Exemplo n.º 1
0
 public RCallServicesREngine(REngine rs, String envir) {
   this.rs = rs;
   try {
     env = rs.parseAndEval(envir);
   } catch (org.rosuda.REngine.REngineException e) {
     e.printStackTrace(); // To change body of catch statement use File | Settings | File
     // Templates.
   } catch (REXPMismatchException e) {
     e.printStackTrace(); // To change body of catch statement use File | Settings | File
     // Templates.
   }
   try {
     rs.parseAndEval(
         "options(error = function() { assign(\"" + ERROR_VAR + "\", geterrmessage()})",
         env,
         true);
   } catch (org.rosuda.REngine.REngineException e) {
     throw new REngineException(e);
   } catch (REXPMismatchException e) {
     throw new REngineException(e);
   }
 }
Exemplo n.º 2
0
  @Override
  protected void doPost(HttpServletRequest req, HttpServletResponse resp)
      throws ServletException, IOException {

    Connection conn = SQLConnectionFactory.getConnection();
    ServletUtil util = new ServletUtil();

    UserSession us = new UserSession();
    long uid = -1;
    try {
      uid = us.getUserId(req, resp, conn);
    } catch (Exception e) {
      util.setResponse(resp, "[\"Error: Error loading session data.\"]");
      try {
        conn.close();
      } catch (SQLException e1) {
        e1.printStackTrace();
      }
      return;
    }

    String network = req.getParameter("network");
    long fid = -1;
    try {
      fid = Long.parseLong(network);
      Util u = new Util();
      if (!u.dataexists(conn, "usersessions.Networks", uid, fid)) {
        util.setResponse(resp, "[\"Error: Error loading network.\"]");
        try {
          conn.close();
        } catch (SQLException e1) {
          e1.printStackTrace();
        }
        return;
      }
    } catch (Exception e) {
      util.setResponse(resp, "[\"Error: Error loading network.\"]");
      try {
        conn.close();
      } catch (SQLException e1) {
        e1.printStackTrace();
      }
      return;
    }

    Gson gson = new Gson();
    String[] genelists = req.getParameterValues("genes[]");
    String[] diseaselists = req.getParameterValues("diseases[]");
    String[] regionlists = req.getParameterValues("regions[]");
    String[] snplists = req.getParameterValues("snps[]");

    // int ts = Integer.parseInt(traitsrc);
    int ts = 2; // Just GWAS for now.

    // boolean promoter = req.getParameter("promoter").equals("true");

    SIIndexUtil siu = new SIIndexUtil();
    Integer[] sids =
        siu.getIndices(conn, uid, fid, ts, genelists, diseaselists, regionlists, snplists);

    String fminsize = req.getParameter("minsize");
    String fmaxsize = req.getParameter("maxsize");

    int minsize = 1;
    int maxsize = Integer.MAX_VALUE;
    try {
      minsize = Integer.parseInt(fminsize);
      maxsize = Integer.parseInt(fmaxsize);
    } catch (NumberFormatException e) {
    }

    AIEJson heatmap = null;
    AnnotationInteractionEnrichment sph = new AnnotationInteractionEnrichment();
    try {
      heatmap = sph.generateHeatmap(conn, fid, sids, minsize, maxsize);
    } catch (SQLException e1) {
      e1.printStackTrace();
    } catch (REngineException e) {
      e.printStackTrace();
    } catch (REXPMismatchException e) {
      e.printStackTrace();
    }

    try {
      conn.close();
    } catch (SQLException e) {
      e.printStackTrace();
    }

    resp.setContentType("application/json");
    PrintWriter out = resp.getWriter();

    out.print(gson.toJson(heatmap, AIEJson.class));
    out.flush();
  }