDigest.getInstance("SHA-256"); } catch (NoSuchAlgorithmException ex) { log.info("No sha-256 available"); try { digest = MessageDigest.getInstance("SHA-1"); } catch (NoSuchAlgorithmException e) { log.fatal("sha-1 is not available", e); throw new RuntimeException("Couldn't get a hash algorithm from Java"); } } try { digest.reset(); digest.update((salt + password).getBytes("UTF-8")); byte hash[] = digest.digest(); return new String(Base64.encodeBase64(hash, false)); } catch (Throwable t) { throw new RuntimeException("Couldn't hash password"); } } | 884,988 |
0 | private void copy(File source, File target) throws IOException { FileChannel in = (new FileInputStream(source)).getChannel(); FileChannel out = (new FileOutputStream(target)).getChannel(); in.transferTo(0, source.length(), out); in.close(); out.close(); } | public BigInteger calculateMd5(String input) throws FileSystemException { try { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(input.getBytes()); byte[] messageDigest = digest.digest(); BigInteger bigInt = new BigInteger(1, messageDigest); return bigInt; } catch (Exception e) { throw new FileSystemException(e); } } | 884,989 |
0 | protected Drawing loadDrawing(ProgressIndicator progress) throws IOException { Drawing drawing = createDrawing(); if (getParameter("datafile") != null) { URL url = new URL(getDocumentBase(), getParameter("datafile")); URLConnection uc = url.openConnection(); if (uc instanceof HttpURLConnection) { ((HttpURLConnection) uc).setUseCaches(false); } int contentLength = uc.getContentLength(); InputStream in = uc.getInputStream(); try { if (contentLength != -1) { in = new BoundedRangeInputStream(in); ((BoundedRangeInputStream) in).setMaximum(contentLength + 1); progress.setProgressModel((BoundedRangeModel) in); progress.setIndeterminate(false); } BufferedInputStream bin = new BufferedInputStream(in); bin.mark(512); IOException formatException = null; for (InputFormat format : drawing.getInputFormats()) { try { bin.reset(); } catch (IOException e) { uc = url.openConnection(); in = uc.getInputStream(); in = new BoundedRangeInputStream(in); ((BoundedRangeInputStream) in).setMaximum(contentLength + 1); progress.setProgressModel((BoundedRangeModel) in); bin = new BufferedInputStream(in); bin.mark(512); } try { bin.reset(); format.read(bin, drawing, true); formatException = null; break; } catch (IOException e) { formatException = e; } } if (formatException != null) { throw formatException; } } finally { in.close(); } } return drawing; } | public String uploadZtree(ArrayList c) { try { String id = generateRandomId(); Iterator iter = c.iterator(); URL url = new URL(ZorobotSystem.props.getProperty("zoro.url") + "auplo1.jsp"); URLConnection connection = url.openConnection(); connection.setDoOutput(true); PrintWriter out = new PrintWriter(connection.getOutputStream()); out.print("id=" + id + "&"); StringBuffer sb = new StringBuffer(); int gg = 0; while (iter.hasNext()) { if (gg++ >= 500) break; String st = (String) iter.next(); sb.append("a="); sb.append(URLEncoder.encode(st, "UTF-8")); if (iter.hasNext() && gg < 500) sb.append("&"); } out.println(sb.toString()); out.close(); BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream())); String inputLine; if ((inputLine = in.readLine()) != null) { if (!inputLine.equals("OK!") && inputLine.length() > 3) { System.out.println("Not OK: " + inputLine); return "xxxxxxxxxx"; } } in.close(); return id; } catch (Exception e) { e.printStackTrace(); } return null; } | 884,990 |
0 | public static void writeURLToFile(String url, String path) throws MalformedURLException, IOException { java.io.BufferedInputStream in = new java.io.BufferedInputStream(new java.net.URL(url).openStream()); java.io.FileOutputStream fos = new java.io.FileOutputStream(path); java.io.BufferedOutputStream bout = new BufferedOutputStream(fos, 1024); byte data[] = new byte[1024]; int count; while ((count = in.read(data, 0, 1024)) != -1) { ; bout.write(data, 0, count); } bout.close(); in.close(); } | @Override public boolean saveCart(Carrito cart, boolean completado, String date, String formPago) { Connection conexion = null; PreparedStatement insertHistorial = null; PreparedStatement insertCarrito = null; boolean exito = false; try { conexion = pool.getConnection(); conexion.setAutoCommit(false); insertHistorial = conexion.prepareStatement("INSERT INTO " + nameBD + ".HistorialCarritos VALUES (?,?,?,?,?,?)"); insertHistorial.setString(1, cart.getUser()); insertHistorial.setString(2, cart.getCodigo()); insertHistorial.setString(3, date); insertHistorial.setDouble(4, cart.getPrecio()); insertHistorial.setString(5, formPago); insertHistorial.setBoolean(6, completado); int filasAfectadas = insertHistorial.executeUpdate(); if (filasAfectadas != 1) { conexion.rollback(); } else { insertCarrito = conexion.prepareStatement("INSERT INTO " + nameBD + ".Carritos VALUES (?,?,?,?,?)"); Iterator<String> iteradorProductos = cart.getArticulos().keySet().iterator(); while (iteradorProductos.hasNext()) { String