Example #1
0
 @Override
 public void render(Parameters blockParameters, Writer w, RenderHints hints)
     throws FrameworkException {
   log.debug("Error rendering " + blockParameters);
   switch (getType()) {
     case BODY:
       try {
         decorateIntro(hints, w, "error");
         w.write("<h1>" + error.status);
         w.write(": ");
         CharTransformer escape = new Xml(Xml.ESCAPE);
         w.write(escape.transform(error.exception.getMessage()));
         w.write(" ");
         w.write(escape.transform(url));
         w.write("</h1>");
         w.write("<pre>");
         HttpServletRequest request = blockParameters.get(Parameter.REQUEST);
         error.getErrorReport(w, request, escape);
         w.write("</pre>");
         decorateOutro(hints, w);
       } catch (IOException eio) {
         throw new FrameworkException(eio.getMessage(), eio);
       }
       break;
     default:
   }
 }
 public String fetchCleanupReviewDirLinkGenXml() {
   String s = null;
   try {
     s = // Organize and Clean Up Section
         "<ReviewDirGenerator class='operator.ReviewDirGenerator' destination.dir='"
             + outputDirectory.getCanonicalPath()
             + "' sample='"
             + outputDirectory.getName()
             + "' submitter='"
             + submitter
             + "' analysis.type='"
             + analysisType
             + "'> \n"
             + "    <finalVariants /> \n"
             + "    <ViewerCSV /> \n"
             + "    <InstanceLog class='buffer.InstanceLogFile' /> \n"
             + "    <finalBAM /> \n"
             + "    <QCOutputFile /> \n"
             + "    <bedForVars /> \n"
             + "</ReviewDirGenerator> \n\n";
   } catch (IOException e) {
     e.printStackTrace();
     Misc.printErrAndExit("\nError fetching clean up and review dir links.\n");
   }
   return s;
 }
Example #3
0
  /**
   * Performs an XPATH lookup in an xml document whose filename is specified by the first parameter
   * (assumed to be in the auxiliary subdirectory) The XPATH expression is supplied as the second
   * string parameter The return value is of type string e.g. this is currently used primarily for
   * looking up the Company Prefix Index for encoding a GS1 Company Prefix into a 64-bit EPC tag
   */
  private String xpathlookup(String xml, String expression) {

    try {

      // Parse the XML as a W3C document.
      DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
      Document document =
          builder.parse(new File(xmldir + File.separator + "auxiliary" + File.separator + xml));

      XPath xpath = XPathFactory.newInstance().newXPath();

      String rv = (String) xpath.evaluate(expression, document, XPathConstants.STRING);

      return rv;

    } catch (ParserConfigurationException e) {
      System.err.println("ParserConfigurationException caught...");
      e.printStackTrace();
      return null;
    } catch (XPathExpressionException e) {
      System.err.println("XPathExpressionException caught...");
      e.printStackTrace();
      return null;
    } catch (SAXException e) {
      System.err.println("SAXException caught...");
      e.printStackTrace();
      return null;
    } catch (IOException e) {
      System.err.println("IOException caught...");
      e.printStackTrace();
      return null;
    }
  }
 /**
  * Get the noun and verb <roots> (i.e. 'the highest' synsets in WordNet) from the particular
  * 'icfile' (Information Content) that you are applying. Store a noun <root>: a synset offset
  * number of type Integer in nounroots: an ArrayList<Integer> defined in the constructor of this
  * class. Store a verb <root>: a synset offset number of type Integer in verbroots: an
  * ArrayList<Integer> defined in the constructor of this class.
  *
  * <p>An example line in an 'icfile', showing a noun <root>: 1740n 128767 ROOT
  */
 private void getRoots() {
   Pattern pn = Pattern.compile("[0-9]+n [0-9]+ ROOT"); // find noun <root>
   Pattern pv = Pattern.compile("[0-9]+v [0-9]+ ROOT"); // find verb <root>
   Matcher m = null;
   String root = "";
   try {
     BufferedReader in = new BufferedReader(new FileReader(icfile));
     String line;
     while ((line = in.readLine()) != null) {
       // nouns
       m = pn.matcher(line);
       if (m.matches()) {
         root = (line.split("\\s")[0]).split("n")[0]; // !!! double split !!!
         nounroots.add(Integer.parseInt(root));
       }
       // verbs
       m = pv.matcher(line);
       if (m.matches()) {
         root = (line.split("\\s")[0]).split("v")[0]; // !!! double split !!!
         verbroots.add(Integer.parseInt(root));
       }
     }
     in.close();
   } catch (IOException e) {
     e.printStackTrace();
   }
 }
Example #5
0
 /**
  * Checks if a given file exists and, if not, create it by copying a default template from
  * resources; used to create default conf files.
  *
  * @param file The path of the file that needs to exist
  * @param template The path of the template for the file
  */
 public static void ensureFileExists(final String file, final String template) {
   if (LAUNCHED_FROM_JAR && !Files.exists(Paths.get(file))) {
     if (Debug.on) printDebug("[Meta] " + file + " does not exist: creating a default one.");
     InputStream stream = Meta.class.getResourceAsStream(template);
     if (stream == null) {
       printDebug(
           "[ WARNING ] template for "
               + template
               + " not found. Won't create a default "
               + file
               + ".");
     } else {
       int readBytes;
       byte[] buffer = new byte[4096];
       try (OutputStream outStream = new FileOutputStream(new File(file))) {
         while ((readBytes = stream.read(buffer)) > 0) {
           outStream.write(buffer, 0, readBytes);
         }
         if (Debug.on)
           printDebug("[Meta] created default file " + file + " from " + template + ".");
       } catch (IOException e) {
         e.printStackTrace();
       } finally {
         try {
           stream.close();
         } catch (IOException ignore) {
         }
       }
     }
   } else {
     if (Meta.LAUNCHED_FROM_JAR && Debug.on) printDebug("[Meta] file exists: " + file + ".");
   }
 }
  /** Returns true if this VM has acquired the right to run this TestTask */
  private static DUnitRun getDUnitRun() {
    if (dunitRun != null) {
      System.out.println("BBB dunitRun not null returning");
      return dunitRun;
    }

