public static void copyDir(
     @NotNull File fromDir, @NotNull File toDir, @Nullable final FileFilter filter)
     throws IOException {
   ensureExists(toDir);
   if (isAncestor(fromDir, toDir, true)) {
     LOG.error(fromDir.getAbsolutePath() + " is ancestor of " + toDir + ". Can't copy to itself.");
     return;
   }
   File[] files = fromDir.listFiles();
   if (files == null)
     throw new IOException(
         CommonBundle.message("exception.directory.is.invalid", fromDir.getPath()));
   if (!fromDir.canRead())
     throw new IOException(
         CommonBundle.message("exception.directory.is.not.readable", fromDir.getPath()));
   for (File file : files) {
     if (filter != null && !filter.accept(file)) {
       continue;
     }
     if (file.isDirectory()) {
       copyDir(file, new File(toDir, file.getName()), filter);
     } else {
       copy(file, new File(toDir, file.getName()));
     }
   }
 }
Example #2
0
  /**
   * Recursive function to enumerate classes inside a classpath folder
   *
   * @param superClass
   * @param classloader
   * @param classes
   * @param packagePath
   * @param packageName
   */
  private static void enumerateDirectory(
      String prefix,
      Class superClass,
      ClassLoader classloader,
      LinkedList<Class> classes,
      File packagePath,
      String packageName) {
    File[] classFiles = packagePath.listFiles();

    for (File classFile : classFiles) {
      if (classFile.isDirectory()) {
        enumerateDirectory(
            prefix,
            superClass,
            classloader,
            classes,
            classFile,
            packageName + classFile.getName() + ".");
      } else {
        if (classFile.getName().endsWith(".class")
            && (prefix == null || classFile.getName().startsWith(prefix))) {
          String classFileName = classFile.getName();
          String className = packageName + classFileName.substring(0, classFileName.length() - 6);
          checkAndAddClass(classloader, superClass, classes, className);
        }
      }
    }
  }
Example #3
0
  private static void index_h(String prefix, File file, IndexWriter indexWriter)
      throws IOException {
    Document doc = null;

    if (file.isDirectory()) {
      File files[] = file.listFiles();
      for (File file1 : files) {
        index_h(prefix + FILE_SEPARATOR + file.getName(), file1, indexWriter);
      }
    } else {
      String content = FileUtils.readFileToString(file, "utf-8");

      System.out.println("==============================================================");
      System.out.println("index_h " + content);
      System.out.println("==============================================================");

      String filename = prefix + FILE_SEPARATOR + file.getName();
      String path = file.getAbsolutePath();

      doc = new Document();
      doc.add(new Field("content", content, Field.Store.YES, Field.Index.ANALYZED));
      doc.add(new Field("relative_path", filename, Field.Store.YES, Field.Index.NOT_ANALYZED));
      indexWriter.addDocument(doc);
    }
  }
Example #4
0
  public static void createAd(@Valid Ad ad, File photo) throws IOException {

    DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd");
    // get current date time with Date()
    Date date = new Date();
    ad.createDate = dateFormat.format(date);
    ad.student = Student.findById(1l);
    // ad.category=Category.findById(ad.category.id);
    File d = new File(Play.applicationPath.getAbsolutePath() + "/public/img/ads");
    // if(d.exists()){
    String suffix = FilenameUtils.getExtension(photo.getName());
    File o = File.createTempFile("ad-", "." + suffix, d);

    InputStream input = new FileInputStream(photo);
    OutputStream output = new FileOutputStream(o);
    ad.image = o.getName();

    ad.save();
    try {
      IOUtils.copy(input, output);
    } finally {
      IOUtils.closeQuietly(output);
      IOUtils.closeQuietly(input);
    }

    Ads.index(1, ad.category.id.toString());
  }
  private void copyAllFilesToLogDir(File node, File parent) throws IOException {
    if (!node.getAbsoluteFile().equals(parent.getAbsoluteFile())
        && node.isFile()
        && !node.getParentFile().equals(parent)) {
      String fileNamePrefix = node.getName().substring(0, node.getName().lastIndexOf('.'));
      String fileNameSuffix = node.getName().substring(node.getName().lastIndexOf('.'));
      String newFilePath =
          node.getParentFile().getAbsolutePath()
              + File.separator
              + fileNamePrefix.replace(".", "_")
              + fileNameSuffix;