key = iteradorProductos.next(); Producto prod = getProduct(key); int cantidad = cart.getArticulos().get(key); insertCarrito.setString(1, cart.getCodigo()); insertCarrito.setString(2, prod.getCodigo()); insertCarrito.setString(3, prod.getNombre()); insertCarrito.setDouble(4, prod.getPrecio()); insertCarrito.setInt(5, cantidad); filasAfectadas = insertCarrito.executeUpdate(); if (filasAfectadas != 1) { conexion.rollback(); break; } insertCarrito.clearParameters(); } conexion.commit(); exito = true; } } catch (SQLException ex) { logger.log(Level.SEVERE, "Error añadiendo carrito al registro", ex); try { conexion.rollback(); } catch (SQLException ex1) { logger.log(Level.SEVERE, "Error haciendo rollback de la transacción para insertar carrito en el registro", ex1); } } finally { cerrarConexionYStatement(conexion, insertCarrito, insertHistorial); } return exito; } | 884,991 |
1 | public static void copy(String sourceName, String destName) throws IOException { File src = new File(sourceName); File dest = new File(destName); BufferedInputStream source = null; BufferedOutputStream destination = null; byte[] buffer; int bytes_read; long byteCount = 0; if (!src.exists()) throw new IOException("Source not found: " + src); if (!src.canRead()) throw new IOException("Source is unreadable: " + src); if (src.isFile()) { if (!dest.exists()) { File parentdir = parent(dest); if (!parentdir.exists()) parentdir.mkdir(); } else if (dest.isDirectory()) { if (src.isDirectory()) dest = new File(dest + File.separator + src); else dest = new File(dest + File.separator + src.getName()); } } else if (src.isDirectory()) { if (dest.isFile()) throw new IOException("Cannot copy directory " + src + " to file " + dest); if (!dest.exists()) dest.mkdir(); } if ((!dest.canWrite()) && (dest.exists())) throw new IOException("Destination is unwriteable: " + dest); if (src.isFile()) { try { source = new BufferedInputStream(new FileInputStream(src)); destination = new BufferedOutputStream(new FileOutputStream(dest)); buffer = new byte[4096]; byteCount = 0; while (true) { bytes_read = source.read(buffer); if (bytes_read == -1) break; destination.write(buffer, 0, bytes_read); byteCount = byteCount + bytes_read; } } finally { if (source != null) source.close(); if (destination != null) destination.close(); } } else if (src.isDirectory()) { String targetfile, target, targetdest; String[] files = src.list(); for (int i = 0; i < files.length; i++) { targetfile = files[i]; target = src + File.separator + targetfile; targetdest = dest + File.separator + targetfile; if ((new File(target)).isDirectory()) { copy(new File(target).getCanonicalPath(), new File(targetdest).getCanonicalPath()); } else { try { byteCount = 0; source = new BufferedInputStream(new FileInputStream(target)); destination = new BufferedOutputStream(new FileOutputStream(targetdest)); buffer = new byte[4096]; while (true) { bytes_read = source.read(buffer); if (bytes_read == -1) break; destination.write(buffer, 0, bytes_read); byteCount = byteCount + bytes_read; } } finally { if (source != null) source.close(); if (destination != null) destination.close(); } } } } } | public static void copyFile(File in, File out) throws IOException { FileChannel sourceChannel = new FileInputStream(in).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); destinationChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); sourceChannel.close(); destinationChannel.close(); } | 884,992 |
1 | private static void main(String mp3Path) throws IOException { String convPath = "http://android.adinterest.biz/wav2mp3.php?k="; String uri = convPath + mp3Path; URL rssurl = new URL(uri); InputStream is = rssurl.openStream(); BufferedReader br = new BufferedReader(new InputStreamReader(is, "UTF-8")); String buf = ""; while ((buf = br.readLine()) != null) { } is.close(); br.close(); } | public static Vector getKeywordsFromURL(String p_url) throws Exception { URL x_url = new URL(p_url); URLConnection x_conn = x_url.openConnection(); InputStreamReader x_is_reader = new InputStreamReader(x_conn.getInputStream()); BufferedReader x_reader = new BufferedReader(x_is_reader); String x_line = null; String x_lc_line = null; Vector x_words = new Vector(1000); int x_body = -1; while ((x_line = x_reader.readLine()) != null) { x_lc_line = x_line.toLowerCase(); x_body = x_lc_line.indexOf("<body"); if (x_body != -1) { x_line = x_line.substring(x_body + 5); break; } } boolean x_status = false; int x_end = -1; if (x_lc_line == null) { System.out.println("No <body start"); return null; } do { x_lc_line = x_line.toLowerCase(); x_end = x_lc_line.indexOf("</body>"); if (x_end != -1) { extractOutsideText(x_line.substring(0, x_end), "<", ">", x_words, x_status); break; } x_status = extractOutsideText(x_line, "<", ">", x_words, x_status); } while ((x_line = x_reader.readLine()) != null); return x_words; } | 884,993 |
