Ejemplo n.º 1
0
  public void loadProperty() {

    try {

      File file = new File(confFileName);

      log.debug("file=" + file.getAbsolutePath());

      confProperties = new Properties();
      confProperties.loadFromXML(new FileInputStream(file));

      bonitaApiHost = confProperties.getProperty("bonita.api.host");
      bonitaApiUsername = confProperties.getProperty("bonita.api.username");
      bonitaApiPassword = confProperties.getProperty("bonita.api.password");
      bonitaApiHttpUsername = confProperties.getProperty("bonita.api.http.username");
      bonitaApiHttpPassword = confProperties.getProperty("bonita.api.http.password");
      bonitaApiPath = confProperties.getProperty("bonita.api.path");

      rallyApiHost = confProperties.getProperty("rally.api.host");
      rallyApiHttpUsername = confProperties.getProperty("rally.api.http.username");
      rallyApiHttpPassword = confProperties.getProperty("rally.api.http.password");
      rallyProjectIds = confProperties.getProperty("rally.project.ids");

      // bonitaProcessId=properties.getProperty("bonita.process.xp_code.id");

      workflowServiceUrl = confProperties.getProperty("service.url");

    } catch (Exception e) {
      log.error("", e);
    }
  }
Ejemplo n.º 2
0
  /**
   * Get dependencies of a source file.
   *
   * @param path The canonical path of source file.
   * @return Path of dependencies.
   */
  private ArrayList<String> getDependencies(String path) {
    if (!dependenceMap.containsKey(path)) {
      ArrayList<String> dependencies = new ArrayList<String>();
      Matcher m = PATTERN_REQUIRE.matcher(read(path, charset));

      while (m.find()) {
        // Decide which root path to use.
        // Path wrapped in <> is related to root path.
        // Path wrapped in "" is related to parent folder of the source file.
        String root = null;

        if (m.group(1).equals("<")) {
          root = this.root;
        } else {
          root = new File(path).getParent();
        }

        // Get path of required file.
        String required = m.group(2);

        File f = new File(root, required);

        if (f.exists()) {
          dependencies.add(canonize(f));
        } else {
          App.exit("Cannot find required file " + required + " in " + path);
        }
      }

      dependenceMap.put(path, dependencies);
    }

    return dependenceMap.get(path);
  }
Ejemplo n.º 3
0
 /**
  * The ActionListener implementation
  *
  * @param event the event.
  */
 public void actionPerformed(ActionEvent event) {
   String searchText = textField.getText().trim();
   if (searchText.equals("") && !saveAs.isSelected() && (fileLength > 10000000)) {
     textPane.setText("Blank search text is not allowed for large IdTables.");
   } else {
     File outputFile = null;
     if (saveAs.isSelected()) {
       outputFile = chooser.getSelectedFile();
       if (outputFile != null) {
         String name = outputFile.getName();
         int k = name.lastIndexOf(".");
         if (k != -1) name = name.substring(0, k);
         name += ".txt";
         File parent = outputFile.getAbsoluteFile().getParentFile();
         outputFile = new File(parent, name);
         chooser.setSelectedFile(outputFile);
       }
       if (chooser.showSaveDialog(this) != JFileChooser.APPROVE_OPTION) System.exit(0);
       outputFile = chooser.getSelectedFile();
     }
     textPane.setText("");
     Searcher searcher = new Searcher(searchText, event.getSource().equals(searchPHI), outputFile);
     searcher.start();
   }
 }
  public void checkPrintFiles() {
    LinkedHashMap<String, File> nameFile = new LinkedHashMap<String, File>();
    nameFile.put("Reference directory", referenceDir);
    nameFile.put("Pipeline.jar", pJar);
    nameFile.put("Pipeline properties", truncPipePropFile);
    nameFile.put("Coverage QC bed", bedForCoverageQC);
    nameFile.put("Variant calling bed", bedForVarCalling);
    nameFile.put("Fasta genome reference", fastaReference);
    nameFile.put("Unfiltered bam", unfilteredBam);
    nameFile.put("Final bam", finalBam);
    nameFile.put("Final vcf", finalVcf);
    if (webRootForLinks != null) nameFile.put("Web links dir", webRootForLinks);
    nameFile.put("Final output dir", outputDirectory);

