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;
 }
  private String listFiles(final File cache, List<File> toDelete) throws Exception {
    boolean stopServices = false;
    if (toDelete == null) {
      toDelete = new ArrayList<File>();
    } else {
      stopServices = true;
    }
    int count = 0;
    Formatter f = new Formatter();

    f.format(" - Cache:%n    * %s%n", cache.getCanonicalPath());
    f.format(" - Commands:%n");
    for (CommandData cdata : getCommands(new File(cache, COMMANDS))) {
      f.format("    * %s \t0 handle for \"%s\"%n", cdata.bin, cdata.name);
      toDelete.add(new File(cdata.bin));
      count++;
    }
    f.format(" - Services:%n");
    for (ServiceData sdata : getServices(new File(cache, SERVICE))) {
      if (sdata != null) {
        f.format("    * %s \t0 service directory for \"%s\"%n", sdata.sdir, sdata.name);
        toDelete.add(new File(sdata.sdir));
        File initd = platform.getInitd(sdata);
        if (initd != null && initd.exists()) {
          f.format("    * %s \t0 init.d file for \"%s\"%n", initd.getCanonicalPath(), sdata.name);
          toDelete.add(initd);
        }
        if (stopServices) {
          Service s = getService(sdata);
          try {
            s.stop();
          } catch (Exception e) {
          }
        }
        count++;
      }
    }
    f.format("%n");

    String result = (count > 0) ? f.toString() : null;
    f.close();
    return result;
  }
Beispiel #3
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  /**
   * Get the canonical path of a file.
   *
   * @param f The file.
   * @return The canonical path.
   */
  private String canonize(File f) {
    String path = null;

    try {
      path = f.getCanonicalPath();
    } catch (IOException e) {
      App.exit(e);
    }

    return path;
  }
  private void executePipelineJob() {
    String[] cmd = null;
    try {
      // write out tempTemplate
      File template = new File(outputDirectory, "pipelineTemplate.xml");
      if (IO.writeString(xmlTemplate, template) == false)
        Misc.printErrAndExit("Problem writing -> " + template);

      // build and execute cmd
      cmd =
          new String[] {
            "java",
            "-jar",
            "-Xmx2G",
            pJar.getCanonicalPath(),
            "-props",
            completePipelinePropFile.getCanonicalPath(),
            template.getCanonicalPath()
          };

      String stringCmd = Misc.stringArrayToString(cmd, " ");
      System.out.println("\nExecuting:\n" + stringCmd);
      System.out.println("\nPipelineOutput:");
      String[] out = IO.executeViaProcessBuilder(cmd, true);

      // check output for possible errors
      for (String line : out) {
        String lcLine = line.toLowerCase();
        // watch out for cases where error is mentioned in a warning output line.
        if (lcLine.contains("error") && lcLine.startsWith("warning") == false)
          Misc.printErrAndExit(
              "\n\nERROR found in Pipeline.jar output, see above. Aborting!\n" + line);
      }

    } catch (Exception e) {
      e.printStackTrace();
      Misc.printErrAndExit("ERROR: executing " + Misc.stringArrayToString(cmd, " "));
    }
  }
  public String what(String key, boolean oneliner) throws Exception {
    byte[] sha;

    Matcher m = SHA_P.matcher(key);
    if (m.matches()) {
      sha = Hex.toByteArray(key);
    } else {
      m = URL_P.matcher(key);
      if (m.matches()) {
        URL url = new URL(key);
        sha = SHA1.digest(url.openStream()).digest();
      } else {
        File jarfile = new File(key);
        if (!jarfile.exists()) {
          reporter.error("File does not exist: %s", jarfile.getCanonicalPath());
        }
        sha = SHA1.digest(jarfile).digest();
      }
    }
    reporter.trace("sha %s", Hex.toHexString(sha));
    Revision revision = library.getRevision(sha);
    if (revision == null) {
      return null;
    }

