Ejemplo n.º 1
0
  private void copy(File workspaceDir, InputStream in, Pattern glob, boolean overwrite)
      throws Exception {

    Jar jar = new Jar("dot", in);
    try {
      for (Entry<String, Resource> e : jar.getResources().entrySet()) {

        String path = e.getKey();
        bnd.trace("path %s", path);

        if (glob != null && !glob.matcher(path).matches()) continue;

        Resource r = e.getValue();
        File dest = Processor.getFile(workspaceDir, path);
        if (overwrite
            || !dest.isFile()
            || dest.lastModified() < r.lastModified()
            || r.lastModified() <= 0) {

          bnd.trace("copy %s to %s", path, dest);

          File dp = dest.getParentFile();
          if (!dp.exists() && !dp.mkdirs()) {
            throw new IOException("Could not create directory " + dp);
          }

          IO.copy(r.openInputStream(), dest);
        }
      }
    } finally {
      jar.close();
    }
  }
Ejemplo n.º 2
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 3
0
  /**
   * Constructor
   *
   * @throws IOException
   */
  public JustAnotherPackageManager(Reporter reporter, Platform platform, File homeDir, File binDir)
      throws IOException {
    this.platform = platform;
    this.reporter = reporter;
    this.homeDir = homeDir;
    if (!homeDir.exists() && !homeDir.mkdirs())
      throw new IllegalArgumentException("Could not create directory " + homeDir);

    repoDir = IO.getFile(homeDir, "repo");
    if (!repoDir.exists() && !repoDir.mkdirs())
      throw new IllegalArgumentException("Could not create directory " + repoDir);

    commandDir = new File(homeDir, COMMANDS);
    serviceDir = new File(homeDir, SERVICE);
    commandDir.mkdir();
    serviceDir.mkdir();
    service = new File(repoDir, SERVICE_JAR_FILE);
    if (!service.isFile()) init();

    this.binDir = binDir;
    if (!binDir.exists() && !binDir.mkdirs())
      throw new IllegalArgumentException("Could not create bin directory " + binDir);
  }
Ejemplo n.º 4
0
 public static void storeImage(BufferedImage image, String s) {
   String ext;
   File f;
   try {
     ext = s.substring(s.lastIndexOf(".") + 1);
     f = new File(s);
     f.mkdirs();
   } catch (Exception e) {
     System.out.println(e);
     return;
   }
   if (!ext.equals("gif") && !ext.equals("jpg") && !ext.equals("png")) {
     System.out.println("Cannot write to file: Illegal extension " + ext);
     return;
   }
   try {
     ImageIO.write(image, ext, f);
   } catch (Exception e) {
     System.out.println(e);
   }
 }
Ejemplo n.º 5
0
  /**
   * @param data
   * @param target
   * @throws Exception
   * @throws IOException
   */
  public String createService(ServiceData data) throws Exception, IOException {

    File sdir = new File(serviceDir, data.name);
    if (!sdir.exists() && !sdir.mkdirs()) {
      throw new IOException("Could not create directory " + data.sdir);
    }
    data.sdir = sdir.getAbsolutePath();

    File lock = new File(data.sdir, LOCK);
    data.lock = lock.getAbsolutePath();

    if (data.work == null) data.work = new File(data.sdir, "work").getAbsolutePath();
    if (data.user == null) data.user = platform.user();

    if (data.user == null) data.user = "******";

    new File(data.work).mkdir();

    if (data.log == null) data.log = new File(data.sdir, "log").getAbsolutePath();

    // TODO
    // if (Data.validate(data) != null)
    // return "Invalid service data: " + Data.validate(data);

    if (service == null)
      throw new RuntimeException(
          "Missing biz.aQute.jpm.service in repo, should have been installed by init, try reiniting");

    data.serviceLib = service.getAbsolutePath();

    platform.chown(data.user, true, new File(data.sdir));

    String s = platform.createService(data, null, false);
    if (s == null) storeData(new File(data.sdir, "data"), data);
    return s;
  }
Ejemplo n.º 6
0
  public void _workspace(WorkspaceOptions opts) throws Exception {
    File base = bnd.getBase();

    String name = opts._arguments().get(0);

    File workspaceDir = Processor.getFile(base, name);
    name = workspaceDir.getName();
    base = workspaceDir.getParentFile();

    if (base == null) {
      bnd.error(
          "You cannot create a workspace in the root (%s). The parent of a workspace %n"
              + "must be a valid directory. Recommended is to dedicate a directory to %n"
              + "all (or related) workspaces.",
          workspaceDir);
      return;
    }

    if (!opts.anyname() && !Verifier.isBsn(name)) {
      bnd.error(
          "You specified a workspace name that does not follow the recommended pattern "
              + "(it should be like a Bundle Symbolic name). It is a bit pedantic but it "
              + "really helps hwne you get many workspaces. If you insist on this name, use the -a/--anyname option.");
      return;
    }

