/** Gets all Genomic Data. */
  private ProfileDataSummary getGenomicData(
      String cancerStudyId,
      HashMap<String, GeneticProfile> defaultGeneticProfileSet,
      SampleList defaultSampleSet,
      String geneListStr,
      ArrayList<SampleList> sampleList,
      HttpServletRequest request,
      HttpServletResponse response)
      throws IOException, ServletException, DaoException {

    // parse geneList, written in the OncoPrintSpec language (except for changes by XSS clean)
    double zScore =
        ZScoreUtil.getZScore(
            new HashSet<String>(defaultGeneticProfileSet.keySet()),
            new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()),
            request);
    double rppaScore = ZScoreUtil.getRPPAScore(request);

    ParserOutput theOncoPrintSpecParserOutput =
        OncoPrintSpecificationDriver.callOncoPrintSpecParserDriver(
            geneListStr,
            new HashSet<String>(defaultGeneticProfileSet.keySet()),
            new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()),
            zScore,
            rppaScore);

    ArrayList<String> geneList = new ArrayList<String>();
    geneList.addAll(theOncoPrintSpecParserOutput.getTheOncoPrintSpecification().listOfGenes());

    ArrayList<ProfileData> profileDataList = new ArrayList<ProfileData>();
    Set<String> warningUnion = new HashSet<String>();

    for (GeneticProfile profile : defaultGeneticProfileSet.values()) {
      try {
        GetProfileData remoteCall =
            new GetProfileData(
                profile, geneList, StringUtils.join(defaultSampleSet.getSampleList(), " "));
        ProfileData pData = remoteCall.getProfileData();
        warningUnion.addAll(remoteCall.getWarnings());
        profileDataList.add(pData);
      } catch (IllegalArgumentException e) {
        e.getStackTrace();
      }
    }

    ProfileMerger merger = new ProfileMerger(profileDataList);
    ProfileData mergedProfile = merger.getMergedProfile();

    ProfileDataSummary dataSummary =
        new ProfileDataSummary(
            mergedProfile,
            theOncoPrintSpecParserOutput.getTheOncoPrintSpecification(),
            zScore,
            rppaScore);
    return dataSummary;
  }
  // Process the request
  private String processRequest(HttpServletRequest request, HttpServletResponse response) {
    HttpSession session = request.getSession();
    String userIDs = (String) session.getAttribute("user.id");
    userIDs = (userIDs != null && userIDs.compareTo(" ") > 0) ? userIDs : "0";
    long userID = Long.parseLong(userIDs);
    String command = request.getParameter("command");
    String template = request.getParameter("template");
    String pageHash = request.getParameter("pagehash");
    String pageTitle = request.getParameter("pagetitle");
    String pageDescription = request.getParameter("pagedescription");

    String outLine = "";
    String nextScript = request.getParameter("nextscript");
    OutputStream toClient;
    boolean success = false;

    // System.out.println("userid=" + userID + ", id=" + id + ", command=" + command);

    command = (command != null && command.compareTo(" ") > 0) ? command : "form";
    nextScript = (nextScript != null && nextScript.compareTo(" ") > 0) ? nextScript : "simple1.jsp";

    //    inputstring = (inputstring != null && inputstring.compareTo(" ") > 0) ? inputstring : "";

    DbConn myConn = null;
    try {

      Context initCtx = new InitialContext();
      // String csiSchema = (String) initCtx.lookup("java:comp/env/csi-schema-path");
      // String acronym = (String) initCtx.lookup("java:comp/env/SystemAcronym");
      myConn = new DbConn();
      String csiSchema = myConn.getSchemaPath();
      if (userID != 0) {
        if (command.equals("add")) {
          outLine = "";
        } else if (command.equals("update")) {
          outLine = "";
        } else if (command.equals("updatepage")) {
          UHash uPage = new UHash(pageHash, myConn);
          // System.out.println("Got Here 1");
          if (template.equals("simple1")) {
            TextItem title = new TextItem(uPage.get("title"), myConn);
            title.setText(pageTitle);
            title.save(myConn);
            TextItem description = new TextItem(uPage.get("description"), myConn);
            description.setText(pageDescription);
            description.save(myConn);
          } else if (template.equals("simple2")) {
          }

        } else if (command.equals("test")) {
          outLine = "test";
        }
        success = true;
      }