      File newNode = new File(newFilePath);
      if (node.renameTo(newNode)) {
        FileUtils.copyFileToDirectory(newNode, parent);
      }
    }
    if (node.isDirectory()) {
      String[] subNote = node.list();
      for (String filename : subNote) {
        copyAllFilesToLogDir(new File(node, filename), parent);
      }
      if (!node.equals(parent)) {
        FileUtils.deleteDirectory(node);
      }
    }
  }
Example #6
0
  public static String[] listFiles(File dir, Boolean includeSubDirs) throws IOException {
    FileFilter fileFilter =
        new FileFilter() {
          public boolean accept(File file) {
            return file.isDirectory();
          }
        };
    File[] subFolders = dir.listFiles(fileFilter);

    List<String> files = new ArrayList<String>();

    List<File> fileArray =
        new ArrayList<File>(
            FileUtils.listFiles(
                dir, TrueFileFilter.INSTANCE, includeSubDirs ? TrueFileFilter.INSTANCE : null));

    for (File file : fileArray) {
      if (file.isFile()) {
        if (includeSubDirs && containsParentFolder(file, subFolders)) {
          files.add(file.getParentFile().getName() + File.separator + file.getName());
        } else {
          files.add(file.getName());
        }
      }
    }

    return (String[]) files.toArray(new String[0]);
  }
  private void updateData(MavenProgressIndicator progress, File newDataDir, boolean fullUpdate)
      throws MavenIndexException {

    IndexData newData = new IndexData(newDataDir);
    try {
      doUpdateIndexData(newData, progress);
      newData.flush();
    } catch (Throwable e) {
      newData.close(true);
      FileUtil.delete(newDataDir);

      if (e instanceof MavenServerIndexerException) throw new MavenIndexException(e);
      if (e instanceof IOException) throw new MavenIndexException(e);
      throw new RuntimeException(e);
    }

    synchronized (this) {
      IndexData oldData = myData;

      myData = newData;
      myDataDirName = newDataDir.getName();

      if (fullUpdate) {
        myUpdateTimestamp = System.currentTimeMillis();
      }

      oldData.close(true);

      for (File each : FileUtil.notNullize(myDir.listFiles())) {
        if (each.getName().startsWith(DATA_DIR_PREFIX) && !each.getName().equals(myDataDirName)) {
          FileUtil.delete(each);
        }
      }
    }
  }
Example #8
0
  private String getTitle(File f) {
    String result = "";
    if (!f.getName().endsWith(".html")) return "not HTML";
    else {
      try {
        BufferedReader reader = new BufferedReader(new FileReader(f));
        String ligne = reader.readLine();
        while (ligne != null && !ligne.contains("<TITLE>") && !ligne.contains("<title>")) {
          ligne = reader.readLine();
        }
        reader.close();
        if (ligne == null) return "No TITLE in page " + f.getName();
        else {
          String fin = "";
          String debut = "";
          if (ligne.contains("</TITLE>")) {
            debut = "<TITLE>";
            fin = "</TITLE>";
          } else if (ligne.contains("</title>")) {
            debut = "<title>";
            fin = "</title>";
          } else return "No title in page " + f.getName();

          int fin_index = ligne.lastIndexOf(fin);
          result = ligne.substring(ligne.indexOf(debut) + 7, fin_index);
          return result;
        }
      } catch (Exception e) {
        LOG.error("Error while reading file " + e);
        return "Error for file " + f.getName();
      }
    }
  }
Example #9
0
 public void saveCache(
     JMXInstrumentedCache<K, V> cache, File savedCachePath, Function<K, byte[]> converter)
     throws IOException {
   long start = System.currentTimeMillis();
   String msgSuffix = " " + savedCachePath.getName() + " for " + cfname + " of " + ksname;
   logger.debug("saving" + msgSuffix);
   int count = 0;
   File tmpFile =
       File.createTempFile(savedCachePath.getName(), null, savedCachePath.getParentFile());
   FileOutputStream fout = new FileOutputStream(tmpFile);
   ObjectOutputStream out = new ObjectOutputStream(new BufferedOutputStream(fout));
   FileDescriptor fd = fout.getFD();
   for (K key : cache.getKeySet()) {
     byte[] bytes = converter.apply(key);
     out.writeInt(bytes.length);
     out.write(bytes);
     ++count;
   }
   out.flush();
   fd.sync();
   out.close();
   if (!tmpFile.renameTo(savedCachePath))
     throw new IOException("Unable to rename cache to " + savedCachePath);
   if (logger.isDebugEnabled())
     logger.debug(
         "saved "
             + count
             + " keys in "
             + (System.currentTimeMillis() - start)
             + " ms from"
             + msgSuffix);
 }
  synchronized void migrateData(DataStore targetStore) {
    ForceLoadAllClaims(this);
    targetStore.ClearInventoryOnJoinPlayers = ClearInventoryOnJoinPlayers;
    // migrate claims
    for (Claim c : this.claims) {
      GriefPrevention.AddLogEntry("Migrating Claim #" + c.getID());
      targetStore.addClaim(c);
    }