    boolean missingFile = false;
    System.out.println("\nResources (name exists path):");
    for (String name : nameFile.keySet()) {
      File f = nameFile.get(name);
      boolean fExists = true;
      if (f == null) {
        fExists = false;
        missingFile = true;
      } else {
        fExists = f.exists();
        if (fExists == false) missingFile = true;
      }
      System.out.println(name + "\t" + fExists + "\t" + f);
    }
    if (missingFile) Misc.printErrAndExit("\nMissing resources! See above.");
  }
 public boolean accept(File pathname) {
   if (pathname.isDirectory()) {
     return true;
   } else {
     return pattern.matcher(pathname.getName()).matches();
   }
 }
Ejemplo n.º 6
0
  public static BufferedReader getBufferedReader(String fileName, String context) throws Throwable {
    includeNames.add(fileName);
    if (fileName.startsWith("http://") || fileName.startsWith("https://")) {
      String hashedFileName = MD5(fileName);
      File remoteCacheFile = new File(cacheDirectoryName + File.separator + hashedFileName);
      if (remoteCacheFile.exists()) {
        return new BufferedReader(new FileReader(remoteCacheFile));
      } else {
        URL input = new URL(fileName);
        BufferedReader remoteReader = new BufferedReader(new InputStreamReader(input.openStream()));
        BufferedWriter cacheWriter =
            new BufferedWriter(
                new FileWriter(cacheDirectoryName + File.separator + hashedFileName));

        String tmpLine = remoteReader.readLine();
        while (tmpLine != null) {
          cacheWriter.write(tmpLine);
          cacheWriter.newLine();
          tmpLine = remoteReader.readLine();
        }
        cacheWriter.close();
        return new BufferedReader(
            new FileReader(cacheDirectoryName + File.separator + hashedFileName));
      }
    } else {
      if (fileName.startsWith(context)) {
        return new BufferedReader(new FileReader(fileName));
      } else {
        return new BufferedReader(new FileReader(context + fileName));
      }
    }
  }
 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;
 }
Ejemplo n.º 8
0
    public void actionPerformed(ActionEvent e) {
      if (readOnly) {
        return;
      }
      JFileChooser fc = getFileChooser();
      File currentDirectory = fc.getCurrentDirectory();

      if (!currentDirectory.exists()) {
        JOptionPane.showMessageDialog(
            fc,
            newFolderParentDoesntExistText,
            newFolderParentDoesntExistTitleText,
            JOptionPane.WARNING_MESSAGE);
        return;
      }

      File newFolder;
      try {
        newFolder = fc.getFileSystemView().createNewFolder(currentDirectory);
        if (fc.isMultiSelectionEnabled()) {
          fc.setSelectedFiles(new File[] {newFolder});
        } else {
          fc.setSelectedFile(newFolder);
        }
      } catch (IOException exc) {
        JOptionPane.showMessageDialog(
            fc,
            newFolderErrorText + newFolderErrorSeparator + exc,
            newFolderErrorText,
            JOptionPane.ERROR_MESSAGE);
        return;
      }

