/**
  * this is the primary method that sends a query to the CIPRes REST service. It expects to receive
  * an XML file, which it returns in Document if the root tag matc hes xmlRootTag
  */
 public Document cipresQuery(HttpClient httpclient, String URL, String xmlRootTag) {
   if (StringUtil.blank(URL)) return null;
   try {
     HttpGet httpget = new HttpGet(URL);
     httpget.addHeader("cipres-appkey", CIPRESkey);
     try {
       HttpResponse response = httpclient.execute(httpget);
       HttpEntity responseEntity = response.getEntity();
       InputStream instream = responseEntity.getContent();
       BufferedReader br = new BufferedReader(new InputStreamReader(instream));
       String line = "";
       StringBuffer sb = new StringBuffer();
       while ((line = br.readLine()) != null) {
         sb.append(line + StringUtil.lineEnding());
       }
       Document cipresResponseDoc = loadXMLFile(xmlRootTag, sb.toString());
       if (cipresResponseDoc != null && verbose) {
         ownerModule.logln(sb.toString());
       }
       if (cipresResponseDoc == null) {
         Document errorDoc = loadXMLFile(sb.toString());
         if (errorDoc != null) reportError(errorDoc, "Error in communicating with CIPRes", true);
       }
       EntityUtils.consume(response.getEntity());
       return cipresResponseDoc;
     } catch (IOException e) {
       Debugg.printStackTrace(e);
     } catch (Exception e) {
       Debugg.printStackTrace(e);
     }
   } catch (Exception e) {
     Debugg.printStackTrace(e);
   }
   return null;
 }
  /** The core method that initiates a job on CIPRes. */
  public boolean postJob(
      HttpClient httpclient, MultipartEntityBuilder builder, MesquiteString jobURL) {
    if (builder == null) return false;
    String URL = baseURL + "/job/" + username;
    HttpPost httppost = new HttpPost(URL);
    httppost.addHeader("cipres-appkey", CIPRESkey);

    // some of this from
    // http://stackoverflow.com/questions/18964288/upload-a-file-through-an-http-form-via-multipartentitybuilder-with-a-progress
    HttpEntity cipresEntity = builder.build();

    httppost.setEntity(cipresEntity);

    try {
      HttpResponse response = httpclient.execute(httppost);

      HttpEntity responseEntity = response.getEntity();
      InputStream instream = responseEntity.getContent();
      BufferedReader br = new BufferedReader(new InputStreamReader(instream));
      StringBuffer sb = new StringBuffer();
      String line = "";
      while ((line = br.readLine()) != null) {
        sb.append(line + StringUtil.lineEnding());
      }

      Document cipresResponseDoc = loadXMLFile("jobstatus", sb.toString()); // let's see how it went
      boolean success = false;
      if (cipresResponseDoc != null) {
        processJobSubmissionResponse(cipresResponseDoc, jobURL);
        if (verbose) ownerModule.logln(sb.toString());
        if (jobURL != null) success = StringUtil.notEmpty(jobURL.getValue());
        else success = true;
      } else {
        cipresResponseDoc = loadXMLFile(sb.toString());
        reportError(cipresResponseDoc, "Error with CIPRes run", false);
      }
      EntityUtils.consume(response.getEntity());
      return success;
    } catch (IOException e) {
      Debugg.printStackTrace(e);
    }
    return false;
  }
 /*.................................................................................................................*/
 public String preparePreferencesForXML() {
   StringBuffer buffer = new StringBuffer(200);
   StringUtil.appendXMLTag(buffer, 2, "username", username);
   StringUtil.appendXMLTag(buffer, 2, "jobNumber", jobNumber);
   return buffer.toString();
 }