source: trunk/www/common/overview/index.jsp @ 5076

<%-- $Id: index.jsp 5076 2009-08-25 09:15:41Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2009 Nicklas Nordborg

  This file is part of BASE - BioArray Software Environment.
  Available at http://base.thep.lu.se/

  BASE is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 3
  of the License, or (at your option) any later version.

  BASE is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with BASE. If not, see <http://www.gnu.org/licenses/>.
  ------------------------------------------------------------------
--%>
<%@ page session="false"
  import="net.sf.basedb.core.SessionControl"
  import="net.sf.basedb.core.DbControl"
  import="net.sf.basedb.core.Item"
  import="net.sf.basedb.core.BasicItem"
  import="net.sf.basedb.core.Project"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.Presets"
  import="net.sf.basedb.core.Presets.Preset"
  import="net.sf.basedb.util.overview.GenericOverview"
  import="net.sf.basedb.util.overview.Node"
  import="net.sf.basedb.util.overview.Validator"
  import="net.sf.basedb.util.overview.ValidationOptions"
  import="net.sf.basedb.util.overview.Severity"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.WebException"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.util.overview.OverviewUtil"
  import="net.sf.basedb.clients.web.util.HTML"
  import="java.util.Map"
  import="java.util.List"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final String ID = sc.getId();
final String cmd = request.getParameter("cmd");
final String root = request.getContextPath()+"/";

String forward = null;
String redirect = null;
String message = null;
DbControl dc = null;
try
{
  if (cmd == null || "Overview".equals(cmd))
  {
    // Display the overview page
    final Item itemType = Item.valueOf(request.getParameter("item_type"));
    final int itemId = Values.getInt(request.getParameter("item_id"));
    dc = sc.newDbControl();
    BasicItem item = itemType.getById(dc, itemId);
    Project project = sc.getActiveProjectId() == 0 ? 
        null : Project.getById(dc, sc.getActiveProjectId());
    GenericOverview overview = OverviewUtil.getNewOrCurrentOverview(dc, item, project);
    overview.getNodeValidatorFactory().setDisabled(true);
    overview.expand(dc, overview.getRootNode(), false);
    dc.close();
    redirect = "frameset.jsp?ID="+ID+"&show_failures="+false;
  }
  else if ("Validate".equals(cmd))
  {
    final Item itemType = Item.valueOf(request.getParameter("item_type"));
    final int itemId = Values.getInt(request.getParameter("item_id"));
    dc = sc.newDbControl();
    BasicItem item = itemType.getById(dc, itemId);
    Project project = sc.getActiveProjectId() == 0 ? 
        null : Project.getById(dc, sc.getActiveProjectId());
    GenericOverview overview = OverviewUtil.getNewOverview(dc, item, project);    
    overview.expand(dc, overview.getRootNode(), true);
    overview.updateFailureCountOnNodes();
    dc.close();
    redirect = "frameset.jsp?ID="+ID+"&item_type="+itemType.name()+"&item_id="+itemId+"&show_failures="+true;
  }
  else if ("SaveValidationOptions".equals(cmd))
  {
    GenericOverview overview = OverviewUtil.getCurrentOverview(sc);
    ValidationOptions options = overview.getValidationOptions();
    Presets presets = OverviewUtil.getValidationPresets(sc);
    for (Map.Entry<String, List<Validator>> entry : OverviewUtil.getValidators().entrySet())
    {
      for (Validator validator : entry.getValue())
      {
        options.setSeverity(validator, Severity.valueOf(request.getParameter(validator.getId())));
      }
    }
    options.setOption(Validator.NONMATCHING_SPOTCOUNT, "threshold", request.getParameter("threshold"));
    options.saveToPreset(presets.getDefault());
    OverviewUtil.saveValidationPresets(sc);
    overview.updateFailureCountOnNodes();
  }
  else if ("SaveAsPreset".equals(cmd))
  {
    Presets presets = OverviewUtil.getValidationPresets(sc);
    String name = request.getParameter("presetName");
    Preset preset = presets.getPreset(name);
    for (Map.Entry<String, List<Validator>> entry : OverviewUtil.getValidators().entrySet())
    {
      for (Validator validator : entry.getValue())
      {
        preset.setSetting(validator.getId(), request.getParameter(validator.getId()));
      }
    }
    preset.setSetting(Validator.NONMATCHING_SPOTCOUNT.getId() + "+threshold", 
        request.getParameter("threshold"));
    OverviewUtil.saveValidationPresets(sc);
    forward = "options.jsp";
  }
  else if ("RemovePreset".equals(cmd))
  {
    Presets presets = OverviewUtil.getValidationPresets(sc);
    String name = request.getParameter("presetName");
    presets.deletePreset(name);
    OverviewUtil.saveValidationPresets(sc);
    redirect = "options.jsp?ID=" + ID;
  }
  else
  {
    throw new WebException("popup", "Invalid command", "The command {1} is not recognised as a valid command.", cmd);
  }
}
finally
{
  if (dc != null) dc.close();
}

if (forward != null)
{
  pageContext.forward(forward);
}
else if (redirect != null)
{
  response.sendRedirect(redirect);
}
else if (message == null)
{
  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&wait=0");
}
else
{
  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&message="+HTML.urlEncode(message));
}
%>