      fc.rescanCurrentDirectory();
    }
Ejemplo n.º 9
0
 void put(final URI uri, ArtifactData data) throws Exception {
   reporter.trace("put %s %s", uri, data);
   File tmp = createTempFile(repoDir, "mtp", ".whatever");
   tmp.deleteOnExit();
   try {
     copy(uri.toURL(), tmp);
     byte[] sha = SHA1.digest(tmp).digest();
     reporter.trace("SHA %s %s", uri, Hex.toHexString(sha));
     ArtifactData existing = get(sha);
     if (existing != null) {
       reporter.trace("existing");
       xcopy(existing, data);
       return;
     }
     File meta = new File(repoDir, Hex.toHexString(sha) + ".json");
     File file = new File(repoDir, Hex.toHexString(sha));
     rename(tmp, file);
     reporter.trace("file %s", file);
     data.file = file.getAbsolutePath();
     data.sha = sha;
     data.busy = false;
     CommandData cmddata = parseCommandData(data);
     if (cmddata.bsn != null) {
       data.name = cmddata.bsn + "-" + cmddata.version;
     } else data.name = Strings.display(cmddata.title, cmddata.bsn, cmddata.name, uri);
     codec.enc().to(meta).put(data);
     reporter.trace("TD = " + data);
   } finally {
     tmp.delete();
     reporter.trace("puted %s %s", uri, data);
   }
 }
Ejemplo n.º 10
0
 @Override
 public void actionPerformed(ActionEvent e) {
   if (td.getTabCount() > 0) {
     JFileChooser f = new JFileChooser();
     f.setFileFilter(new MyFileFilter());
     int choose = f.showSaveDialog(getContentPane());
     if (choose == JFileChooser.APPROVE_OPTION) {
       BufferedWriter brw = null;
       try {
         File file = f.getSelectedFile();
         brw = new BufferedWriter(new FileWriter(file));
         int i = td.getSelectedIndex();
         TextDocument ta = (TextDocument) td.getComponentAt(i);
         ta.write(brw);
         ta.fileName = file.getName(); // 將檔案名稱更新為存檔的名稱
         td.setTitleAt(td.getSelectedIndex(), ta.fileName);
         ta.file = file;
         ta.save = true; // 設定已儲存
         System.out.println("Save as pass!");
         td.setTitleAt(i, ta.fileName); // 更新標題名稱
       } catch (Exception exc) {
         exc.printStackTrace();
       } finally {
         try {
           brw.close();
         } catch (Exception ecx) {
           ecx.printStackTrace();
         }
       }
     }
   } else {
     JOptionPane.showMessageDialog(null, "沒有檔案可以儲存!");
   }
 }
Ejemplo n.º 11
0
 private byte[] loadClassData(String className) throws IOException {
   Playground.println("Loading class " + className + ".class", warning);
   File f = new File(System.getProperty("user.dir") + "/" + className + ".class");
   byte[] b = new byte[(int) f.length()];
   new FileInputStream(f).read(b);
   return b;
 }
Ejemplo n.º 12
0
 @Override
 public void actionPerformed(ActionEvent e) {
   JFileChooser f = new JFileChooser();
   f.setFileFilter(new MyFileFilter()); // 設定檔案選擇器
   int choose = f.showOpenDialog(getContentPane()); // 顯示檔案選取
   if (choose == JFileChooser.OPEN_DIALOG) { // 有開啟檔案的話,開始讀檔
     BufferedReader br = null;
     try {
       File file = f.getSelectedFile();
       br = new BufferedReader(new FileReader(file));
       TextDocument ta = new TextDocument(file.getName(), file);
       ta.addKeyListener(new SystemTrackSave());
       ta.read(br, null);
       td.add(ta);
       td.setTitleAt(docCount++, file.getName());
     } catch (Exception exc) {
       exc.printStackTrace();
     } finally {
       try {
         br.close();
       } catch (Exception ecx) {
         ecx.printStackTrace();
       }
     }
   }
 }
Ejemplo n.º 13
0
 private static void tryResUrls(Picture picture) {
   String hi_res = "";
   String url = picture.media_url.toString();
   for (String ending : Main.endings) {
     try {
       hi_res = url.replace(url.substring(url.lastIndexOf("_"), url.lastIndexOf(".")), ending);
       URL hi_url = new URL(hi_res);
       File hi_name = Helper.extractMediaFileNameFromURL(hi_url);
       if (hi_name.equals(picture.media_name)) {
         picture.hi_url = hi_url;
         picture.hi_name = hi_name;
         picture.downloaded_hi = true;
         break;
       } else {
         boolean success = Helper.downloadFileFromURLToFileInTemp(hi_url, hi_name);
         if (success) {
           picture.hi_url = hi_url;
           picture.hi_name = hi_name;
           picture.downloaded_hi = true;
           Helper.moveTempImageToStore(hi_name, new File(Main.blogdir, picture.md5_id));
           break;
         }
       }
     } catch (MalformedURLException ex) {
       Main.error(String.format("Attempted hi res url %s is a malformed URL.", hi_res));
     }
   }
 }
Ejemplo n.º 14
0
 public static File directoryOf(Class clazz) {
   File location = locationOf(clazz);
   if (location.isDirectory()) {
     return location;
   }
   return location.getParentFile();
 }
Ejemplo n.º 15
0
  private Service getService(File base) throws Exception {
    File dataFile = new File(base, "data");
    if (!dataFile.isFile()) return null;

