Example #1
0
  public static String showSecurity(HttpServletRequest req, String role) {
    StringBuilder sbuff = new StringBuilder();

    sbuff.append("Security Info\n");
    sbuff.append(" req.getRemoteUser(): ").append(req.getRemoteUser()).append("\n");
    sbuff.append(" req.getUserPrincipal(): ").append(req.getUserPrincipal()).append("\n");
    sbuff
        .append(" req.isUserInRole(")
        .append(role)
        .append("):")
        .append(req.isUserInRole(role))
        .append("\n");
    sbuff.append(" ------------------\n");

    return sbuff.toString();
  }
Example #2
0
  /**
   * Show details about the request
   *
   * @param servlet used to get teh servlet context, may be null
   * @param req the request
   * @return string showing the details of the request.
   */
  public static String showRequestDetail(HttpServlet servlet, HttpServletRequest req) {
    StringBuilder sbuff = new StringBuilder();

    sbuff.append("Request Info\n");
    sbuff.append(" req.getServerName(): ").append(req.getServerName()).append("\n");
    sbuff.append(" req.getServerPort(): ").append(req.getServerPort()).append("\n");
    sbuff.append(" req.getContextPath:").append(req.getContextPath()).append("\n");
    sbuff.append(" req.getServletPath:").append(req.getServletPath()).append("\n");
    sbuff.append(" req.getPathInfo:").append(req.getPathInfo()).append("\n");
    sbuff.append(" req.getQueryString:").append(req.getQueryString()).append("\n");
    sbuff
        .append(" getQueryStringDecoded:")
        .append(EscapeStrings.urlDecode(req.getQueryString()))
        .append("\n");
    /*try {
      sbuff.append(" getQueryStringDecoded:").append(URLDecoder.decode(req.getQueryString(), "UTF-8")).append("\n");
    } catch (UnsupportedEncodingException e1) {
      e1.printStackTrace();
    }*/
    sbuff.append(" req.getRequestURI:").append(req.getRequestURI()).append("\n");
    sbuff.append(" getRequestBase:").append(getRequestBase(req)).append("\n");
    sbuff.append(" getRequestServer:").append(getRequestServer(req)).append("\n");
    sbuff.append(" getRequest:").append(getRequest(req)).append("\n");
    sbuff.append("\n");

    sbuff.append(" req.getPathTranslated:").append(req.getPathTranslated()).append("\n");
    String path = req.getPathTranslated();
    if ((path != null) && (servlet != null)) {
      ServletContext context = servlet.getServletContext();
      sbuff.append(" getMimeType:").append(context.getMimeType(path)).append("\n");
    }
    sbuff.append("\n");
    sbuff.append(" req.getScheme:").append(req.getScheme()).append("\n");
    sbuff.append(" req.getProtocol:").append(req.getProtocol()).append("\n");
    sbuff.append(" req.getMethod:").append(req.getMethod()).append("\n");
    sbuff.append("\n");
    sbuff.append(" req.getContentType:").append(req.getContentType()).append("\n");
    sbuff.append(" req.getContentLength:").append(req.getContentLength()).append("\n");

    sbuff.append(" req.getRemoteAddr():").append(req.getRemoteAddr());
    try {
      sbuff
          .append(" getRemoteHost():")
          .append(java.net.InetAddress.getByName(req.getRemoteHost()).getHostName())
          .append("\n");
    } catch (java.net.UnknownHostException e) {
      sbuff.append(" getRemoteHost():").append(e.getMessage()).append("\n");
    }
    sbuff.append(" getRemoteUser():").append(req.getRemoteUser()).append("\n");

    sbuff.append("\n");
    sbuff.append("Request Parameters:\n");
    Enumeration params = req.getParameterNames();
    while (params.hasMoreElements()) {
      String name = (String) params.nextElement();
      String values[] = req.getParameterValues(name);
      if (values != null) {
        for (int i = 0; i < values.length; i++) {
          sbuff
              .append("  ")
              .append(name)
              .append("  (")
              .append(i)
              .append("): ")
              .append(values[i])
              .append("\n");
        }
      }
    }
    sbuff.append("\n");