    } catch (IllegalArgumentException e) {
      outLine = outLine + "IllegalArgumentException caught: " + e.getMessage();
      ALog.logActivity(userID, "csi", 0, pageHash + " error: '" + outLine + "'");
      // log(outLine);
    } catch (NullPointerException e) {
      outLine = outLine + "NullPointerException caught: " + e.getMessage();
      ALog.logActivity(userID, "csi", 0, pageHash + " error: '" + outLine + "'");
      // log(outLine);
    }

    // catch (IOException e) {
    //    outLine = outLine + "IOException caught: " + e.getMessage();
    //    ALog.logActivity(userID, "csi", 0, pageHash + " error: '" + outLine + "'");
    //    //log(outLine);
    // }

    catch (Exception e) {
      outLine = outLine + "Exception caught: " + e.getMessage();
      ALog.logActivity(userID, "csi", 0, pageHash + " error: '" + outLine + "'");
      // log(outLine);
    } finally {
      try {
        generateResponse(outLine, command, nextScript, success, response);
      } catch (Exception i) {
      }

      myConn.release();
      // log("Test log message\n");
    }

    return outLine;
  }
Exemple #3
0
  // Process the request
  private String processRequest(HttpServletRequest request, HttpServletResponse response) {
    String command = request.getParameter("command");
    String id = request.getParameter("id");
    String description = request.getParameter("description");
    String status = request.getParameter("rstatus");
    status = (status != null && status.compareTo(" ") > 0) ? status : null;
    String outLine = "";
    // String nextScript = "home.jsp";
    String nextScript = request.getParameter("nextscript");
    OutputStream toClient;
    HttpSession session = request.getSession();
    boolean success = false;
    String userIDs = (String) session.getAttribute("user.id");
    long userID = Long.parseLong(userIDs);

    command = (command != null && command.compareTo(" ") > 0) ? command : "form";
    nextScript = (nextScript != null && nextScript.compareTo(" ") > 0) ? nextScript : "roles.jsp";

    //    inputstring = (inputstring != null && inputstring.compareTo(" ") > 0) ? inputstring : "";

    DbConn myConn = null;
    try {

      Context initCtx = new InitialContext();
      // String csiSchema = (String) initCtx.lookup("java:comp/env/csi-schema-path");
      String acronym = (String) initCtx.lookup("java:comp/env/SystemAcronym");
      myConn = new DbConn();
      String csiSchema = myConn.getSchemaPath();
      if (command.equals("add")) {
        Role item = new Role();
        item.setDescription(description);
        item.setStatus(status);
        getPermissions(request, item);
        getPositions(request, item);
        item.add(myConn, userID);
        GlobalMembership.refresh(myConn);
        success = true;
        outLine = "";

      } else if (command.equals("update")) {
        Role item = new Role(myConn, Long.parseLong(id));
        item.setDescription(description);
        item.setStatus(status);
        getPermissions(request, item);
        getPositions(request, item);
        item.save(myConn, userID);
        GlobalMembership.refresh(myConn);
        success = true;
        outLine = "";
      } else if (command.equals("drop")) {
        Role item = new Role(myConn, Long.parseLong(id));
        item.drop(myConn, userID);
        success = true;
        outLine = "Role " + item.getDescription() + " Removed";
      } else if (command.equals("test")) {
        outLine = "test";
      }

    } catch (IllegalArgumentException e) {
      outLine = outLine + "IllegalArgumentException caught: " + e.getMessage();
      ALog.logActivity(userID, "csi", 0, "Role error: '" + outLine + "'");
      // log(outLine);
    } catch (NullPointerException e) {
      outLine = outLine + "NullPointerException caught: " + e.getMessage();
      ALog.logActivity(userID, "csi", 0, "Role error: '" + outLine + "'");
      // log(outLine);
    }

    // catch (IOException e) {
    //    outLine = outLine + "IOException caught: " + e.getMessage();
    //    ALog.logActivity(userID, "csi", 0, "Role error: '" + outLine + "'");
    //    //log(outLine);
    // }

    catch (Exception e) {
      outLine = outLine + "Exception caught: " + e.getMessage();
      ALog.logActivity(userID, "csi", 0, "Role error: '" + outLine + "'");
      // log(outLine);
    } finally {
      try {
        generateResponse(outLine, command, nextScript, success, response);
      } catch (Exception i) {
      }

      myConn.release();
      // log("Test log message\n");
    }

    return outLine;
  }