source: trunk/www/views/experiments/spotdata/index.jsp @ 4476

<%-- $Id: index.jsp 4476 2008-09-05 15:14:42Z jari $
  ------------------------------------------------------------------
  Copyright (C) 2006 Jari Hakkinen, 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 this program; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place - Suite 330,
  Boston, MA  02111-1307, USA.
  ------------------------------------------------------------------

  @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.BioAssaySet"
  import="net.sf.basedb.core.BioAssay"
  import="net.sf.basedb.core.RawDataType"
  import="net.sf.basedb.core.RawDataTypes"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.DynamicSpotQuery"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.WebException"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.clients.web.util.HTML"
  import="java.util.Map"
  import="java.util.HashMap"
  import="java.util.Collections"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%!
  private static final Map<RawDataType, ItemContext> defaultContexts = 
    new HashMap<RawDataType, ItemContext>();

  static
  {
    for (RawDataType rdt : RawDataTypes.getRawDataTypes())
    {
      // Default visible columns are: position, ch1, ch2, ...
      StringBuilder columns = new StringBuilder("POSITION");
      for (int ch = 1; ch <= rdt.getChannels(); ++ch)
      {
        columns.append(",ch").append(ch);
      }
      defaultContexts.put(rdt, 
        Base.createDefaultContext("POSITION", columns.toString()));
    }
  }
  private static final Item itemType = Item.SPOTDATA;
%>
<%
final int bioAssayId = Values.getInt(request.getParameter("bioassay_id"));
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 mode = request.getParameter("mode");
final String callback = request.getParameter("callback");
final String itemId = request.getParameter("item_id");
final String listPage = "list_spotdata.jsp?ID="+ID
  +"&bioassay_id="+bioAssayId+"&bioassayset_id="+bioAssaySetId
  +(mode == null ? "" : "&mode="+mode)
  +(callback == null ? "" : "&callback="+callback)
  +(itemId == null ? "" : "&item_id="+itemId);

String forward = null;
String redirect = null;
String message = null;
DbControl dc = null;

try
{
  dc = sc.newDbControl();
  final BioAssay ba = bioAssayId == 0 ? null : BioAssay.getById(dc, bioAssayId);
  final BioAssaySet bas = ba != null ? ba.getBioAssaySet() : BioAssaySet.getById(dc, bioAssaySetId);
  dc.close();
  final RawDataType rawDataType = bas.getRawDataType();
  final ItemContext defaultContext = defaultContexts.get(rawDataType);
  final String subContext = rawDataType.getId();
  
  if (cmd == null || "List".equals(cmd))
  {
    // Display the list page without updatinging the current context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, subContext, null, defaultContext);
    redirect = listPage;
  }
  else if ("UpdateContext".equals(cmd))
  {
    // Display the list page after updating the current context from the request parameters
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, subContext, pageContext, defaultContext);
    redirect = listPage;
  }
  else if ("LoadContext".equals(cmd))
  {
    // Display the list page after loading a saved context
    int contextId = Values.getInt(request.getParameter("context"));
    Base.loadContext(sc, contextId, defaultContext);
    redirect = listPage;
  }
  else if ("ExportItems".equals(cmd))
  {
    // Run an export plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    dc = sc.newDbControl();
    if (bas != null) dc.reattachItem(bas);
    if (ba != null) dc.reattachItem(ba);
    final DynamicSpotQuery query = ba != null ? ba.getSpotData() : bas.getSpotData();
    //cc.configureQuery(query, true);
    dc.close();
    cc.setQuery(query);
    redirect = "../../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+spot+data";
  }
  else if ("CreateReporterList".equals(cmd))
  {
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, subContext, pageContext, defaultContext);
    dc = sc.newDbControl();
    if (bas != null) dc.reattachItem(bas);
    if (ba != null) dc.reattachItem(ba);
    final DynamicSpotQuery query = ba != null ? ba.getSpotData() : bas.getSpotData();
    cc.configureQuery(dc, query, Collections.singletonList("@id"));
    cc.setQuery(query);
    redirect = "../../../views/reporterlists/index.jsp?ID="+ID+
      "&cmd=NewItem&addReporters=1&formId=spotdata&fromContext=SPOTDATA&subContext=" + subContext +
      "&name=" + HTML.urlEncode(ba != null ? ba.getName() : bas.getName());
  }
  
  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));
}
%>