    // migrate groups
    Iterator<String> groupNamesEnumerator = this.permissionToBonusBlocksMap.keySet().iterator();
    while (groupNamesEnumerator.hasNext()) {
      String groupName = groupNamesEnumerator.next();
      targetStore.saveGroupBonusBlocks(groupName, this.permissionToBonusBlocksMap.get(groupName));
    }

    // migrate players
    for (PlayerData pdata : getAllPlayerData()) {

      targetStore.playerNameToPlayerDataMap.put(pdata.playerName, pdata);
      targetStore.savePlayerData(pdata.playerName, pdata);
    }

    // migrate next claim ID
    if (this.nextClaimID > targetStore.nextClaimID) {
      targetStore.setNextClaimID(this.nextClaimID);
    }

    // rename player and claim data folders so the migration won't run again
    int i = 0;
    File claimsBackupFolder;
    File playersBackupFolder;
    do {
      String claimsFolderBackupPath = claimDataFolderPath;
      if (i > 0) claimsFolderBackupPath += String.valueOf(i);
      claimsBackupFolder = new File(claimsFolderBackupPath);

      String playersFolderBackupPath = playerDataFolderPath;
      if (i > 0) playersFolderBackupPath += String.valueOf(i);
      playersBackupFolder = new File(playersFolderBackupPath);
      i++;
    } while (claimsBackupFolder.exists() || playersBackupFolder.exists());

    File claimsFolder = new File(claimDataFolderPath);
    File playersFolder = new File(playerDataFolderPath);

    claimsFolder.renameTo(claimsBackupFolder);
    playersFolder.renameTo(playersBackupFolder);

    GriefPrevention.AddLogEntry(
        "Backed your file system data up to "
            + claimsBackupFolder.getName()
            + " and "
            + playersBackupFolder.getName()
            + ".");
    GriefPrevention.AddLogEntry(
        "If your migration encountered any problems, you can restore those data with a quick copy/paste.");
    GriefPrevention.AddLogEntry(
        "When you're satisfied that all your data have been safely migrated, consider deleting those folders.");
  }
  /**
   * Gets a list of <code>IIOImage</code> objects for an image file.
   *
   * @param imageFile input image file. It can be any of the supported formats, including TIFF,
   *     JPEG, GIF, PNG, BMP, JPEG, and PDF if GPL Ghostscript is installed
   * @return a list of <code>IIOImage</code> objects
   * @throws Exception
   */
  public static List<IIOImage> getIIOImageList(File imageFile) throws IOException {
    File workingTiffFile = null;

    ImageReader reader = null;
    ImageInputStream iis = null;

    try {
      // convert PDF to TIFF
      if (imageFile.getName().toLowerCase().endsWith(".pdf")) {
        workingTiffFile = PdfUtilities.convertPdf2Tiff(imageFile);
        imageFile = workingTiffFile;
      }

      List<IIOImage> iioImageList = new ArrayList<IIOImage>();