    try {
      SwarmBB.getBB().getSharedLock().lock();
      Integer runId = (Integer) SwarmBB.getBB().getSharedMap().get(SwarmBB.RUN_ID);
      System.out.println("BBB runID=" + runId);
      if (runId != null) {
        dunitRun = Swarm.getDUnitRun(runId);
        System.out.println("BBB lookedUp RUN:" + dunitRun);
      } else {
        dunitRun = Swarm.generateNewDUnitRun();
        System.out.println(
            "BBB GENNED UP A RUN:" + dunitRun + " mapping to id:" + dunitRun.getId());
        SwarmBB.getBB().getSharedMap().put(SwarmBB.RUN_ID, dunitRun.getId());
      }
    } catch (SQLException e) {
      e.printStackTrace();
    } catch (IOException e) {
      e.printStackTrace();
    } finally {
      SwarmBB.getBB().getSharedLock().unlock();
    }
    return dunitRun;
  }
Example #7
0
 private void dumpFailedLaunchInfo(Process process) {
   try {
     dumpStream(process.getErrorStream());
     dumpStream(process.getInputStream());
   } catch (IOException e) {
     MessageOutput.println("Unable to display process output:", e.getMessage());
   }
 }
 static void searchFiles() {
   try {
     for (int i = 0; i < options.filenames.length; i++) {
       Scanner input = new Scanner(new File(options.filenames[i]));
       scanfile(input, options.filenames[i], options.pattern);
       input.close();
     }
   } catch (IOException e) {
     messages.warn(e.getMessage());
     messages.exit_status = messages.EXIT_NOMATCH;
   }
 }
Example #9
0
  /** The main program for ReTrace. */
  public static void main(String[] args) {
    if (args.length < 1) {
      System.err.println(
          "Usage: java proguard.ReTrace [-verbose] <mapping_file> [<stacktrace_file>]");
      System.exit(-1);
    }

    String regularExpresssion = STACK_TRACE_EXPRESSION;
    boolean verbose = false;

    int argumentIndex = 0;
    while (argumentIndex < args.length) {
      String arg = args[argumentIndex];
      if (arg.equals(REGEX_OPTION)) {
        regularExpresssion = args[++argumentIndex];
      } else if (arg.equals(VERBOSE_OPTION)) {
        verbose = true;
      } else {
        break;
      }

      argumentIndex++;
    }

    if (argumentIndex >= args.length) {
      System.err.println(
          "Usage: java proguard.ReTrace [-regex <regex>] [-verbose] <mapping_file> [<stacktrace_file>]");
      System.exit(-1);
    }

    File mappingFile = new File(args[argumentIndex++]);
    File stackTraceFile = argumentIndex < args.length ? new File(args[argumentIndex]) : null;

    ReTrace reTrace = new ReTrace(regularExpresssion, verbose, mappingFile, stackTraceFile);

    try {
      // Execute ReTrace with its given settings.
      reTrace.execute();
    } catch (IOException ex) {
      if (verbose) {
        // Print a verbose stack trace.
        ex.printStackTrace();
      } else {
        // Print just the stack trace message.
        System.err.println("Error: " + ex.getMessage());
      }