    Workspace ws = bnd.getWorkspace((File) null);

    if (ws != null && ws.isValid()) {
      bnd.error(
          "You are currently in a workspace already (%s) in %s. You can only create a new workspace outside an existing workspace",
          ws, base);
      return;
    }

    File eclipseDir = workspaceDir;
    workspaceDir.mkdirs();

    if (!opts.single()) workspaceDir = new File(workspaceDir, "scm");

    workspaceDir.mkdirs();

    if (!base.isDirectory()) {
      bnd.error("Could not create directory for the bnd workspace %s", base);
    } else if (!eclipseDir.isDirectory()) {
      bnd.error("Could not create directory for the Eclipse workspace %s", eclipseDir);
    }

    if (!workspaceDir.isDirectory()) {
      bnd.error("Could not create the workspace directory %s", workspaceDir);
      return;
    }

    if (!opts.update() && !opts.force() && workspaceDir.list().length > 0) {
      bnd.error(
          "The workspace directory %s is not empty, specify -u/--update to update or -f/--force to replace",
          workspaceDir);
    }

    InputStream in = getClass().getResourceAsStream("/templates/enroute.zip");
    if (in == null) {
      bnd.error("Cannot find template in this jar %s", "/templates/enroute.zip");
      return;
    }

    Pattern glob = Pattern.compile("[^/]+|cnf/.*|\\...+/.*");

    copy(workspaceDir, in, glob, opts.force());

    File readme = new File(workspaceDir, "README.md");
    if (readme.isFile()) IO.copy(readme, bnd.out);

    bnd.out.printf(
        "%nWorkspace %s created.%n%n" //
            + " Start Eclipse:%n" //
            + "   1) Select the Eclipse workspace %s%n" //
            + "   2) Package Explorer context menu: Import/General/Existing Projects from %s%n"
            + "%n"
            + "", //
        workspaceDir.getName(), eclipseDir, workspaceDir);
  }
  /** This method will process each argument and assign new variables */
  public void processArgs(String[] args) {
    Pattern pat = Pattern.compile("-[a-z]");
    System.out.println(
        "\n" + IO.fetchUSeqVersion() + " Arguments: " + Misc.stringArrayToString(args, " ") + "\n");
    for (int i = 0; i < args.length; i++) {
      String lcArg = args[i].toLowerCase();
      Matcher mat = pat.matcher(lcArg);
      if (mat.matches()) {
        char test = args[i].charAt(1);
        try {
          switch (test) {
            case 'o':
              jobId = args[++i];
              break;
            case 's':
              sampleId = args[++i];
              break;
            case 'm':
              submitter = args[++i];
              break;
            case 'y':
              analysisType = args[++i];
              break;
            case 'w':
              webRootForLinks = new File(args[++i]);
              break;
            case 'e':
              snpEffGenome = args[++i];
              break;
            case 'i':
              minimumReadDepth = args[++i];
              break;
            case 't':
              threads = args[++i];
              break;
            case 'l':
              uploadVarsToNGSWeb = true;
              break;
            case 'j':
              pJar = new File(args[++i]);
              break;
            case 'p':
              truncPipePropFile = new File(args[++i]);
              break;
            case 'q':
              bedForCoverageQC = new File(args[++i]);
              break;
            case 'b':
              bedForVarCalling = new File(args[++i]);
              break;
            case 'r':
              fastaReference = new File(args[++i]);
              break;
            case 'u':
              unfilteredBam = new File(args[++i]);
              break;
            case 'f':
              finalBam = new File(args[++i]);
              break;
            case 'v':
              finalVcf = new File(args[++i]);
              break;
            case 'd':
              outputDirectory = new File(args[++i]);
              break;
            case 'c':
              referenceDir = new File(args[++i]);
              break;
            case 'h':
              printDocs();
              System.exit(0);
            default:
              Misc.printErrAndExit("\nProblem, unknown option! " + mat.group());
          }
        } catch (Exception e) {
          Misc.printErrAndExit(
              "\nSorry, something doesn't look right with this parameter: -" + test + "\n");
        }
      }
    }

    // check output dir and if needed set sampleId
    if (outputDirectory != null) {
      outputDirectory.mkdirs();
      if (sampleId.length() == 0) sampleId = outputDirectory.getName();
    }
    // check root directory if needed
    if (webRootForLinks != null) {
      if (webRootForLinks.exists() == false) webRootForLinks.mkdirs();
      // links dir?
      File links = new File(webRootForLinks, "links");
      if (links.exists() == false) links.mkdirs();
    }

    // look for required fields and files
    checkPrintFields();
    checkPrintFiles();
    checkForGzippedVcf();
  }