source: trunk/www/lims/plates/wells/index.jsp @ 4866

<%-- $Id: index.jsp 4866 2009-03-31 07:36:06Z martin $
  ------------------------------------------------------------------
  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 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.Plate"
  import="net.sf.basedb.core.Well"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.DataQuery"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.core.data.ReporterData"
  import="net.sf.basedb.core.query.Hql"
  import="net.sf.basedb.core.query.Orders"
  import="net.sf.basedb.util.RemovableUtil"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.WebException"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.util.formatter.WellCoordinateFormatter"
  import="java.util.List"
  import="java.util.Collections"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
<%!
  private static final ItemContext defaultContext = Base.createDefaultContext("row", "row,column,reporter.name,reporter.externalId");
  private static final Item itemType = Item.WELL;
  
  private static void registerExportFormatters(ItemContext cc)
  {
    cc.setObject("export.formatter.row", new WellCoordinateFormatter(true));
    cc.setObject("export.formatter.column", new WellCoordinateFormatter(false));
  }
%>
<%
final int plateId = Values.getInt(request.getParameter("plate_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_wells.jsp?ID="+ID
  +"&plate_id="+plateId
  +(mode == null ? "" : "&mode="+mode)
  +(callback == null ? "" : "&callback="+callback)
  +(itemId == null ? "" : "&item_id="+itemId);
final String viewPage = "view_well.jsp?ID="+ID+"&plate_id="+plateId;
final String editPage = "edit_well.jsp?ID="+ID+"&plate_id="+plateId;

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

try
{
  if (cmd == null || "List".equals(cmd))
  {
    // Display the list page without updatinging the current context
    Base.getAndSetCurrentContext(sc, itemType, null, defaultContext, true);
    redirect = listPage;
  }
  else if ("UpdateContext".equals(cmd))
  {
    // Display the list page after updating the current context from the request parameters
    Base.getAndSetCurrentContext(sc, itemType, 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 ("ViewItem".equals(cmd))
  {
    // Display the view page for a single item 
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    forward = viewPage;
  }
  else if ("EditItem".equals(cmd))
  {
    // Display the edit page for a single item (should be opened in a popup)
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = editPage;
  }
  else if ("UpdateItem".equals(cmd))
  {
    // Update the properties on an item (will close the popup)
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, defaultContext);
    dc = sc.newDbControl();
    Well well = (Well)cc.getObject("item");
    dc.reattachItem(well);
    message = "Well updated";
    
    // Annotations tab
    Base.updateAnnotations(dc, well, well, request);
    
    dc.commit();
    cc.removeObject("item");
  }
  else if ("ExportItems".equals(cmd))
  {
    // Run an export plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    dc = sc.newDbControl();
    final Plate plate = Plate.getById(dc, plateId);
    dc.close();
    final ItemQuery<Well> query = plate.getWells();
    cc.configureQuery(query, true);
    if (!"row".equals(cc.getSortProperty()))
    {
      query.order(Orders.asc(Hql.property("row")));
    }
    if (!"column".equals(cc.getSortProperty()))
    {
      query.order(Orders.asc(Hql.property("column")));
    }
    registerExportFormatters(cc);
    
    cc.setQuery(query);
    redirect = "../../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+wells";
  }
  else if ("ExportItem".equals(cmd))
  {
    // Run an export plugin in single-item context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    registerExportFormatters(cc);
    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+well";
  }
  else if ("ImportItems".equals(cmd))
  {
    // Run an import plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    dc = sc.newDbControl();
    final Plate plate = Plate.getById(dc, plateId);
    dc.close();
    final ItemQuery<Well> query = plate.getWells();
    cc.configureQuery(query, true);
    cc.setQuery(query);
    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+wells";
  }
  else if ("ImportItem".equals(cmd))
  {
    // Run an import plugin in single-item context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Import+well";
  }
  else if ("RunListPlugin".equals(cmd))
  {
    // Run another plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    dc = sc.newDbControl();
    final Plate plate = Plate.getById(dc, plateId);
    dc.close();
    final ItemQuery<Well> query = plate.getWells();
    cc.configureQuery(query, true);
    cc.setQuery(query);
    redirect = "../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&main_type=OTHER&title=Run+plugin";
  }
  else if ("RunPlugin".equals(cmd))
  {
    // Run another plugin in single-item context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = "../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&main_type=OTHER&title=Run+plugin";
  }
  else if ("CreateReporterList".equals(cmd))
  {
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    dc = sc.newDbControl();   
    final Plate plate = Plate.getById(dc, plateId);
    final DataQuery<ReporterData> query = plate.getReporters();
    cc.configureQuery(query, true);
    cc.setQuery(query);
    redirect = "../../../views/reporterlists/index.jsp?ID="+ID+
      "&cmd=NewItem&addReporters=1&formId=wells&fromContext=WELL"+
      "&name=" + HTML.urlEncode(plate.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));
}

%>