      System.exit(1);
    }

    System.exit(0);
  }
Example #10
0
 /* attach to running target vm */
 private VirtualMachine attachTarget() {
   AttachingConnector attacher = (AttachingConnector) connector;
   try {
     return attacher.attach(connectorArgs);
   } catch (IOException ioe) {
     ioe.printStackTrace();
     MessageOutput.fatalError("Unable to attach to target VM.");
   } catch (IllegalConnectorArgumentsException icae) {
     icae.printStackTrace();
     MessageOutput.fatalError("Internal debugger error.");
   }
   return null; // Shuts up the compiler
 }
 public static void main(String[] args) {
   File f = new File(args[0]);
   try {
     Parser<GeneOrthologyEntry> entries =
         new Parser<GeneOrthologyEntry>(f, new GeneOrthologyEntry.ParsingMapper());
     while (entries.hasNext()) {
       GeneOrthologyEntry entry = entries.next();
     }
   } catch (IOException e) {
     // TODO Auto-generated catch block
     e.printStackTrace();
   }
 }
 public Class<?> findClass(String s) {
   try {
     byte[] bytes = loadClassData(s);
     return defineClass(s, bytes, 0, bytes.length);
   } catch (IOException ioe) {
     try {
       return super.loadClass(s);
     } catch (ClassNotFoundException ignore) {
     }
     ioe.printStackTrace(System.out);
     return null;
   }
 }
Example #13
0
    // Writes the program to a source file, compiles it, and runs it.
    private void compileAndRun(String fileName, String code) {
      // Exceptions here can pick and choose what font to use, as needed.
      // Exceptions thrown by the program, that cause the Playground to be unstable, should be in
      // blue.

      println("Deleting old temp files...", progErr);
      new File(fileName + ".java").delete();
      new File(fileName + ".class").delete();

      println("Creating source file...", progErr);
      file = new File(fileName + ".java");

      println("Writing code to source file...", progErr);
      try {
        new FileWriter(file).append(code).close();
      } catch (IOException i) {
        println("Had an IO Exception when trying to write the code. Stack trace:", error);
        i.printStackTrace();
        return; // Exit on error
      }

      println("Compiling code...", progErr);
      // This should only ever be called if the JDK isn't installed. How you'd get here, I don't
      // know.
      if (compiler == null) {
        println("Fatal Error: JDK not installed. Go to java.sun.com and install.", error);
        return;
      }

      // Tries to compile. Success code is 0, so if something goes wrong, do stuff.
      int result =
          compiler.run(
              null,
              null,
              null,
              file
                  .getAbsolutePath()); // Possibly add a new outputstream to parse through the
                                       // compiler errors
      if (result != 0) {
        displayLog();
        println("Failed to compile.", error);
        return; // Return on error
      }

      println("Code compiled with 0 errors.", progErr);

      println("Attempting to run code...", progErr);
      run(fileName);
    }
  public static void main(String[] args) {
    try {
      BufferedReader br = new BufferedReader(new FileReader(args[0]));
      int tIndex = 0;
      int pIndex = 0;

      // This will probably change soon (name and implementation)
      NgramParser tnp = new NgramParser(args[1]);

      ArrayList<String> triplet = tnp.getTriplet();
      ArrayList<String> polarity = tnp.getPolarity();

      FileWriter sw = new FileWriter(args[2]);
      String line = null;

      while (((line = br.readLine()) != null)
          && (tIndex < triplet.size())
          && (pIndex < polarity.size())) {
        if (line.matches("^[\\d]*:")) {
          // System.out.println(line);
          sw.write(line + "\n");
        } else {
          Scanner sc = new Scanner(line);
          String trip = sc.findInLine(Pattern.compile("[a-zA-Z]+#[a-z]+[#]?[0-9]*"));
          // if (trip != null && trip.equals(triplet.get(tIndex))) {
          System.out.println(trip);
          if (trip != null && !trip.toLowerCase().contains("no#cl")) {
            // System.out.println(triplet.get(tIndex) + ":" +polarity.get(pIndex));
            String pol = polarity.get(pIndex);
            sw.write(line + " " + pol + "\n");
            sc.close();
            tIndex++;
            pIndex++;
          } else {
            String pol = "neg";
            sw.write("no#a#1" + " " + pol + "\n");
            sc.close();
          }
        }

        // sw.flush();
      }

      sw.close();

    } catch (IOException e) {
      e.printStackTrace();
    }
  }
Example #15
0
 public void run() {
   for (; ; ) {
     try {
       int n = sel.select();
       if (n > 0) processSelectedKeys();
       processPendingTargets();
       if (shutdown) {
         sel.close();
         return;
       }
     } catch (IOException x) {
       x.printStackTrace();
     }
   }
 }
  public BackupHdfs() {
    try {
      m_wrMkdirs = new PrintWriter(new BufferedWriter(new FileWriter("hdfs-mkdirs.sh")));
      m_wrMkdirs.println("hadoop fs -mkdir /mapred");
      m_wrMkdirs.println("hadoop fs -mkdir /mapred/system");

