source: branches/3.5-stable/www/lims/arraydesigns/features/index.jsp @ 6949

<%-- $Id: index.jsp 6949 2015-09-10 12:34:16Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2006 Jari Häkkinen, 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 pageEncoding="UTF-8" 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.ItemQuery"
  import="net.sf.basedb.core.DataQuery"
  import="net.sf.basedb.core.DataResultIterator"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.core.ArrayDesign"
  import="net.sf.basedb.core.data.FeatureData"
  import="net.sf.basedb.core.data.ReporterData"
  import="net.sf.basedb.core.query.Hql"
  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="net.sf.basedb.core.plugin.GuiContext"
  import="net.sf.basedb.util.extensions.ExtensionsInvoker"
  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
  import="net.sf.basedb.clients.web.extensions.JspContext"
  import="net.sf.basedb.clients.web.extensions.list.ListColumnExportRenderer"
  import="net.sf.basedb.clients.web.extensions.list.ListColumnUtil"
  import="java.util.List"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
<%!
  private static final ItemContext defaultContext = Base.createDefaultContext("position", 
    "position,externalId,block,row,column,reporter.name,reporter.externalId");
  private static final Item itemType = Item.FEATURE;
  
  private static void registerExportFormatters(ItemContext cc)
  {
    cc.setObject("export.formatter.well.row", new WellCoordinateFormatter(true));
    cc.setObject("export.formatter.well.column", new WellCoordinateFormatter(false));
  }
%>
<%
final int arrayDesignId = Values.getInt(request.getParameter("arraydesign_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 listPage = "list_features.jsp?ID="+ID+"&arraydesign_id="+arrayDesignId;
final String viewPage = "view_feature.jsp?ID="+ID+"&arraydesign_id="+arrayDesignId;

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 ("ExportItems".equals(cmd))
  {
    // Run an export plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    dc = sc.newDbControl();   
    final ArrayDesign arrayDesign = ArrayDesign.getById(dc, arrayDesignId);
    final DataQuery<FeatureData> query = arrayDesign.getFeatures();
    query.join(Hql.leftJoin(null, "reporter", "rpt", null, true));
    cc.configureQuery(dc, query, true);
    cc.setQuery(query);
    registerExportFormatters(cc);
    JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.list(itemType), null);
    ExtensionsInvoker listInvoker = ListColumnUtil.useExtensions(jspContext);
    listInvoker.render(new ListColumnExportRenderer(cc));
    dc.close();
    redirect = "../../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+features+of+array+design";
  }
  else if ("CreateReporterList".equals(cmd))
  {
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    dc = sc.newDbControl();   
    final ArrayDesign arrayDesign = ArrayDesign.getById(dc, arrayDesignId);
    final DataQuery<ReporterData> query = arrayDesign.getReporters();
    query.join(Hql.leftJoin("reporter", "rpt"));
    cc.configureQuery(dc, query, true);
    dc.close();
    cc.setQuery(query);
    redirect = "../../../views/reporterlists/index.jsp?ID="+ID+
      "&cmd=NewItem&addReporters=1&formId=features&fromContext=FEATURE" +
      "&name=" + HTML.urlEncode(arrayDesign.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)
{
  sc.setSessionSetting("alert-message", message);
  pageContext.forward(forward);
}
else if (redirect != null)
{
  sc.setSessionSetting("alert-message", message);
  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));
}

%>