    ServiceData data = getData(ServiceData.class, dataFile);
    return new Service(this, data);
  }
Ejemplo n.º 16
0
 public static void main(String[] args) {
   File path = new File(".");
   String[] list;
   if (args.length == 0) list = path.list();
   else list = path.list(new DirFilter(args[0]));
   Arrays.sort(list, String.CASE_INSENSITIVE_ORDER);
   for (String dirItem : list) System.out.println(dirItem);
 }
Ejemplo n.º 17
0
    public void valueChanged(ListSelectionEvent evt) {
      if (!evt.getValueIsAdjusting()) {
        JFileChooser chooser = getFileChooser();
        FileSystemView fsv = chooser.getFileSystemView();
        JList list = (JList) evt.getSource();

        int fsm = chooser.getFileSelectionMode();
        boolean useSetDirectory = usesSingleFilePane && (fsm == JFileChooser.FILES_ONLY);

        if (chooser.isMultiSelectionEnabled()) {
          File[] files = null;
          Object[] objects = list.getSelectedValues();
          if (objects != null) {
            if (objects.length == 1
                && ((File) objects[0]).isDirectory()
                && chooser.isTraversable(((File) objects[0]))
                && (useSetDirectory || !fsv.isFileSystem(((File) objects[0])))) {
              setDirectorySelected(true);
              setDirectory(((File) objects[0]));
            } else {
              ArrayList<File> fList = new ArrayList<File>(objects.length);
              for (Object object : objects) {
                File f = (File) object;
                boolean isDir = f.isDirectory();
                if ((chooser.isFileSelectionEnabled() && !isDir)
                    || (chooser.isDirectorySelectionEnabled() && fsv.isFileSystem(f) && isDir)) {
                  fList.add(f);
                }
              }
              if (fList.size() > 0) {
                files = fList.toArray(new File[fList.size()]);
              }
              setDirectorySelected(false);
            }
          }
          chooser.setSelectedFiles(files);
        } else {
          File file = (File) list.getSelectedValue();
          if (file != null
              && file.isDirectory()
              && chooser.isTraversable(file)
              && (useSetDirectory || !fsv.isFileSystem(file))) {

            setDirectorySelected(true);
            setDirectory(file);
            if (usesSingleFilePane) {
              chooser.setSelectedFile(null);
            }
          } else {
            setDirectorySelected(false);
            if (file != null) {
              chooser.setSelectedFile(file);
            }
          }
        }
      }
    }
Ejemplo n.º 18
0
 public boolean accept(File f) {
   if (f == null) {
     return false;
   }
   if (f.isDirectory()) {
     return true;
   }
   return pattern.matcher(f.getName()).matches();
 }
Ejemplo n.º 19
0
 public boolean accept(File f) {
   if (f.isDirectory()) {
     return true;
   }
   String fn = f.getName();
   if (fn.toLowerCase().endsWith(".java") || fn.toLowerCase().endsWith(".txt")) {
     return true;
   }
   return false;
 }
  public void init(Editor _editor) {
    this.m_editor = _editor;

    File toolRoot = null;
    try {
      toolRoot =
          new File(
                  SequantoAutomationTool.class
                      .getProtectionDomain()
                      .getCodeSource()
                      .getLocation()
                      .toURI())
              .getParentFile()
              .getParentFile();
    } catch (java.net.URISyntaxException ex) {
      toolRoot =
          new File(
                  SequantoAutomationTool.class
                      .getProtectionDomain()
                      .getCodeSource()
                      .getLocation()
                      .getPath())
              .getParentFile()
              .getParentFile();
    }