    sbuff.append("Request Headers:\n");
    Enumeration names = req.getHeaderNames();
    while (names.hasMoreElements()) {
      String name = (String) names.nextElement();
      Enumeration values = req.getHeaders(name); // support multiple values
      if (values != null) {
        while (values.hasMoreElements()) {
          String value = (String) values.nextElement();
          sbuff.append("  ").append(name).append(": ").append(value).append("\n");
        }
      }
    }
    sbuff.append(" ------------------\n");

    return sbuff.toString();
  }
  public void doPost(HttpServletRequest request, HttpServletResponse response)
      throws ServletException, IOException {

    // set the response

    Shepherd myShepherd = new Shepherd();

    Vector rEncounters = new Vector();

    // setup data dir
    String rootWebappPath = getServletContext().getRealPath("/");
    File webappsDir = new File(rootWebappPath).getParentFile();
    File shepherdDataDir = new File(webappsDir, CommonConfiguration.getDataDirectoryName());
    // if(!shepherdDataDir.exists()){shepherdDataDir.mkdir();}
    File encountersDir = new File(shepherdDataDir.getAbsolutePath() + "/encounters");
    // if(!encountersDir.exists()){encountersDir.mkdir();}

    // set up the files
    String gisFilename = "geneGIS_export_" + request.getRemoteUser() + ".csv";
    File gisFile = new File(encountersDir.getAbsolutePath() + "/" + gisFilename);

    myShepherd.beginDBTransaction();

    try {

      // set up the output stream
      FileOutputStream fos = new FileOutputStream(gisFile);
      OutputStreamWriter outp = new OutputStreamWriter(fos);

      try {

        EncounterQueryResult queryResult =
            EncounterQueryProcessor.processQuery(
                myShepherd, request, "year descending, month descending, day descending");
        rEncounters = queryResult.getResult();

        int numMatchingEncounters = rEncounters.size();

        // build the CSV file header
        StringBuffer locusString = new StringBuffer("");
        int numLoci = 2; // most covered species will be loci
        try {
          numLoci = (new Integer(CommonConfiguration.getProperty("numLoci"))).intValue();
        } catch (Exception e) {
          System.out.println("numPloids configuration value did not resolve to an integer.");
          e.printStackTrace();
        }

        for (int j = 0; j < numLoci; j++) {
          locusString.append(",Locus" + (j + 1) + " A1,Locus" + (j + 1) + " A2");
        }
        // out.println("<html><body>");
        // out.println("Individual ID,Other ID 1,Date,Time,Latitude,Longitude,Area,Sub
        // Area,Sex,Haplotype"+locusString.toString());

        outp.write(
            "Individual ID,Other ID 1,Date,Time,Latitude,Longitude,Area,Sub Area,Sex,Haplotype"
                + locusString.toString()
                + "\n");

        for (int i = 0; i < numMatchingEncounters; i++) {

          Encounter enc = (Encounter) rEncounters.get(i);
          String assembledString = "";
          if (enc.getIndividualID() != null) {
            assembledString += enc.getIndividualID();
          }
          if (enc.getAlternateID() != null) {
            assembledString += "," + enc.getAlternateID();
          } else {
            assembledString += ",";
          }

          String dateString = ",";
          if (enc.getYear() > 0) {
            dateString += enc.getYear();
            if (enc.getMonth() > 0) {
              dateString += ("-" + enc.getMonth());
              if (enc.getDay() > 0) {
                dateString += ("-" + enc.getDay());
              }
            }
          }
          assembledString += dateString;

