/*.................................................................................................................*/
 public void processOutputFiles(String jobURL) {
   if (rootDir != null) {
     downloadWorkingResults(jobURL, rootDir, true);
     if (outputFileProcessor != null && outputFilePaths != null && lastModified != null) {
       String[] paths = outputFileProcessor.modifyOutputPaths(outputFilePaths);
       for (int i = 0; i < paths.length && i < lastModified.length; i++) {
         File file = new File(paths[i]);
         long lastMod = file.lastModified();
         if (!MesquiteLong.isCombinable(lastModified[i]) || lastMod > lastModified[i]) {
           outputFileProcessor.processOutputFile(paths, i);
           lastModified[i] = lastMod;
         }
       }
     }
   }
 }
  /*.................................................................................................................*/
  public boolean monitorAndCleanUpShell(String jobURL) {
    boolean stillGoing = true;

    if (!checkUsernamePassword(true)) {
      return false;
    }
    lastModified = null;
    if (outputFilePaths != null) {
      lastModified = new long[outputFilePaths.length];
      LongArray.deassignArray(lastModified);
    }
    String status = "";
    while (!jobCompleted(jobURL) && stillGoing) {
      if (StringUtil.blank(status))
        ownerModule.logln(
            "CIPRes Job Status: " + getJobStatus(jobURL) + "  (" + StringUtil.getDateTime() + ")");

      //	if (jobSubmitted(jobURL))
      //		processOutputFiles();
      try {
        Thread.sleep(minPollIntervalSeconds * 1000);
      } catch (InterruptedException e) {
        MesquiteMessage.notifyProgrammer("InterruptedException in CIPRes monitoring");
        return false;
      }

      stillGoing = watcher == null || watcher.continueShellProcess(null);
      String newStatus = getJobStatus(jobURL);
      if (newStatus != null && !newStatus.equalsIgnoreCase(status)) {
        ownerModule.logln(
            "CIPRes Job Status: " + newStatus + "  (" + StringUtil.getDateTime() + ")");
        status = newStatus;
      } else ownerModule.log(".");
      if (newStatus != null && newStatus.equalsIgnoreCase("SUBMITTED")) { // job is running
        processOutputFiles(jobURL);
      }
    }
    ownerModule.logln("CIPRes job completed.");
    if (outputFileProcessor != null) {
      if (rootDir != null) {
        ownerModule.logln("About to download results from CIPRes.");
        if (downloadResults(jobURL, rootDir, false))
          outputFileProcessor.processCompletedOutputFiles(outputFilePaths);
        else return false;
      }
    }

    return true;
  }