0 | public void save(File f, AudioFileFormat.Type t) throws IOException { if (t.getExtension().equals("raw")) { IOUtils.copy(makeInputStream(), new FileOutputStream(f)); } else { AudioSystem.write(makeStream(), t, f); } } | protected static boolean isLatestVersion(double myVersion, String referenceAddress) { Scanner scanner = null; try { URL url = new URL(referenceAddress); InputStream iS = url.openStream(); scanner = new Scanner(iS); String firstLine = scanner.nextLine(); double latestVersion = Double.valueOf(firstLine.trim()); return myVersion >= latestVersion; } catch (Exception e) { displaySimpleAlert(null, "Cannot check latest version...check internet connection?"); return false; } } | 884,994 |
1 | public static void writeEntry(File file, File input) throws PersistenceException { try { File temporaryFile = File.createTempFile("pmMDA_zargo", ARGOUML_EXT); temporaryFile.deleteOnExit(); ZipOutputStream output = new ZipOutputStream(new FileOutputStream(temporaryFile)); FileInputStream inputStream = new FileInputStream(input); ZipEntry entry = new ZipEntry(file.getName().substring(0, file.getName().indexOf(ARGOUML_EXT)) + XMI_EXT); output.putNextEntry(new ZipEntry(entry)); IOUtils.copy(inputStream, output); output.closeEntry(); inputStream.close(); entry = new ZipEntry(file.getName().substring(0, file.getName().indexOf(ARGOUML_EXT)) + ".argo"); output.putNextEntry(new ZipEntry(entry)); output.write(ArgoWriter.getArgoContent(file.getName().substring(0, file.getName().indexOf(ARGOUML_EXT)) + XMI_EXT).getBytes()); output.closeEntry(); output.close(); temporaryFile.renameTo(file); } catch (IOException ioe) { throw new PersistenceException(ioe); } } | @Test public void testWriteAndRead() throws Exception { JCFS.configureLoopback(dir); RFile file = new RFile("testreadwrite.txt"); RFileOutputStream out = new RFileOutputStream(file); out.write("test".getBytes("utf-8")); out.close(); RFileInputStream in = new RFileInputStream(file); byte[] buffer = new byte[4]; int readCount = in.read(buffer); in.close(); assertEquals(4, readCount); String resultRead = new String(buffer, "utf-8"); assertEquals("test", resultRead); } | 884,995 |
0 | public static Image getPluginImage(Object plugin, String name) { try { try { URL url = getPluginImageURL(plugin, name); if (m_URLImageMap.containsKey(url)) return m_URLImageMap.get(url); InputStream is = url.openStream(); Image image; try { image = getImage(is); m_URLImageMap.put(url, image); } finally { is.close(); } return image; } catch (Throwable e) { } } catch (Throwable e) { } return null; } | public static long copyFile(File source, File target) throws IOException { FileInputStream fileInputStream = null; FileOutputStream fileOutputStream = null; try { fileInputStream = new FileInputStream(source); fileOutputStream = new FileOutputStream(target); FileChannel in = fileInputStream.getChannel(); FileChannel out = fileOutputStream.getChannel(); return out.transferFrom(in, 0, source.length()); } finally { if (fileInputStream != null) fileInputStream.close(); if (fileOutputStream != null) fileOutputStream.close(); } } | 884,996 |
1 | public static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } | public static void copyFile(File file, String pathExport) throws IOException { File out = new File(pathExport); FileChannel sourceChannel = new FileInputStream(file).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); } | 884,997 |
0 | private static void backupFile(File file) { FileChannel in = null, out = null; try { if (!file.getName().endsWith(".bak")) { in = new FileInputStream(file).getChannel(); out = new FileOutputStream(new File(file.toString() + ".bak")).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } } catch (Exception e) { e.getMessage(); } finally { try { System.gc(); if (in != null) in.close(); if (out != null) out.close(); } catch (Exception e) { e.getMessage(); } } } | public Document load(java.net.URL url) throws DOMTestLoadException { Document doc = null; try { java.io.InputStream stream = url.openStream(); Object tidyObj = tidyConstructor.newInstance(new Object[0]); doc = (Document) parseDOMMethod.invoke(tidyObj, new Object[] { stream, null }); } catch (InvocationTargetException ex) { throw new DOMTestLoadException(ex.getTargetException()); } catch (Exception ex) { throw new DOMTestLoadException(ex); } return doc; } | 884,998 |
0 | public static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } | public String computeMD5(String string) throws ServiceException { try { MessageDigest digest = MessageDigest.getInstance("md5"); digest.reset(); digest.update(string.getBytes(Invoker.ENCODING)); return convertToHex(digest.digest()); } catch (NoSuchAlgorithmException exception) { String message = "Could not create properly the MD5 digest"; log.error(message, exception); throw new ServiceException(message, exception); } catch (UnsupportedEncodingException exception) { String message = "Could not encode properly the MD5 digest"; log.error(message, exception); throw new ServiceException(message, exception); } } | 884,999 |
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