      String imageFileName = imageFile.getName();
      String imageFormat = imageFileName.substring(imageFileName.lastIndexOf('.') + 1);
      if (imageFormat.matches("(pbm|pgm|ppm)")) {
        imageFormat = "pnm";
      } else if (imageFormat.equals("jp2")) {
        imageFormat = "jpeg2000";
      }
      Iterator<ImageReader> readers = ImageIO.getImageReadersByFormatName(imageFormat);
      reader = readers.next();

      if (reader == null) {
        throw new RuntimeException(
            "Need to install JAI Image I/O package.\nhttps://jai-imageio.dev.java.net");
      }

      iis = ImageIO.createImageInputStream(imageFile);
      reader.setInput(iis);

      int imageTotal = reader.getNumImages(true);

      for (int i = 0; i < imageTotal; i++) {
        //                IIOImage oimage = new IIOImage(reader.read(i), null,
        // reader.getImageMetadata(i));
        IIOImage oimage = reader.readAll(i, reader.getDefaultReadParam());
        iioImageList.add(oimage);
      }

      return iioImageList;
    } finally {
      try {
        if (iis != null) {
          iis.close();
        }
        if (reader != null) {
          reader.dispose();
        }
      } catch (Exception e) {
        // ignore
      }
      if (workingTiffFile != null && workingTiffFile.exists()) {
        workingTiffFile.delete();
      }
    }
  }
  private String getPlayerDataFile(String sPlayerName) {
    String retval = null;
    try {

      String strPath = playerDataFolderPath + File.separator;

      String scaseSensitive = strPath + sPlayerName;
      String scaseInsensitive = strPath + sPlayerName.toLowerCase();

      File examinepath = new File(strPath);

      File CaseSensitive = null;
      File CaseInsensitive = null;

      // search for file.
      for (File iterate : examinepath.listFiles()) {
        // if it equals the name case-sensitively,

        if (iterate.getName().equals(sPlayerName)) {
          // assign our case sensitive name

          CaseSensitive = iterate;
        } else if (iterate.getName().equalsIgnoreCase(sPlayerName)
            && iterate.getName().toLowerCase().equals(iterate.getName())) {
          // otherwise assign our case insensitive name.

          CaseInsensitive = iterate;
          scaseInsensitive = CaseInsensitive.getName();
        }
      }

      if (CaseSensitive != null
          && CaseInsensitive != null
          && !scaseInsensitive.equals(scaseSensitive)) {
        try {

          // delete caseinsensitive file...
          new File(scaseInsensitive).delete();
          // copy case sensitive version in it's place.

          copyFile(CaseSensitive, CaseInsensitive);
          // CaseInsensitive.renameTo(new File(scaseInsensitive + "-backup"));
          // delete the case sensitive file.

          CaseSensitive.delete();

        } catch (IOException iox) {
          // ignore
        }
      }
      return retval = scaseInsensitive;

    } finally {
      Debugger.Write(
          "Flat: Player Data retrieved for " + sPlayerName + ":" + retval,
          Debugger.DebugLevel.Verbose);
    }
  }
Example #13
0
 private void visit(Set<String> names, String prefix, File file) {
   for (File child : file.listFiles()) {
     if (child.isFile()) {
       names.add(prefix + child.getName());
     } else if (child.isDirectory()) {
       visit(names, prefix + child.getName() + "/", child);
     }
   }
 }
Example #14
0
 /**
  * @param guid
  * @throws IOException
  */
 public void delete(int guid) throws IOException {
   // delete file
   File file = new File(Integer.toString(guid));
   if (file.delete()) {
     System.out.println(file.getName() + " deleted");
   } else {
     System.out.println("Failed to delete " + file.getName());
   }
 }
 private void analyze(File f) throws IOException {
   String[] list = f.list();
   if (list != null) {
     for (int i = 0; i < list.length; i++)
       analyze(new File(f.getCanonicalPath() + "\\" + list[i]));
   } else {
     if (f.getName().endsWith(".ma") || f.getName().endsWith(".fg")) count(f);
   }
 }
Example #16
0
 private void runFromDir(File folder) throws IOException {
   System.out.println(
       "LongevityRecordedTests.testAllInFolder running longjevity test from data in folder "
           + folder);
   if (folder.getName().indexOf("_") < 0) return;
   String branchName = folder.getName().substring(0, folder.getName().indexOf("_"));
   run(folder.getCanonicalPath(), branchName);
   printStats(branchName);
 }
Example #17
0
  /**
   * Crea el fichero de indices con la informacion inicial necesaria para un archivo concreto.
   *
   * @param fichero es el fichero de indices que tendra toda la informacion.
   * @param archivo es el objeto que representa el archivo en concreto.
   * @param fragmentos es la lista de fragmentos que faltan de dicho archivo.
   */
  public void crearFicheroIndices(File fichero, Archivo archivo, Vector<Fragmento> fragmentos) {
    Vector<Fragmento> fragTengo = new Vector<Fragmento>(), fragFaltan = fragmentos;
    Indices indices = new Indices(archivo, fragTengo, fragFaltan);
    ByteArrayOutputStream bs = new ByteArrayOutputStream();
    try {
      ObjectOutputStream os = new ObjectOutputStream(bs);
      os.writeObject(indices);
      os.close();