          String timeString = ",";
          if (enc.getHour() > -1) {
            timeString += enc.getHour() + ":" + enc.getMinutes();
          }
          assembledString += timeString;

          if ((enc.getDecimalLatitude() != null) && (enc.getDecimalLongitude() != null)) {
            assembledString += "," + enc.getDecimalLatitude();
            assembledString += "," + enc.getDecimalLongitude();
          } else {
            assembledString += ",,";
          }

          assembledString += "," + enc.getVerbatimLocality();
          assembledString += "," + enc.getLocationID();
          assembledString += "," + enc.getSex();

          // find and print the haplotype
          String haplotypeString = ",";
          if (enc.getHaplotype() != null) {
            haplotypeString += enc.getHaplotype();
          }

          // find and print the ms markers
          String msMarkerString = "";
          List<TissueSample> samples = enc.getTissueSamples();
          int numSamples = samples.size();
          boolean foundMsMarkers = false;
          for (int k = 0; k < numSamples; k++) {
            if (!foundMsMarkers) {
              TissueSample t = samples.get(k);
              List<GeneticAnalysis> analyses = t.getGeneticAnalyses();
              int aSize = analyses.size();
              for (int l = 0; l < aSize; l++) {
                GeneticAnalysis ga = analyses.get(l);
                if (ga.getAnalysisType().equals("MicrosatelliteMarkers")) {
                  foundMsMarkers = true;
                  MicrosatelliteMarkersAnalysis ga2 = (MicrosatelliteMarkersAnalysis) ga;
                  List<Locus> loci = ga2.getLoci();
                  int localLoci = loci.size();
                  for (int m = 0; m < localLoci; m++) {
                    Locus locus = loci.get(m);
                    if (locus.getAllele0() != null) {
                      msMarkerString += "," + locus.getAllele0();
                    } else {
                      msMarkerString += ",";
                    }
                    if (locus.getAllele1() != null) {
                      msMarkerString += "," + locus.getAllele1();
                    } else {
                      msMarkerString += ",";
                    }
                  }
                }
              }
            }
          }

          // out.println("<p>"+assembledString+haplotypeString+msMarkerString+"</p>");
          outp.write(assembledString + haplotypeString + msMarkerString + "\n");
        }
        outp.close();
        outp = null;

        // now write out the file
        response.setContentType("text/csv");
        response.setHeader("Content-Disposition", "attachment;filename=" + gisFilename);
        ServletContext ctx = getServletContext();
        // InputStream is = ctx.getResourceAsStream("/encounters/"+gisFilename);
        InputStream is = new FileInputStream(gisFile);

        int read = 0;
        byte[] bytes = new byte[BYTES_DOWNLOAD];
        OutputStream os = response.getOutputStream();

        while ((read = is.read(bytes)) != -1) {
          os.write(bytes, 0, read);
        }
        os.flush();
        os.close();

      } catch (Exception ioe) {
        ioe.printStackTrace();
        response.setContentType("text/html");
        PrintWriter out = response.getWriter();
        out.println(ServletUtilities.getHeader(request));
        out.println(
            "<html><body><p><strong>Error encountered</strong> with file writing. Check the relevant log.</p>");
        out.println(
            "<p>Please let the webmaster know you encountered an error at: EncounterSearchExportGeneGISFormat servlet</p></body></html>");
        out.println(ServletUtilities.getFooter());
        out.close();
        outp.close();
        outp = null;
      }

    } catch (Exception e) {
      e.printStackTrace();
      response.setContentType("text/html");
      PrintWriter out = response.getWriter();
      out.println(ServletUtilities.getHeader(request));
      out.println("<html><body><p><strong>Error encountered</strong></p>");
      out.println(
          "<p>Please let the webmaster know you encountered an error at: EncounterSearchExportGeneGISFormat servlet</p></body></html>");
      out.println(ServletUtilities.getFooter());
      out.close();
    }
    myShepherd.rollbackDBTransaction();
    myShepherd.closeDBTransaction();
  }