    StringBuilder sb = new StringBuilder();
    Formatter f = new Formatter(sb);
    Justif justif = new Justif(120, 20, 70, 20, 75);
    DateFormat dateFormat = DateFormat.getDateInstance();

    try {
      if (oneliner) {
        f.format("%20s %s%n", Hex.toHexString(revision._id), createCoord(revision));
      } else {
        f.format("Artifact: %s%n", revision.artifactId);
        if (revision.organization != null && revision.organization.name != null) {
          f.format(" (%s)", revision.organization.name);
        }
        f.format("%n");
        f.format("Coordinates\t0: %s%n", createCoord(revision));
        f.format("Created\t0: %s%n", dateFormat.format(new Date(revision.created)));
        f.format("Size\t0: %d%n", revision.size);
        f.format("Sha\t0: %s%n", Hex.toHexString(revision._id));
        f.format("URL\t0: %s%n", createJpmLink(revision));
        f.format("%n");
        f.format("%s%n", revision.description);
        f.format("%n");
        f.format("Dependencies\t0:%n");
        boolean flag = false;
        Iterable<RevisionRef> closure = library.getClosure(revision._id, true);
        for (RevisionRef dep : closure) {
          f.format(
              " - %s \t2- %s \t3- %s%n",
              dep.name, createCoord(dep), dateFormat.format(new Date(dep.created)));
          flag = true;
        }
        if (!flag) {
          f.format("     None%n");
        }
        f.format("%n");
      }
      f.flush();
      justif.wrap(sb);
      return sb.toString();
    } finally {
      f.close();
    }
  }
  public CommandData parseCommandData(ArtifactData artifact) throws Exception {
    File source = new File(artifact.file);
    if (!source.isFile()) throw new FileNotFoundException();

    CommandData data = new CommandData();
    data.sha = artifact.sha;
    data.jpmRepoDir = repoDir.getCanonicalPath();
    JarFile jar = new JarFile(source);
    try {
      reporter.trace("Parsing %s", source);
      Manifest m = jar.getManifest();
      Attributes main = m.getMainAttributes();
      data.name = data.bsn = main.getValue("Bundle-SymbolicName");
      String version = main.getValue("Bundle-Version");
      if (version == null) data.version = Version.LOWEST;
      else data.version = new Version(version);

      data.main = main.getValue("Main-Class");
      data.description = main.getValue("Bundle-Description");
      data.title = main.getValue("JPM-Name");

      reporter.trace("name " + data.name + " " + data.main + " " + data.title);
      DependencyCollector path = new DependencyCollector(this);
      path.add(artifact);
      DependencyCollector bundles = new DependencyCollector(this);
      if (main.getValue("JPM-Classpath") != null) {
        Parameters requires = OSGiHeader.parseHeader(main.getValue("JPM-Classpath"));

        for (Map.Entry<String, Attrs> e : requires.entrySet()) {
          path.add(e.getKey(), e.getValue().get("name")); // coordinate
        }
      } else if (!artifact.local) { // No JPM-Classpath, falling back to
        // server's revision
        // Iterable<RevisionRef> closure =
        // library.getClosure(artifact.sha,
        // false);
        // System.out.println("getting closure " + artifact.url + " " +
        // Strings.join("\n",closure));

        // if (closure != null) {
        // for (RevisionRef ref : closure) {
        // path.add(Hex.toHexString(ref.revision));
        // }
        // }
      }

      if (main.getValue("JPM-Runbundles") != null) {
        Parameters jpmrunbundles = OSGiHeader.parseHeader(main.getValue("JPM-Runbundles"));

        for (Map.Entry<String, Attrs> e : jpmrunbundles.entrySet()) {
          bundles.add(e.getKey(), e.getValue().get("name"));
        }
      }

      reporter.trace("collect digests runpath");
      data.dependencies.addAll(path.getDigests());
      reporter.trace("collect digests bundles");
      data.runbundles.addAll(bundles.getDigests());

      Parameters command = OSGiHeader.parseHeader(main.getValue("JPM-Command"));
      if (command.size() > 1) reporter.error("Only one command can be specified");

      for (Map.Entry<String, Attrs> e : command.entrySet()) {
        data.name = e.getKey();

        Attrs attrs = e.getValue();

        if (attrs.containsKey("jvmargs")) data.jvmArgs = attrs.get("jvmargs");

        if (attrs.containsKey("title")) data.title = attrs.get("title");

        if (data.title != null) data.title = data.name;
      }
      return data;
    } finally {
      jar.close();
    }
  }