    } catch (IOException e) {
      /*System.out.println("Error -> posibles causas: ");
      System.out.println( "\tProblemas al crear un flujo de bytes serializable" );
      System.out.println( "\tProblemas al serializar el objeto indice" );
      System.out.println( "\tProblemas al cerrar el flujo serializable" );*/
      ControlDeErrores.getInstancia()
          .registrarError(
              ErrorEGorilla.ERROR_DISCO,
              "Error -> posibles causas: "
                  + "\tProblemas al crear un flujo de bytes serializable"
                  + "\tProblemas al serializar el objeto indice"
                  + "\tProblemas al cerrar el flujo serializable");
      // e.printStackTrace();
    }

    byte[] bytes = bs.toByteArray(); // devuelve byte[]

    try {
      if (fichero.exists() == true) {
        String nombreNuevoFichero = fichero.getName();
        nombreNuevoFichero += "_" + archivo.getHash();
        fichero = new File(nombreNuevoFichero);
      }
      FileOutputStream ficheroIndices = new FileOutputStream(fichero);
      BufferedOutputStream bufferedOutput = new BufferedOutputStream(ficheroIndices);
      bufferedOutput.write(bytes, 0, bytes.length);
      bufferedOutput.close();
      // creo que tambien hace falta cerrar el otro
      ficheroIndices.close();
    } catch (FileNotFoundException e) {
      System.out.println("No existe el fichero <" + fichero.getName() + ">");
    } catch (IOException e) {
      /*System.out.println("Error -> posibles causas: ");
      System.out.println( "\tProblemas al escribir en el fichero <"+fichero.getName()+">" );
      System.out.println( "\tProblemas al cerrar el flujo o el fichero <"+fichero.getName()+">" );*/
      ControlDeErrores.getInstancia()
          .registrarError(
              ErrorEGorilla.ERROR_DISCO,
              "Error -> posibles causas: "
                  + "\tProblemas al escribir en el fichero <"
                  + fichero.getName()
                  + ">"
                  + "\tProblemas al cerrar el flujo o el fichero <"
                  + fichero.getName()
                  + ">");
      // e.printStackTrace();
    }
  }
Example #18
0
 public static String stripExtension(File file) {
   try {
     int i = file.getName().lastIndexOf(".");
     String s = file.getName().substring(0, i);
     return s;
   } catch (Exception ex) {
     return null;
   }
 }
Example #19
0
 // http://stackoverflow.com/questions/3154488/best-way-to-iterate-through-a-directory-in-java
 public void showFiles(File[] files) {
   for (File file : files) {
     if (file.isDirectory()) {
       System.out.println("Directory: " + file.getName());
       showFiles(file.listFiles()); // Calls same method again.
     } else {
       System.out.println("File: " + file.getName());
     }
   }
 }
Example #20
0
  protected long getTotalFileSizeSupport(File file) throws TOTorrentException {

    String name = file.getName();

    /////////////////////////////////////////

    /////////////////////////////////////

    if (name.equals(".") || name.equals("..")) {

      return (0);
    }

    if (!file.exists()) {

      throw (new TOTorrentException(
          "TOTorrentCreate: file '" + file.getName() + "' doesn't exist",
          TOTorrentException.RT_FILE_NOT_FOUND));
    }

    if (file.isFile()) {

      if (!ignoreFile(name)) {

        total_file_count++;

        return (file.length());