      m_wrChmods = new PrintWriter(new BufferedWriter(new FileWriter("hdfs-chmods.sh")));
      m_wrChmods.println("hadoop fs -chmod 775 /");
      m_wrChmods.println("hadoop fs -chown hdfs:hadoop /");
      m_wrChmods.println("hadoop fs -chown mapred:hadoop /mapred/system");
      m_wrChmods.println("hadoop fs -chmod 700 /mapred/system");
    } catch (IOException e) {
      System.err.println("ERROR: failed to open files for writing: " + e.toString());
    }
  }
Example #17
0
  public static void lookingCode() {

    int procura = 0;
    boolean entrou = false;

    do {
      procura = Entrada.leiaInt("Digite o código da carta: ");
    } while (procura < 0 || procura > 32);

    try {
      FileReader arq = new FileReader(FileManenger.fileName);
      BufferedReader lerArq = new BufferedReader(arq);
      String linha = lerArq.readLine();

      while (linha != null) {

        // procura na string '.'
        if (linha.toLowerCase().contains(".".toLowerCase())) {

          // separ em um array a linha que tem o nome do personagem ex: 1.CARLOS
          String columnArray[] = linha.split(Pattern.quote("."));

          // testa se o codigo é o que ele procura
          if (procura == Integer.parseInt(columnArray[0])) {

            // achou o codigo que ele procura
            entrou = true;
          }
        }

        // testa se a linha é igual a * se for ele já não é mais o personagem que procuramos
        if (linha.equals("*")) {
          entrou = false;
        }

        // mostra as inforamações do personagem
        if (entrou) {
          System.out.println(linha);
        }

        linha = lerArq.readLine();
      }

      arq.close();
    } catch (IOException e) {
      System.err.printf("Erro na abertura do arquivo: %s.\n", e.getMessage());
    }
  }
Example #18
0
 /* listen for connection from target vm */
 private VirtualMachine listenTarget() {
   ListeningConnector listener = (ListeningConnector) connector;
   try {
     String retAddress = listener.startListening(connectorArgs);
     MessageOutput.println("Listening at address:", retAddress);
     vm = listener.accept(connectorArgs);
     listener.stopListening(connectorArgs);
     return vm;
   } catch (IOException ioe) {
     ioe.printStackTrace();
     MessageOutput.fatalError("Unable to attach to target VM.");
   } catch (IllegalConnectorArgumentsException icae) {
     icae.printStackTrace();
     MessageOutput.fatalError("Internal debugger error.");
   }
   return null; // Shuts up the compiler
 }
Example #19
0
 private void dumpStream(InputStream stream) throws IOException {
   BufferedReader in = new BufferedReader(new InputStreamReader(stream));
   int i;
   try {
     while ((i = in.read()) != -1) {
       MessageOutput.printDirect((char) i); // Special case: use
       //   printDirect()
     }
   } catch (IOException ex) {
     String s = ex.getMessage();
     if (!s.startsWith("Bad file number")) {
       throw ex;
     }
     // else we got a Bad file number IOException which just means
     // that the debuggee has gone away.  We'll just treat it the
     // same as if we got an EOF.
   }
 }
Example #20
0
  public static void readFile() {

    try {

      FileReader arq = new FileReader(FileManenger.fileName);
      BufferedReader lerArq = new BufferedReader(arq);
      String linha =
          lerArq
              .readLine(); // lê a primeira linha a variável "linha" recebe o valor "null" quando o
                           // processo  de repetição atingir o final do arquivo texto
      while (linha != null) {
        System.out.println(linha);
        linha = lerArq.readLine(); // lê da segunda até a última linha
      }
      arq.close();

    } catch (IOException e) {
      System.err.printf("Erro na abertura do arquivo: %s.\n", e.getMessage());
    }
  }
  public static void main(String[] args) {
    try {
      Genome g = Organism.findGenome(args[0]);
      File blasttab = new File(args[1]);
      ProbesFromPrimers pfp = new ProbesFromPrimers(g, blasttab);
      Collection<NamedRegion> probes = pfp.parseProbes();

      for (NamedRegion probe : probes) {
        String probeName = probe.getName();
        System.out.println(
            String.format(
                "%s\t%s\t%d\t%d", probeName, probe.getChrom(), probe.getStart(), probe.getEnd()));
      }

