source: trunk/www/views/experiments/explorer/view/index.jsp @ 5111

<%-- $Id: index.jsp 5111 2009-09-30 10:56:51Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2006 Nicklas Nordborg

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

  This file is part of BASE.

  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/>.
  ------------------------------------------------------------------

  @author Nicklas
  @version 2.0
--%>
<%@ 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.ItemContext"
  import="net.sf.basedb.core.BioAssaySet"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.ExperimentExplorer"
  import="net.sf.basedb.clients.web.WebException"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.clients.web.util.HTML"
  import="java.util.Set"
  import="java.util.Arrays"
%>
<%
final int bioAssaySetId = Values.getInt(request.getParameter("bioassayset_id"));
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final String ID = sc.getId();
final String cmd = request.getParameter("cmd");
final String root = request.getContextPath()+"/";

final String viewPage = "view.jsp?ID="+ID+"&bioassayset_id="+bioAssaySetId;

String forward = null;
String redirect = null;
String message = null;

DbControl dc = null;
try
{
  dc = sc.newDbControl();
  BioAssaySet bioAssaySet = BioAssaySet.getById(dc, bioAssaySetId);
  ExperimentExplorer explorer = ExperimentExplorer.getExplorer(bioAssaySet);
  if (cmd == null || "Explore".equals(cmd))
  {
    redirect = viewPage;
  }
  else if ("UpdateContext".equals(cmd))
  {
    ItemContext cc = explorer.getAndSetSpotContext(sc, pageContext);
    redirect = viewPage;
  }
  else if ("SetReporterColumns".equals(cmd))
  {
    ItemContext cc = explorer.getAndSetSpotContext(sc, null);
    cc.setSetting("reporter-columns", Values.getString(request.getParameter("columns"), cc.getSetting("reporter-columns")));
    redirect = viewPage;
  }
  else if ("SetReporterIndex".equals(cmd))
  {
    explorer.setReporterIndex(Values.getInt(request.getParameter("reporterIndex")));
    redirect = viewPage;
  }
  else if ("SetSpotIndex".equals(cmd))
  {
    explorer.setPositionIndex(Values.getInt(request.getParameter("spotIndex")));
    redirect = viewPage;
  }
  else if ("SetAnnotationType".equals(cmd))
  {
    Integer[] annotationTypes = Values.getInt(request.getParameter("annotationtype_id").split("|"));
    Set<Integer> tmp = explorer.getAnnotationTypeIds();
    tmp.clear();
    tmp.addAll(Arrays.asList(annotationTypes));
    
    // If an annotation type is selected the annotation column must be visible as the first column
    ItemContext cc = explorer.getAndSetSpotContext(sc, null);
    String columns = cc.getSetting("columns");
    columns = columns.replaceAll("annotation\\.\\d+,", "");
    for (Integer atId : annotationTypes)
    {
      columns = "annotation." + atId + "," + columns;
    }
    cc.setSetting("columns", columns);
    redirect = viewPage;
  }
  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));
}

%>