      } else {

        return (0);
      }
    } else {

      File[] dir_files = file.listFiles();

      if (dir_files == null) {

        throw (new TOTorrentException(
            "TOTorrentCreate: directory '"
                + file.getAbsolutePath()
                + "' returned error when listing files in it",
            TOTorrentException.RT_FILE_NOT_FOUND));
      }

      long length = 0;

      for (int i = 0; i < dir_files.length; i++) {

        length += getTotalFileSizeSupport(dir_files[i]);
      }

      return (length);
    }
  }
  /**
   * Perform recovery on commit logs located in the directory specified by the config file.
   *
   * @return the number of mutations replayed
   */
  public int recover() throws IOException {
    // If createReserveSegments is already flipped, the CLSM is running and recovery has already
    // taken place.
    if (allocator.createReserveSegments) return 0;

    // Allocator could be in the process of initial startup with 0 active and available segments. We
    // need to wait for
    // the allocation manager to finish allocation and add it to available segments so we don't get
    // an invalid response
    // on allocator.manages(...) below by grabbing a file off the filesystem before it's added to
    // the CLQ.
    allocator.allocatingFrom();

    FilenameFilter unmanagedFilesFilter =
        new FilenameFilter() {
          public boolean accept(File dir, String name) {
            // we used to try to avoid instantiating commitlog (thus creating an empty segment ready
            // for writes)
            // until after recover was finished.  this turns out to be fragile; it is less
            // error-prone to go
            // ahead and allow writes before recover(), and just skip active segments when we do.
            return CommitLogDescriptor.isValid(name) && !allocator.manages(name);
          }
        };

    // submit all existing files in the commit log dir for archiving prior to recovery -
    // CASSANDRA-6904
    for (File file :
        new File(DatabaseDescriptor.getCommitLogLocation()).listFiles(unmanagedFilesFilter)) {
      archiver.maybeArchive(file.getPath(), file.getName());
      archiver.maybeWaitForArchiving(file.getName());
    }

    assert archiver.archivePending.isEmpty()
        : "Not all commit log archive tasks were completed before restore";
    archiver.maybeRestoreArchive();

    File[] files =
        new File(DatabaseDescriptor.getCommitLogLocation()).listFiles(unmanagedFilesFilter);
    int replayed = 0;
    if (files.length == 0) {
      logger.info("No commitlog files found; skipping replay");
    } else {
      Arrays.sort(files, new CommitLogSegmentFileComparator());
      logger.info("Replaying {}", StringUtils.join(files, ", "));
      replayed = recover(files);
      logger.info("Log replay complete, {} replayed mutations", replayed);

      for (File f : files) allocator.recycleSegment(f);
    }

    allocator.enableReserveSegmentCreation();
    return replayed;
  }
Example #22
0
 public boolean edtImport(File fi, String date, String tags) {
   if (!fi.exists()) {
     System.err.println("import: file " + fi.getAbsolutePath() + " doesnt exist");
     return false;
   }
   String pname = fi.getName();
   if (store.containsEntry(pname)) {
     System.err.println("import: already have a file named " + pname);
     return false;
   }
   long size = fi.length() / KILOBYTE;
   File save = sec.encryptMainFile(fi, storeLocs.get(0), true);
   if (save == null) {
     System.err.println("import: Encryption failure");
     return false;
   }
   if (checkImports) {
     boolean success = true;
     File checkfi = new File(idx + ".check");
     File checkOut = sec.encryptSpecialFile(save, checkfi, false);
     if (checkOut == null) success = false;
     else {
       String fiHash = sec.digest(fi);
       String outHash = sec.digest(checkOut);
       if (fiHash == null || outHash == null || fiHash.length() < 1 || !fiHash.equals(outHash))
         success = false;
     }
     checkfi.delete();
     if (!success) {
       save.delete();
       if (JOptionPane.showConfirmDialog(
               frm,
               "Confirming "
                   + fi.getName()
                   + "failed\n\n - Would you like to re-import the file?",
               "Import failed",
               JOptionPane.YES_NO_OPTION)
           == JOptionPane.YES_OPTION) {
         String j = impJob(fi, date, tags);
         synchronized (jobs) {
           if (priorityExport) jobs.addLast(j);
           else jobs.addFirst(j);
         }
       }
       return false;
     }
   }
   if (!fi.delete()) {
     System.err.println("import: Couldnt delete old file - continuing");
   }
   store.add(save.getName(), pname, date, size, tags, 0);
   needsSave = true;
   return true;
 }
  public static void main(String[] args) {