    } catch (NotFoundException e) {
      e.printStackTrace();
    } catch (IOException e) {
      e.printStackTrace();
    }
  }
Example #22
0
 /* launch child target vm */
 private VirtualMachine launchTarget() {
   LaunchingConnector launcher = (LaunchingConnector) connector;
   try {
     VirtualMachine vm = launcher.launch(connectorArgs);
     process = vm.process();
     displayRemoteOutput(process.getErrorStream());
     displayRemoteOutput(process.getInputStream());
     return vm;
   } catch (IOException ioe) {
     ioe.printStackTrace();
     MessageOutput.fatalError("Unable to launch target VM.");
   } catch (IllegalConnectorArgumentsException icae) {
     icae.printStackTrace();
     MessageOutput.fatalError("Internal debugger error.");
   } catch (VMStartException vmse) {
     MessageOutput.println("vmstartexception", vmse.getMessage());
     MessageOutput.println();
     dumpFailedLaunchInfo(vmse.process());
     MessageOutput.fatalError("Target VM failed to initialize.");
   }
   return null; // Shuts up the compiler
 }
Example #23
0
  protected void getDimensionsFromLogFile(BufferedReader reader, PicText text) {
    if (reader == null) {
      return;
    }
    String line = ""; // il rale si j'initialise pas ...
    boolean finished = false;
    while (!finished) {
      try {
        line = reader.readLine();
      } catch (IOException ioex) {
        ioex.printStackTrace();
        return;
      }
      if (line == null) {
        System.out.println("Size of text not found in log file...");
        return;
      }

      System.out.println(line);
      Matcher matcher = LogFilePattern.matcher(line);

      if (line != null && matcher.find()) {
        System.out.println("FOUND :" + line);
        finished = true;
        try {
          text.setDimensions(
              0.3515 * Double.parseDouble(matcher.group(1)), // height, pt->mm (1pt=0.3515 mm)
              0.3515 * Double.parseDouble(matcher.group(2)), // width
              0.3515 * Double.parseDouble(matcher.group(3))); // depth
          areDimensionsComputed = true;
        } catch (NumberFormatException e) {
          System.out.println("Logfile number format problem: $line" + e.getMessage());
        } catch (IndexOutOfBoundsException e) {
          System.out.println("Logfile regexp problem: $line" + e.getMessage());
        }
      }
    }
    return;
  }
Example #24
0
 /**
  * Searches for the directory 'dirPath'; if not found, tries to create it, then returns a File
  * object for that directory.
  */
 public static File ensureDirExists(final String dirPath) {
   File dirpath = new File(dirPath);
   if (!dirpath.isDirectory()) {
     if (!dirpath.exists()) {
       printDebug("[Meta] " + dirpath + " does not exist: creating it...");
       try {
         Files.createDirectories(Paths.get(dirpath.getPath()));
         return dirpath;
       } catch (IOException e) {
         printDebug("[Meta] Exception while creating directory:");
         e.printStackTrace();
         return null;
       }
     } else {
       printDebug(
           "[Meta] Error: path `"
               + dirpath
               + "' is not a valid directory path, and could not create it.");
       return null;
     }
   } else return dirpath;
 }
  // Takes a PImage and compresses it into a JPEG byte stream
  // Adapted from Dan Shiffman's UDP Sender code
  public byte[] compressImage(PImage img) {
    // We need a buffered image to do the JPG encoding
    BufferedImage bimg = new BufferedImage(img.width, img.height, BufferedImage.TYPE_INT_RGB);

    img.loadPixels();
    bimg.setRGB(0, 0, img.width, img.height, img.pixels, 0, img.width);

    // Need these output streams to get image as bytes for UDP communication
    ByteArrayOutputStream baStream = new ByteArrayOutputStream();
    BufferedOutputStream bos = new BufferedOutputStream(baStream);

    // Turn the BufferedImage into a JPG and put it in the BufferedOutputStream
    // Requires try/catch
    try {
      ImageIO.write(bimg, "jpg", bos);
    } catch (IOException e) {
      e.printStackTrace();
    }

    // Get the byte array, which we will send out via UDP!
    return baStream.toByteArray();
  }
Example #26
0
    // Creates a new thread, runs the program in that thread, and reports any errors as needed.
    private void run(String clazz) {
      try {
        // Makes sure the JVM resets if it's already running.
        if (JVMrunning) kill();

        // Some String constants for java path and OS-specific separators.
        String separator = System.getProperty("file.separator");
        String path = System.getProperty("java.home") + separator + "bin" + separator + "java";

        // Tries to run compiled code.
        ProcessBuilder builder = new ProcessBuilder(path, clazz);

        // Should be good now! Everything past this is on you. Don't mess it up.
        println(
            "Build succeeded on " + java.util.Calendar.getInstance().getTime().toString(), progErr);
        println("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~", progErr);

        JVM = builder.start();

        // Note that as of right now, there is no support for input. Only output.
        Reader errorReader = new InputStreamReader(JVM.getErrorStream());
        Reader outReader = new InputStreamReader(JVM.getInputStream());
        // Writer inReader = new OutputStreamWriter(JVM.getOutputStream());

        redirectErr = redirectIOStream(errorReader, err);
        redirectOut = redirectIOStream(outReader, out);
        // redirectIn = redirectIOStream(null, inReader);

      } catch (IOException e) {
        // JVM = builder.start() can throw this.
        println("IOException when running the JVM.", progErr);
        e.printStackTrace();
        displayLog();
        return;
      }
    }
  /**
   * Compare the checksums of the hdfs file as well as the local copied file.
   *
   * @author [email protected]
   * @date Fri Jan 27 06:06:00 2012
   */
  boolean compareChecksums(FileSystem fs, Path p, String sFsPath) {
    try {
      // get hdfs file info
      FileStatus stat = fs.getFileStatus(p);

