source: trunk/www/views/rawbioassays/rawdata/index.jsp @ 6192

<%-- $Id: index.jsp 6192 2012-10-31 12:34:19Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2005 Nicklas Nordborg
  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.data.RawData"
  import="net.sf.basedb.core.data.ReporterData"
  import="net.sf.basedb.core.RawBioAssay"
  import="net.sf.basedb.core.RawDataType"
  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.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,block,row,column,reporter.name,reporter.externalId");
  private static final Item itemType = Item.RAWDATA;
  
  private static void registerExportFormatters(ItemContext cc)
  {
    cc.setObject("export.formatter.feature.well.row", new WellCoordinateFormatter(true));
    cc.setObject("export.formatter.feature.well.column", new WellCoordinateFormatter(false));
  }
%>
<%
final int rawBioAssayId = Values.getInt(request.getParameter("rawbioassay_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_rawdata.jsp?ID="+ID+"&rawbioassay_id="+rawBioAssayId;
final String viewPage = "view_rawdata.jsp?ID="+ID+"&rawbioassay_id="+rawBioAssayId;
sc.getCurrentContext(Item.RAWBIOASSAY).setId(rawBioAssayId);

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

try
{
  dc = sc.newDbControl();
  RawBioAssay rba = RawBioAssay.getById(dc, rawBioAssayId);
  RawDataType rawDataType = rba.getRawDataType();

  if (cmd == null || "List".equals(cmd))
  {
    // Display the list page without updatinging the current context
    Base.getAndSetCurrentContext(sc, itemType, rawDataType.getId(), null, defaultContext);
    redirect = listPage;
  }
  else if ("UpdateContext".equals(cmd))
  {
    // Display the list page after updating the current context from the request parameters
    Base.getAndSetCurrentContext(sc, itemType, rawDataType.getId(), 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, rawDataType.getId(), pageContext, defaultContext);
    forward = viewPage;
  }
  else if ("ExportItems".equals(cmd))
  {
    // Run an export plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, rawDataType.getId(), pageContext, defaultContext);
    final DataQuery<RawData> query = rba.getRawData();
    query.join(Hql.leftJoin(null, "reporter", "r", null, true));
    query.join(Hql.leftJoin(null, "feature", "f", null, true));
    cc.configureQuery(dc, query, true);
    cc.setQuery(query);
    registerExportFormatters(cc);
    JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.list(itemType, rawDataType.getId()), null);
    ExtensionsInvoker listInvoker = ListColumnUtil.useExtensions(jspContext);
    listInvoker.render(new ListColumnExportRenderer(cc));
    redirect = "../../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&subcontext="+rawDataType.getId()+"&context_type=LIST&title=Export+raw+data";
  }
  else if ("ImportItems".equals(cmd))
  {
    // Run an import plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, rawDataType.getId(), pageContext, defaultContext);
    final DataQuery<RawData> query = rba.getRawData();
    query.join(Hql.leftJoin(null, "reporter", "r", null, true));
    query.join(Hql.leftJoin(null, "feature", "f", null, true));
    cc.configureQuery(dc, query, true);
    cc.setQuery(query);
    redirect = "../../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&subcontext="+rawDataType.getId()+"&context_type=LIST&title=Import+raw+data";
  }
  else if ("RunListPlugin".equals(cmd))
  {
    // Run another plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, rawDataType.getId(), pageContext, defaultContext);
    final DataQuery<RawData> query = rba.getRawData();
    query.join(Hql.leftJoin(null, "reporter", "r", null, true));
    query.join(Hql.leftJoin(null, "feature", "f", null, true));
    cc.configureQuery(dc, query, true);
    cc.setQuery(query);
    redirect = "../../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&subcontext="+rawDataType.getId()+"&context_type=LIST&main_type=OTHER&title=Run+plugin";
  }
  else if ("CreateReporterList".equals(cmd))
  {
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, rawDataType.getId(), pageContext, defaultContext);
    final DataQuery<ReporterData> query = rba.getReporters();
    cc.configureQuery(dc, query, true);
    cc.setQuery(query);
    redirect = "../../../views/reporterlists/index.jsp?ID="+ID+
      "&cmd=NewItem&addReporters=1&formId=rawdata&fromContext=RAWDATA&subContext="+rawDataType.getId()+
      "&name=" + HTML.urlEncode(rba.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));
}

%>