    BackgroundEstimation estimation = new BolstadEMBackgroundEstimation();
    // BackgroundEstimation estimation = new UniformBackgroundEstimation();

    String key = args[0];

    WorkflowProperties props = new WorkflowProperties();
    File fplus = new File(props.getDirectory(), String.format("%s_plus.raw", key));
    File fminus = new File(props.getDirectory(), String.format("%s_negative.raw", key));

    // LogTransform transform = LogTransform.NONE;
    LogTransform transform = LogTransform.LOG_TO_EXP;

    BackgroundRemoval norm = new BackgroundRemoval(estimation, transform);

    try {
      System.out.println(String.format("Loading: %s", fplus.getName()));
      norm.load(new WorkflowDataLoader(fplus));
      System.out.println(String.format("Loading: %s", fminus.getName()));
      norm.load(new WorkflowDataLoader(fminus));

      WorkflowIndexing indexing = props.getIndexing(key);

      System.out.println(String.format("Removing background..."));
      norm.removeBackground();

      Filter<ProbeLine, ProbeLine> plus =
          new Filter<ProbeLine, ProbeLine>() {
            public ProbeLine execute(ProbeLine p) {
              return p.strand.equals("+") ? p : null;
            }
          };
      Filter<ProbeLine, ProbeLine> minus =
          new Filter<ProbeLine, ProbeLine>() {
            public ProbeLine execute(ProbeLine p) {
              return p.strand.equals("-") ? p : null;
            }
          };

      System.out.println(String.format("Outputting background-removed results..."));
      File plusOut = new File(props.getDirectory(), String.format("%s_plus.corrected", key));
      File minusOut = new File(props.getDirectory(), String.format("%s_negative.corrected", key));

      outputProbes(new FilterIterator<ProbeLine, ProbeLine>(plus, norm.iterator()), plusOut);
      System.out.println(String.format("\t%s", plusOut.getAbsolutePath()));

      outputProbes(new FilterIterator<ProbeLine, ProbeLine>(minus, norm.iterator()), minusOut);
      System.out.println(String.format("\t%s", minusOut.getAbsolutePath()));

    } catch (IOException e) {
      e.printStackTrace();
    }
  }
Example #24
0
 /**
  * public char[] jetPass(){ JPasswordField psf = new JPasswordField(); psf.grabFocus(); int opt =
  * JOptionPane.showConfirmDialog(frm, psf, "Password", JOptionPane.PLAIN_MESSAGE); if(opt ==
  * JOptionPane.OK_OPTION) return psf.getPassword(); return null; }
  *
  * <p>public String jetString(String msg, String ttl){ return JOptionPane.showInputDialog(frm,
  * msg, ttl, JOptionPane.QUESTION_MESSAGE); }*
  */
 public static String jobString(String job) {
   if (job.charAt(0) == IMPORT_FLAG) {
     String[] brk = job.split(",", 4); // 4 parts to an import string
     File inf = new File(brk[1]);
     return "import " + inf.getName();
   } else {
     String[] brk = job.split(",", 3); // 3 parts to export string
     File plf = new File(brk[2]);
     return "export " + plf.getName();
   }
 }
Example #25
0
 public void postProcessCmdLineArgs(CmdLineParser cmdLineParser) throws CmdLineException {
   for (File inputFile : inputFiles) {
     if (inputFile.getName().endsWith(".xml")
         || inputFile.getName().endsWith(".vtt")
         || inputFile.getName().endsWith(".dfxp")) {
       throw new CmdLineException(
           cmdLineParser,
           new AbstractEncryptOrNotCommand.Message(
               "Subtitle files must either be supplied via command line option --subtitles or --closed-captions"));
     }
   }
 }
Example #26
0
 public static void upload(File[] files) throws FileNotFoundException {
   Files f = null;
   for (File file : files) {
     f = new Files();
     f.name = file.getName();
     f.path = "";
     f.image = new Blob();
     f.image.set(new FileInputStream(file), MimeTypes.getContentType(file.getName()));
     f.save();
     renderText(f.id);
   }
 }
Example #27
0
 public void save(File file) throws IOException {
   if (file.getName().endsWith(".gif")) {
     ImageIO.write(_i, "png", file);
   } else if (file.getName().endsWith(".jpg")) {
     ImageIO.write(_i, "jpg", file);
   } else {
     if (!file.getName().endsWith(".png")) {
       file = new File(file.toString() + ".png");
     }
     ImageIO.write(_i, "png", file);
   }
 }
 /** Find the corresponding meta data file from a given block file */
 private static long parseGenerationStamp(File blockFile, File metaFile) throws IOException {
   String metaname = metaFile.getName();
   String gs =
       metaname.substring(
           blockFile.getName().length() + 1, metaname.length() - METADATA_EXTENSION.length());
   try {
     return Long.parseLong(gs);
   } catch (NumberFormatException nfe) {
     throw (IOException)
         new IOException("blockFile=" + blockFile + ", metaFile=" + metaFile).initCause(nfe);
   }
 }
  /**
   * @param verificationMapFromUnpackedFiles Map of BBI files names to their corresponding
   *     verifications
   * @param listOfBBIfiles List with BBI files extracted from the archive
   * @return List of DTOs containing BBI filename, verification id, outcome of parsing (true/false),
   *     and reason of rejection (if the bbi file was rejected)
   */
  private List<BBIOutcomeDTO> processListOfBBIFiles(
      Map<String, Map<String, String>> verificationMapFromUnpackedFiles,
      List<File> listOfBBIfiles,
      User calibratorEmployee)
      throws ParseException {
    List<BBIOutcomeDTO> resultsOfBBIProcessing = new ArrayList<>();