      // get HDFS checksum
      FileChecksum ck = fs.getFileChecksum(p);
      String sCk, sCkShort;
      if (ck == null) {
        sCk = sCkShort = "<null>";
      } else {
        sCk = ck.toString();
        sCkShort = sCk.replaceAll("^.*:", "");
      }

      // System.out.println(p.toUri().getPath() + " len=" + stat.getLen()
      // + " " + stat.getOwner() + "/" + stat.getGroup()
      // + " checksum=" + sCk);

      // find the local file
      File fLocal = new File(sFsPath);
      if (!fLocal.exists()) {
        System.out.println("CHECKSUM-ERROR: file does not exist: " + sFsPath);
        return false;
      }
      if (!fLocal.isFile()) {
        System.out.println("CHECKSUM-ERROR: path is not a file: " + sFsPath);
        return false;
      }
      if (stat.getLen() != fLocal.length()) {
        System.out.println(
            "CHECKSUM-ERROR: length mismatch: "
                + sFsPath
                + " hdfslen="
                + stat.getLen()
                + " fslen="
                + fLocal.length());
        return false;
      }

      // get local fs checksum
      FileChecksum ckLocal = getLocalFileChecksum(sFsPath);
      if (ckLocal == null) {
        System.out.println("ERROR Failed to get checksum for local file " + sFsPath);
        return false;
      }

      // compare checksums as a string, after stripping the
      // algorithm name from the beginning
      String sCkLocal = ckLocal.toString();
      String sCkLocalShort = sCkLocal.replaceAll("^.*:", "");

      if (false == sCkShort.equals(sCkLocalShort)) {
        System.out.println(
            "CHECKSUM-ERROR: checksum mismatch: "
                + sFsPath
                + "\nhdfs = "
                + sCk
                + "\nlocal= "
                + sCkLocal);
        return false;
      }

      return true;
    } catch (IOException e) {
      System.out.println("CHECKSUM-ERROR: " + sFsPath + " exception " + e.toString());
    }

    return false;
  }
Example #28
0
  public void init() throws ServletException {

    final String CONFIG_PATH = getServletContext().getRealPath("/") + "config.ini";
    final String APPLICATION_NAME = getServletContext().getServletContextName();

    BasicConfigurator.configure();

    FileInputStream config_file = null;
    File config = new File(CONFIG_PATH);

    if (config.canRead()) {
      log.debug("Parsing " + CONFIG_PATH);
      try {
        config_file = new FileInputStream(CONFIG_PATH);
      } catch (java.io.FileNotFoundException e) {
        throw new ServletException(e);
      }

      Properties config_prop = new Properties();

      try {
        config_prop.load(config_file);
      } catch (java.io.IOException e) {
        throw new ServletException(e);
      }
      this.config = config_prop;

      log.debug("Parsing finished");
    } else {
      log.fatal("Error, cannot read " + CONFIG_PATH);
    }

    log.debug("maximumRecords : " + this.config.getProperty("default_maximumRecords"));
    log.debug("srw_header_file: " + this.config.getProperty("srw_header_file"));
    log.debug("srw_diag: " + this.config.getProperty("srw_diag_file"));
    // log.debug("server_list:     " + this.config.getProperty("server_list"));

    try {
      FileReader fis =
          new FileReader(
              getServletContext().getRealPath("/") + this.config.getProperty("srw_header_file"));
      BufferedReader in1 = new BufferedReader(fis);
      fis =
          new FileReader(
              getServletContext().getRealPath("/") + this.config.getProperty("srw_footer_file"));
      BufferedReader in2 = new BufferedReader(fis);
      fis =
          new FileReader(
              getServletContext().getRealPath("/") + this.config.getProperty("srw_diag_file"));
      BufferedReader in3 = new BufferedReader(fis);
      try {
        String line = null;

        while ((line = in1.readLine()) != null) {
          this.SRW_HEADER = this.SRW_HEADER + line;
        }
        while ((line = in2.readLine()) != null) {
          this.SRW_FOOTER = this.SRW_FOOTER + line;
        }
        while ((line = in3.readLine()) != null) {
          this.SRW_DIAG = this.SRW_DIAG + line;
        }
      } finally {
        in1.close();
        in2.close();
        in3.close();
      }

    } catch (IOException ex) {
      ex.printStackTrace();
    }
  }
Example #29
0
  /** Performs the subsequent ReTrace operations. */
  public void execute() throws IOException {
    // Read the mapping file.
    MappingReader mappingReader = new MappingReader(mappingFile);
    mappingReader.pump(this);