    m_generatorPy =
        new File(new File(toolRoot, "generator"), "generate_automation_defines.py")
            .getAbsolutePath();
    m_isWindows = System.getProperty("os.name").toLowerCase().contains("win");
    if (m_isWindows) {
      for (File root : File.listRoots()) {
        File[] files =
            root.listFiles(
                new FileFilter() {
                  public boolean accept(File f) {
                    return f.getName().toLowerCase().startsWith("python");
                  }
                });
        if (files != null) {
          for (File directory : files) {
            m_pythonPath = new File(directory, "python.exe");
            break;
          }
        }
      }
      if (m_pythonPath == null) {
        Base.showMessage(
            "ERROR",
            String.format(
                "Could not python interpreter - Generate Automation tool will not work."));
      }
    }
  }
 private void checkForGzippedVcf() {
   String vcfName = finalVcf.getName();
   if (vcfName.endsWith(".gz")) {
     File uncomp = new File(finalVcf.getParentFile(), vcfName.substring(0, vcfName.length() - 3));
     if (uncomp.exists() == false) {
       deleteTempVcf = true;
       if (IO.uncompress(finalVcf, uncomp) == null)
         Misc.printErrAndExit("ERROR: failed to uncompress -> " + finalVcf);
     }
     finalVcf = uncomp;
   }
 }
Ejemplo n.º 22
0
Archivo: Macro.java Proyecto: bramk/bnd
 public String _isdir(String args[]) {
   if (args.length < 2) {
     domain.warning("Need at least one file name for ${isdir;...}");
     return null;
   }
   boolean isdir = true;
   for (int i = 1; i < args.length; i++) {
     File f = new File(args[i]).getAbsoluteFile();
     isdir &= f.isDirectory();
   }
   return isdir ? "true" : "false";
 }
 public static File getBuildFolder(Sketch data) throws IOException {
   File buildFolder;
   if (PreferencesData.get("build.path") != null) {
     buildFolder = BaseNoGui.absoluteFile(PreferencesData.get("build.path"));
     Files.createDirectories(buildFolder.toPath());
   } else {
     buildFolder =
         FileUtils.createTempFolder("build", DigestUtils.md5Hex(data.getMainFilePath()) + ".tmp");
     DeleteFilesOnShutdown.add(buildFolder);
   }
   return buildFolder;
 }
Ejemplo n.º 24
0
  @Nonnull
  private static File getOutputFileCreatingDirIfNeeded(
      @Nonnull String outputDir, @Nonnull String sourceFilePath) {
    File outputFile = getOutputFile(outputDir, sourceFilePath);
    File parentDir = outputFile.getParentFile();

    if (!parentDir.exists()) {
      boolean outputDirCreated = parentDir.mkdirs();
      assert outputDirCreated : "Failed to create output dir: " + outputDir;
    }

    return outputFile;
  }
Ejemplo n.º 25
0
  public List<CommandData> getCommands(File commandDir) throws Exception {
    List<CommandData> result = new ArrayList<CommandData>();

    if (!commandDir.exists()) {
      return result;
    }

    for (File f : commandDir.listFiles()) {
      CommandData data = getData(CommandData.class, f);
      if (data != null) result.add(data);
    }
    return result;
  }
Ejemplo n.º 26
0
  private ArrayList GetFolderTree(String s_Dir, String s_Flag, int n_Indent, int n_TreeIndex) {
    String s_List = "";
    ArrayList aSubFolders = new ArrayList();

    File file = new File(s_Dir);
    File[] filelist = file.listFiles();

    if (filelist != null && filelist.length > 0) {
      for (int i = 0; i < filelist.length; i++) {
        if (filelist[i].isDirectory()) {
          aSubFolders.add(filelist[i].getName());
        }
      }

      int n_Count = aSubFolders.size();
      String s_LastFlag = "";
      String s_Folder = "";
      for (int i = 1; i <= n_Count; i++) {
        if (i < n_Count) {
          s_LastFlag = "0";
        } else {
          s_LastFlag = "1";
        }

        s_Folder = aSubFolders.get(i - 1).toString();
        s_List =
            s_List
                + "arr"
                + s_Flag
                + "["
                + String.valueOf(n_TreeIndex)
                + "]=new Array(\""
                + s_Folder
                + "\","
                + String.valueOf(n_Indent)
                + ", "
                + s_LastFlag
                + ");\n";
        n_TreeIndex = n_TreeIndex + 1;
        ArrayList a_Temp =
            GetFolderTree(s_Dir + s_Folder + sFileSeparator, s_Flag, n_Indent + 1, n_TreeIndex);
        s_List = s_List + a_Temp.get(0).toString();
        n_TreeIndex = Integer.valueOf(a_Temp.get(1).toString()).intValue();
      }
    }

