예제 #1
0
  /**
   * This constructor is used when running this for QC. Analysis_level, annotation_level, and
   * normalize_method are all hard-coded for this call.
   */
  public AsyncAffyPowerTools(Dataset selectedDataset, HttpSession session) {

    log = Logger.getRootLogger();

    this.selectedDataset = selectedDataset;
    this.newDatasetVersion = selectedDataset.new DatasetVersion();
    this.newDatasetVersion.setVersion_path(selectedDataset.getPath());
    this.session = session;
    this.analysis_level = "transcript";
    this.annotation_level = "core";
    this.normalize_method = "rma-sketch";
    this.userLoggedIn = (User) session.getAttribute("userLoggedIn");
  }
예제 #2
0
  public void run() throws RuntimeException {

    Thread thisThread = Thread.currentThread();
    log.debug("Starting run method of AsyncAffyPowerTools. thisThread = " + thisThread.getName());
    String fileName = "";
    try {
      //
      // If this thread is interrupted, throw an Exception
      //
      ThreadReturn.ifInterruptedStop();

      fileName = newDatasetVersion.getVersion_path() + "AffyPowerTools";

      String aptDir = (String) session.getAttribute("aptDir");
      log.debug("aptDir = " + aptDir + ", fileName = " + fileName);
      boolean mouse = (selectedDataset.getOrganism().equals("Mm") ? true : false);
      String mousePrefix = "Mo";
      String ratPrefix = "Ra";
      String filePrefix = (mouse ? mousePrefix : ratPrefix) + "Ex-1_0-st-v1.r2.";
      String version = (mouse ? "mm8." : "rn5.");
      String masked = (probeMask.equals("T") ? "MASKED." : "");

      String probeSetFile = aptDir + filePrefix + masked + "pgf";
      String clfFile = aptDir + filePrefix + "clf";
      String gcBackgroundFile = aptDir + filePrefix + "antigenomic.bgp";
      String transcriptsFile =
          aptDir + filePrefix + "dt1." + version + annotation_level + "." + masked + "mps";
      String probesetsFile =
          aptDir + filePrefix + "dt1." + version + annotation_level + "." + masked + "ps";
      String qcProbesetsFile = aptDir + filePrefix + "qcc";
      String analysisPathway = "dabg";
      String outputDir = newDatasetVersion.getVersion_path();
      String celFileListing = selectedDataset.getPath() + selectedDataset.getFileListingName();
      log.debug("outputDir = " + outputDir + ", celFileListing = " + celFileListing);

      // Create parameter value records?

      String function = aptDir + "apt-probeset-summarize";
      List<String> functionArgsList =
          new ArrayList<String>(
              Arrays.asList(
                  function,
                  "-p",
                  probeSetFile,
                  "-c",
                  clfFile,
                  "-a",
                  normalize_method,
                  "-b",
                  gcBackgroundFile,
                  "--qc-probesets",
                  qcProbesetsFile,
                  "-a",
                  analysisPathway,
                  "-o",
                  outputDir,
                  "--cel-files",
                  celFileListing));

      if (analysis_level.equals("probeset")) {
        functionArgsList.add("-s");
        functionArgsList.add(probesetsFile);
      } else {
        functionArgsList.add("-m");
        functionArgsList.add(transcriptsFile);
      }
      String[] functionArgs =
          (String[]) functionArgsList.toArray(new String[functionArgsList.size()]);
      log.debug("functionArgs = ");
      myDebugger.print(functionArgs);

      String[] envVariables = new String[] {"PATH=$PATH:" + aptDir};
      log.debug("envVariables = ");
      new Debugger().print(envVariables);

      ExecHandler myExecHandler = new ExecHandler(aptDir, functionArgs, envVariables, fileName);

      log.debug("starting APT exec process");
      myExecHandler.runExec();
      log.debug("just finished APT exec process");
      //
      // If this thread is interrupted, throw an Exception
      //
      ThreadReturn.ifInterruptedStop();

    } catch (Throwable t) {
      log.error("in exception of AsyncAffyPowerTools", t);

      if (t instanceof ThreadException) {
        log.error("throwable exception is a ThreadException. cause = " + t.getCause().getMessage());
        //
        // This saves the Throwable object so an Exception can be detected
        // by the calling program
        //
        ThreadReturn.save(t);
      } else if (t instanceof ThreadInterruptedException) {
        log.error("throwable exception is a ThreadInterruptedException");
        ThreadReturn.save(new Throwable("ThreadInterruptedException in AsyncAffyPowerTools", t));
      } else if (t instanceof RException) {
        log.error("throwable exception is an RException");
        ThreadReturn.save(
            new Throwable("RException in AsyncAffyPowerTools is " + t.getMessage(), t));
      } else {
        log.error("exception caused AsyncAffyPowerTools");
        ThreadReturn.save(t);
      }

      Email myEmail = new Email();
      myEmail.setTo(userLoggedIn.getEmail());
      myEmail.setSubject("Affymetrix Power Tools process had errors");

      String mainContent =
          userLoggedIn.getFormal_name()
              + ",\n\n"
              + "Thank you for using the PhenoGen Informatics website.  "
              + "The Affymetrix Power Tools process that you initiated ";
      String errorContent =
          mainContent
              + "was not completed successfully.  "
              + "The system administrator has been notified of the error. "
              + "\n"
              + "You will be contacted via email once the problem is resolved.";

      String adminErrorContent =
          "The following email was sent to "
              + userLoggedIn.getEmail()
              + ":\n"
              + errorContent
              + "\n"
              + "The file is "
              + fileName
              + "\n"
              + "The error cause was "
              + t.getCause()
              + (t.getCause() != null ? t.getCause().getMessage() : t.getMessage())
              + "\n and the Message = "
              + t.getMessage();
      try {
        myEmail.setContent(errorContent);
        myEmail.sendEmail();
        myEmail.setContent(adminErrorContent);
        myEmail.sendEmailToAdministrator("");
        log.debug("just sent email to administrator notifying of Affymetrix Power Tools errors");
      } catch (MessagingException e2) {
        log.error("in exception of AsyncAffyPowerTools while sending email", e2);
        throw new RuntimeException();
      }
      // throw new RuntimeException(e.getMessage());
    } finally {
      log.debug("executing finally clause in AsyncAffyPowerTools");
    }
    log.debug("done with AsyncAffyPowerTools run method");
  }