    StringBuffer expressionBuffer = new StringBuffer(regularExpression.length() + 32);
    char[] expressionTypes = new char[32];
    int expressionTypeCount = 0;
    int index = 0;
    while (true) {
      int nextIndex = regularExpression.indexOf('%', index);
      if (nextIndex < 0
          || nextIndex == regularExpression.length() - 1
          || expressionTypeCount == expressionTypes.length) {
        break;
      }

      expressionBuffer.append(regularExpression.substring(index, nextIndex));
      expressionBuffer.append('(');

      char expressionType = regularExpression.charAt(nextIndex + 1);
      switch (expressionType) {
        case 'c':
          expressionBuffer.append(REGEX_CLASS);
          break;

        case 'C':
          expressionBuffer.append(REGEX_CLASS_SLASH);
          break;

        case 'l':
          expressionBuffer.append(REGEX_LINE_NUMBER);
          break;

        case 't':
          expressionBuffer.append(REGEX_TYPE);
          break;

        case 'f':
          expressionBuffer.append(REGEX_MEMBER);
          break;

        case 'm':
          expressionBuffer.append(REGEX_MEMBER);
          break;

        case 'a':
          expressionBuffer.append(REGEX_ARGUMENTS);
          break;
      }

      expressionBuffer.append(')');

      expressionTypes[expressionTypeCount++] = expressionType;

      index = nextIndex + 2;
    }

    expressionBuffer.append(regularExpression.substring(index));

    Pattern pattern = Pattern.compile(expressionBuffer.toString());

    // Read the stack trace file.
    LineNumberReader reader =
        new LineNumberReader(
            stackTraceFile == null
                ? (Reader) new InputStreamReader(System.in)
                : (Reader) new BufferedReader(new FileReader(stackTraceFile)));

    try {
      StringBuffer outLine = new StringBuffer(256);
      List extraOutLines = new ArrayList();

      String className = null;

      // Read the line in the stack trace.
      while (true) {
        String line = reader.readLine();
        if (line == null) {
          break;
        }

        Matcher matcher = pattern.matcher(line);

        if (matcher.matches()) {
          int lineNumber = 0;
          String type = null;
          String arguments = null;

          // Figure out a class name, line number, type, and
          // arguments beforehand.
          for (int expressionTypeIndex = 0;
              expressionTypeIndex < expressionTypeCount;
              expressionTypeIndex++) {
            int startIndex = matcher.start(expressionTypeIndex + 1);
            if (startIndex >= 0) {
              String match = matcher.group(expressionTypeIndex + 1);

              char expressionType = expressionTypes[expressionTypeIndex];
              switch (expressionType) {
                case 'c':
                  className = originalClassName(match);
                  break;

                case 'C':
                  className = originalClassName(ClassUtil.externalClassName(match));
                  break;

                case 'l':
                  lineNumber = Integer.parseInt(match);
                  break;

                case 't':
                  type = originalType(match);
                  break;

                case 'a':
                  arguments = originalArguments(match);
                  break;
              }
            }
          }

          // Actually construct the output line.
          int lineIndex = 0;

          outLine.setLength(0);
          extraOutLines.clear();

          for (int expressionTypeIndex = 0;
              expressionTypeIndex < expressionTypeCount;
              expressionTypeIndex++) {
            int startIndex = matcher.start(expressionTypeIndex + 1);
            if (startIndex >= 0) {
              int endIndex = matcher.end(expressionTypeIndex + 1);
              String match = matcher.group(expressionTypeIndex + 1);

              // Copy a literal piece of input line.
              outLine.append(line.substring(lineIndex, startIndex));

              char expressionType = expressionTypes[expressionTypeIndex];
              switch (expressionType) {
                case 'c':
                  className = originalClassName(match);
                  outLine.append(className);
                  break;

                case 'C':
                  className = originalClassName(ClassUtil.externalClassName(match));
                  outLine.append(ClassUtil.internalClassName(className));
                  break;

                case 'l':
                  lineNumber = Integer.parseInt(match);
                  outLine.append(match);
                  break;

                case 't':
                  type = originalType(match);
                  outLine.append(type);
                  break;

                case 'f':
                  originalFieldName(className, match, type, outLine, extraOutLines);
                  break;

                case 'm':
                  originalMethodName(
                      className, match, lineNumber, type, arguments, outLine, extraOutLines);
                  break;

                case 'a':
                  arguments = originalArguments(match);
                  outLine.append(arguments);
                  break;
              }

              // Skip the original element whose processed version
              // has just been appended.
              lineIndex = endIndex;
            }
          }

          // Copy the last literal piece of input line.
          outLine.append(line.substring(lineIndex));

          // Print out the main line.
          System.out.println(outLine);