    ArrayList a_Return = new ArrayList();
    a_Return.add(s_List);
    a_Return.add(String.valueOf(n_TreeIndex));
    return a_Return;
  }
Ejemplo n.º 27
0
 /**
  * Takes a line and looks for an archive group tag. If one is found, the information from the tag
  * is returned as an <CODE>ArchiveGroup</CODE>. If a tag is found, the data in the tag is stored
  * in the <CODE>HashMap</CODE> provided.
  *
  * @param currentLine The line in which to look for the archive tag.
  * @param template The <CODE>Template</CODE> to which the <CODE>ArchiveGroup</CODE> belongs.
  * @return The archive request tag data as an instance of <CODE>ArchiveGroup</CODE>, <CODE>null
  *     </CODE> if the line passed in does not contain an arFile tag.
  */
 private ArchiveGroup parseArchiveGroupTag(String currentLine, Template template) {
   ArchiveGroup archiveTag;
   Matcher currentMatcher = archiveRequestPattern.matcher(currentLine);
   if (currentMatcher.find()) {
     String fileName = currentMatcher.group(1);
     archiveTag = template.getArchiveGroup(fileName);
     if (archiveTag == null) {
       File groupFile = new File(fileName);
       archiveTag = new ArchiveGroup(groupFile.getParent(), groupFile.getName());
       template.addArchiveGroup(archiveTag);
     }
   } else archiveTag = null;
   return archiveTag;
 }
Ejemplo n.º 28
0
Archivo: Macro.java Proyecto: bramk/bnd
  public String _fmodified(String args[]) throws Exception {
    verifyCommand(args, _fmodifiedHelp, null, 2, Integer.MAX_VALUE);

    long time = 0;
    Collection<String> names = new ArrayList<String>();
    for (int i = 1; i < args.length; i++) {
      Processor.split(args[i], names);
    }
    for (String name : names) {
      File f = new File(name);
      if (f.exists() && f.lastModified() > time) time = f.lastModified();
    }
    return "" + time;
  }
Ejemplo n.º 29
0
  public List<ServiceData> getServices(File serviceDir) throws Exception {
    List<ServiceData> result = new ArrayList<ServiceData>();

    if (!serviceDir.exists()) {
      return result;
    }

    for (File sdir : serviceDir.listFiles()) {
      File dataFile = new File(sdir, "data");
      ServiceData data = getData(ServiceData.class, dataFile);
      result.add(data);
    }
    return result;
  }
Ejemplo n.º 30
0
Archivo: Macro.java Proyecto: bramk/bnd
  String ls(String args[], boolean relative) {
    if (args.length < 2)
      throw new IllegalArgumentException(
          "the ${ls} macro must at least have a directory as parameter");

    File dir = domain.getFile(args[1]);
    if (!dir.isAbsolute())
      throw new IllegalArgumentException(
          "the ${ls} macro directory parameter is not absolute: " + dir);

    if (!dir.exists())
      throw new IllegalArgumentException(
          "the ${ls} macro directory parameter does not exist: " + dir);

    if (!dir.isDirectory())
      throw new IllegalArgumentException(
          "the ${ls} macro directory parameter points to a file instead of a directory: " + dir);

    Collection<File> files = new ArrayList<File>(new SortedList<File>(dir.listFiles()));

    for (int i = 2; i < args.length; i++) {
      Instructions filters = new Instructions(args[i]);
      files = filters.select(files, true);
    }

    List<String> result = new ArrayList<String>();
    for (File file : files) result.add(relative ? file.getName() : file.getAbsolutePath());

    return Processor.join(result, ",");
  }