Ejemplo n.º 1
0
  /** {@inheritDoc} */
  @Override
  public ActionForward execute(
      ComponentContext context,
      ActionMapping mapping,
      ActionForm form,
      HttpServletRequest request,
      HttpServletResponse response)
      throws Exception {
    HttpSession session = request.getSession();
    final InterMineAPI im = SessionMethods.getInterMineAPI(session);

    InterMineBag imBag = (InterMineBag) request.getAttribute("bag");
    WebConfig webConfig = SessionMethods.getWebConfig(request);
    Model model = im.getModel();
    TemplateManager templateManager = im.getTemplateManager();

    Map<Class, ApiTemplate> conversionTypesMap =
        TypeConverter.getConversionTemplates(
            templateManager.getConversionTemplates(),
            TypeUtil.instantiate(model.getPackageName() + "." + imBag.getType()));
    ArrayList<String> conversionTypes = new ArrayList<String>();
    Map<Type, Boolean> fastaMap = new HashMap<Type, Boolean>();
    for (Class<?> clazz : conversionTypesMap.keySet()) {
      conversionTypes.add(TypeUtil.unqualifiedName(clazz.getName()));
      Type type = webConfig.getTypes().get(clazz.getName());
      FieldConfig fieldConfig = type.getFieldConfigMap().get("length");
      if (fieldConfig != null && fieldConfig.getDisplayer() != null) {
        fastaMap.put(type, Boolean.TRUE);
      } else {
        fastaMap.put(type, Boolean.FALSE);
      }
    }
    // Use custom converters
    BagQueryConfig bagQueryConfig = im.getBagQueryConfig();
    String bagType = imBag.getType();
    Set<AdditionalConverter> additionalConverters = bagQueryConfig.getAdditionalConverters(bagType);
    request.setAttribute("customConverters", additionalConverters);
    request.setAttribute("conversionTypes", conversionTypes);
    request.setAttribute("fastaMap", fastaMap);
    return null;
  }
Ejemplo n.º 2
0
  /**
   * Forward to the correct method based on the button pressed
   *
   * @param mapping The ActionMapping used to select this instance
   * @param form The optional ActionForm bean for this request (if any)
   * @param request The HTTP request we are processing
   * @param response The HTTP response we are creating
   * @return an ActionForward object defining where control goes next
   * @exception Exception if the application business logic throws an exception
   */
  @Override
  public ActionForward execute(
      ActionMapping mapping,
      ActionForm form,
      HttpServletRequest request,
      HttpServletResponse response)
      throws Exception {
    HttpSession session = request.getSession();
    final InterMineAPI im = SessionMethods.getInterMineAPI(session);
    Profile profile = SessionMethods.getProfile(session);

    Model model = im.getModel();
    ModifyBagDetailsForm mbdf = (ModifyBagDetailsForm) form;
    BagManager bagManager = im.getBagManager();

    InterMineBag imBag = bagManager.getBag(profile, mbdf.getBagName());
    String bagIdentifier = "bag." + imBag.getName();

    if (request.getParameter("removeFromBag") != null) {
      PagedTable pc = SessionMethods.getResultsTable(session, bagIdentifier);
      String msg = "";

      if (pc.isAllRowsSelected()) {
        // TODO these messages need to be moved to properties file
        msg = "You can't remove all items from your list.  Try deleting your list instead.";
      } else {
        int removed = pc.removeSelectedFromBag(imBag, session);
        msg = "You have removed " + removed + " items from your list.";
      }
      SessionMethods.recordMessage(msg, session);
      // return new ForwardParameters(mapping.findForward("bagDetails"))
      // .addParameter("bagName", mbdf.getBagName()).forward();

      // pass an extra parameter telling the JSP to open up the results table
      return new ForwardParameters(mapping.findForward("bagDetails"))
          .addParameter("bagName", mbdf.getBagName())
          .addParameter("table", "open")
          .forward();

    } else if (request.getParameter("addToBag") != null) {
      InterMineBag newBag = bagManager.getBag(profile, mbdf.getExistingBagName());
      String msg = "";
      if (newBag.getType().equals(imBag.getType())) {
        PagedTable pc = SessionMethods.getResultsTable(session, bagIdentifier);
        int oldSize = newBag.size();
        pc.addSelectedToBag(newBag);
        int newSize = newBag.size();
        int added = newSize - oldSize;
        msg =
            "You have added "
                + added
                + " items from list <strong>"
                + imBag.getName()
                + "</strong> to list <strong>"
                + newBag.getName()
                + "</strong>";
      } else {
        msg = "You can only add objects to other lists of the same type";
      }
      SessionMethods.recordMessage(msg, session);
      // orthologues form
    } else if (request.getParameter("convertToThing") != null) {
      BagQueryConfig bagQueryConfig = im.getBagQueryConfig();
      Set<AdditionalConverter> additionalConverters =
          bagQueryConfig.getAdditionalConverters(imBag.getType());
      if (additionalConverters != null && !additionalConverters.isEmpty()) {
        for (AdditionalConverter additionalConverter : additionalConverters) {
          BagConverter bagConverter =
              PortalHelper.getBagConverter(
                  im, SessionMethods.getWebConfig(request), additionalConverter.getClassName());
          List<Integer> converted =
              bagConverter.getConvertedObjectIds(
                  profile, imBag.getType(), imBag.getContentsAsIds(), mbdf.getExtraFieldValue());

          if (converted.size() == 1) {
            return goToReport(mapping, converted.get(0).toString());
          }

          String bagName =
              NameUtil.generateNewName(
                  profile.getSavedBags().keySet(),
                  mbdf.getExtraFieldValue() + " orthologues of " + imBag.getName());

          InterMineBag newBag = profile.createBag(bagName, imBag.getType(), "", im.getClassKeys());
          return createBagAndGoToBagDetails(mapping, newBag, converted);
        }
      }

      // "use in bag" link
    } else if (request.getParameter("useBag") != null) {
      PagedTable pc = SessionMethods.getResultsTable(session, bagIdentifier);
      PathQuery pathQuery = pc.getWebTable().getPathQuery().clone();
      SessionMethods.setQuery(session, pathQuery);
      session.setAttribute("path", imBag.getType());
      session.setAttribute("prefix", imBag.getType());
      String msg = "You can now create a query using your list " + imBag.getName();
      SessionMethods.recordMessage(msg, session);
      return mapping.findForward("query");

      // convert links
    } else if (request.getParameter("convert") != null && request.getParameter("bagName") != null) {
      String type2 = request.getParameter("convert");
      TemplateManager templateManager = im.getTemplateManager();
      PathQuery q =
          BagConversionHelper.getConvertedObjects(
              session,
              templateManager.getConversionTemplates(),
              TypeUtil.instantiate(model.getPackageName() + "." + imBag.getType()),
              TypeUtil.instantiate(model.getPackageName() + "." + type2),
              imBag);
      q.setTitle(type2 + "s from list '" + imBag.getName() + "'");
      SessionMethods.loadQuery(q, session, response);
      String qid = SessionMethods.startQueryWithTimeout(request, false, q);
      Thread.sleep(200); // slight pause in the hope of avoiding holding page
      final String trail = "|bag." + imBag.getName();
      return new ForwardParameters(mapping.findForward("waiting"))
          .addParameter("trail", trail)
          .addParameter("qid", qid)
          .forward();
    }
    return new ForwardParameters(mapping.findForward("bagDetails"))
        .addParameter("bagName", mbdf.getBagName())
        .forward();
  }