    for (File bbiFile : listOfBBIfiles) {
      Map<String, String> correspondingVerificationMap =
          verificationMapFromUnpackedFiles.get(bbiFile.getName());
      String correspondingVerification =
          correspondingVerificationMap.get(Constants.VERIFICATION_ID);
      BBIOutcomeDTO.ReasonOfRejection reasonOfRejection = null;
      if (correspondingVerification == null) {
        try {
          correspondingVerification =
              createNewVerificationFromMap(correspondingVerificationMap, calibratorEmployee);
          parseAndSaveBBIFile(bbiFile, correspondingVerification, bbiFile.getName());
          Verification verification = verificationService.findById(correspondingVerification);
          verification.setStatus(Status.CREATED_BY_CALIBRATOR);
          verificationService.saveVerification(verification);
        } catch (NoSuchElementException e) {
          reasonOfRejection = BBIOutcomeDTO.ReasonOfRejection.INVALID_COUNTER_SIZE_AND_SYMBOL;
          logger.info(e);
        } catch (Exception e) {
          reasonOfRejection = BBIOutcomeDTO.ReasonOfRejection.BBI_IS_NOT_VALID;
          logger.info(e);
        }
      } else {
        try {
          updateVerificationFromMap(correspondingVerificationMap, correspondingVerification);
          parseAndSaveBBIFile(bbiFile, correspondingVerification, bbiFile.getName());
        } catch (NoSuchElementException e) {
          reasonOfRejection = BBIOutcomeDTO.ReasonOfRejection.INVALID_COUNTER_SIZE_AND_SYMBOL;
          logger.info(e);
        } catch (IOException e) {
          reasonOfRejection = BBIOutcomeDTO.ReasonOfRejection.BBI_IS_NOT_VALID;
          logger.info(e);
        } catch (Exception e) {
          reasonOfRejection = BBIOutcomeDTO.ReasonOfRejection.INVALID_VERIFICATION_CODE;
          logger.info(e);
        }
      }
      if (reasonOfRejection == null) {
        resultsOfBBIProcessing.add(
            BBIOutcomeDTO.accept(bbiFile.getName(), correspondingVerification));
      } else {
        resultsOfBBIProcessing.add(
            BBIOutcomeDTO.reject(bbiFile.getName(), correspondingVerification, reasonOfRejection));
      }
    }
    return resultsOfBBIProcessing;
  }
  private void deleteListImpl(final ShelvedChangeList changeList) {
    File file = new File(changeList.PATH);
    myFileProcessor.delete(file.getName());

    for (ShelvedBinaryFile binaryFile : changeList.getBinaryFiles()) {
      final String path = binaryFile.SHELVED_PATH;
      if (path != null) {
        File binFile = new File(path);
        myFileProcessor.delete(binFile.getName());
      }
    }
  }