          // Print out any additional lines.
          for (int extraLineIndex = 0; extraLineIndex < extraOutLines.size(); extraLineIndex++) {
            System.out.println(extraOutLines.get(extraLineIndex));
          }
        } else {
          // Print out the original line.
          System.out.println(line);
        }
      }
    } catch (IOException ex) {
      throw new IOException("Can't read stack trace (" + ex.getMessage() + ")");
    } finally {
      if (stackTraceFile != null) {
        try {
          reader.close();
        } catch (IOException ex) {
          // This shouldn't happen.
        }
      }
    }
  }
Example #30
0
  // Thread's run method aimed at creating a bitmap asynchronously
  public void run() {
    Drawing drawing = new Drawing();
    PicText rawPicText = new PicText();
    String s = ((PicText) element).getText();
    rawPicText.setText(s);
    drawing.add(
        rawPicText); // bug fix: we must add a CLONE of the PicText, otherwise it loses it former
                     // parent... (then pb with the view )
    drawing.setNotparsedCommands(
        "\\newlength{\\jpicwidth}\\settowidth{\\jpicwidth}{"
            + s
            + "}"
            + CR_LF
            + "\\newlength{\\jpicheight}\\settoheight{\\jpicheight}{"
            + s
            + "}"
            + CR_LF
            + "\\newlength{\\jpicdepth}\\settodepth{\\jpicdepth}{"
            + s
            + "}"
            + CR_LF
            + "\\typeout{JPICEDT INFO: \\the\\jpicwidth, \\the\\jpicheight,  \\the\\jpicdepth }"
            + CR_LF);
    RunExternalCommand.Command commandToRun = RunExternalCommand.Command.BITMAP_CREATION;
    // RunExternalCommand command = new RunExternalCommand(drawing, contentType,commandToRun);
    boolean isWriteTmpTeXfile = true;
    String bitmapExt = "png"; // [pending] preferences
    String cmdLine =
        "{i}/unix/tetex/create_bitmap.sh {p} {f} "
            + bitmapExt
            + " "
            + fileDPI; // [pending] preferences
    ContentType contentType = getContainer().getContentType();
    RunExternalCommand.isGUI = false; // System.out, no dialog box // [pending] debug
    RunExternalCommand command =
        new RunExternalCommand(drawing, contentType, cmdLine, isWriteTmpTeXfile);
    command
        .run(); // synchronous in an async. thread => it's ok (anyway, we must way until the LaTeX
                // process has completed)

    if (wantToComputeLatexDimensions) {
      // load size of text:
      try {
        File logFile = new File(command.getTmpPath(), command.getTmpFilePrefix() + ".log");
        BufferedReader reader = null;
        try {
          reader = new BufferedReader(new FileReader(logFile));
        } catch (FileNotFoundException fnfe) {
          System.out.println("Cannot find log file! " + fnfe.getMessage());
          System.out.println(logFile);
        } catch (IOException ioex) {
          System.out.println("Log file IO exception");
          ioex.printStackTrace();
        } // utile ?
        System.out.println("Log file created! file=" + logFile);
        getDimensionsFromLogFile(reader, (PicText) element);
        syncStringLocation(); // update dimensions
        syncBounds();
        syncFrame();
        SwingUtilities.invokeLater(
            new Thread() {
              public void run() {
                repaint(null);
              }
            });
        // repaint(null); // now that dimensions are available, we force a repaint() [pending]
        // smart-repaint ?
      } catch (Exception e) {
        e.printStackTrace();
      }
    }

    if (wantToGetBitMap) {
      // load image:
      try {
        File bitmapFile =
            new File(command.getTmpPath(), command.getTmpFilePrefix() + "." + bitmapExt);
        this.image = ImageIO.read(bitmapFile);
        System.out.println(
            "Bitmap created! file="
                + bitmapFile
                + ", width="
                + image.getWidth()
                + "pixels, height="
                + image.getHeight()
                + "pixels");
        if (image == null) return;
        syncStringLocation(); // sets strx, stry, and dimensions of text
        syncBounds();
        // update the AffineTransform that will be applied to the bitmap before displaying on screen
        PicText te = (PicText) element;
        text2ModelTr.setToIdentity(); // reset
        PicPoint anchor = te.getCtrlPt(TextEditable.P_ANCHOR, ptBuf);
        text2ModelTr.rotate(getRotation(), anchor.x, anchor.y); // rotate along P_ANCHOR !
        text2ModelTr.translate(te.getLeftX(), te.getTopY());
        text2ModelTr.scale(
            te.getWidth() / image.getWidth(),
            -(te.getHeight() + te.getDepth()) / image.getHeight());
        // [pending]  should do something special to avoid dividing by 0 or setting a rescaling
        // factor to 0 [non invertible matrix] (java will throw an exception)
        syncFrame();
        SwingUtilities.invokeLater(
            new Thread() {
              public void run() {
                repaint(null);
              }
            });
        // repaint(null); // now that bitmap is available, we force a repaint() [pending]
        // smart-repaint ?
      } catch (Exception e) {
        e.printStackTrace();
      }
    }
  }