source: trunk/www/views/itemlists/members/index.jsp @ 6743

<%-- $Id: index.jsp 6278 2013-05-24 10:41:55Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2008 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 2.10
--%>
<%@page import="net.sf.basedb.core.Listable"%>
<%@ 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.Type"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.ItemResultIterator"
  import="net.sf.basedb.core.ItemList"
  import="net.sf.basedb.core.BasicItem"
  import="net.sf.basedb.core.Sample"
  import="net.sf.basedb.core.Extract"
  import="net.sf.basedb.core.PhysicalBioAssay"
  import="net.sf.basedb.core.BioPlateEventType"
  import="net.sf.basedb.core.OwnedItem"
  import="net.sf.basedb.core.query.Restrictions"
  import="net.sf.basedb.core.query.Expressions"
  import="net.sf.basedb.core.query.Hql"
  import="net.sf.basedb.core.query.Orders"
  import="net.sf.basedb.core.MultiPermissions"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.WebException"
  import="net.sf.basedb.util.ShareableUtil"
  import="net.sf.basedb.util.RemovableUtil"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.core.plugin.GuiContext"
  import="net.sf.basedb.util.extensions.ExtensionsInvoker"
  import="net.sf.basedb.util.formatter.NameableFormatter"
  import="net.sf.basedb.util.formatter.WellCoordinateFormatter"
  import="net.sf.basedb.util.formatter.ItemTypeFormatter"
  import="net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter"
  import="net.sf.basedb.clients.web.plugins.ItemQueryLoader"
  import="net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoader"
  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.Arrays"
  import="java.util.Collections"
  import="java.util.Set"
  import="java.util.HashSet"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%!
  private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,itemSubtype,description");

  private static void registerExportUtils(ItemContext cc)
  {
    Item memberType = cc.getItemType();
    if (memberType == Item.BIOSOURCE)
    {
      // Register formatters
      cc.setObject("export.formatter.&children(name)", new NameableFormatter());
          
      // Register dataloaders
      String bioSourceParameter = "bioSource";
      final ItemQuery<Sample> sampleQuery = Sample.getQuery();
      sampleQuery.include(cc.getInclude());
      sampleQuery.restrict(Restrictions.eq(Hql.property("parent"), Expressions.parameter(bioSourceParameter)));
      sampleQuery.order(Orders.asc(Hql.property("name")));
      cc.setObject("export.dataloader.&children(name)", new ItemQueryLoader(sampleQuery, bioSourceParameter));
    }
    else if (memberType == Item.SAMPLE)
    {
      // Register formatters
      cc.setObject("export.formatter.bioWell.row", new WellCoordinateFormatter(true));
      cc.setObject("export.formatter.bioWell.column", new WellCoordinateFormatter(false));
      cc.setObject("export.formatter.&creationEvent.sources(bioMaterial.name)", new BioMaterialEventSourceFormatter());
      cc.setObject("export.formatter.&childCreationEvents(event.bioMaterial.name)", new NameableFormatter());
      cc.setObject("export.formatter.&children(name)", new NameableFormatter());
      cc.setObject("export.formatter.parentType", new ItemTypeFormatter());
      
      // Register dataloaders
      String sampleParameter = "sample";

      // Child extracts
      ItemQuery<Extract> extractQuery = Extract.getQuery();
      extractQuery.include(cc.getInclude());
      extractQuery.restrict(Restrictions.eq(Hql.property("parent"), Expressions.parameter(sampleParameter)));
      extractQuery.order(Orders.asc(Hql.property("name")));
      cc.setObject("export.dataloader.&children(name)", new ItemQueryLoader(extractQuery, sampleParameter));

      // Child samples
      ItemQuery<Sample> childSamplesQuery = Sample.getQuery();
      childSamplesQuery.join(Hql.innerJoin("creationEvent", "ce"));
      childSamplesQuery.join(Hql.innerJoin("ce", "sources", "src"));
      childSamplesQuery.restrict(Restrictions.eq(Hql.property("src", "bioMaterial"), Expressions.parameter(sampleParameter)));
      childSamplesQuery.order(Orders.asc(Hql.property("name")));
      childSamplesQuery.include(cc.getInclude());
      cc.setObject("export.dataloader.&childCreationEvents(event.bioMaterial.name)", new ItemQueryLoader(childSamplesQuery, sampleParameter));
      
      // Parent samples
      cc.setObject("export.dataloader.&creationEvent.sources(bioMaterial.name)", new ParentBioMaterialEventSourceLoader());
    }
    else if (memberType == Item.EXTRACT)
    {
      cc.setObject("export.formatter.bioWell.row", new WellCoordinateFormatter(true));
      cc.setObject("export.formatter.bioWell.column", new WellCoordinateFormatter(false));
      cc.setObject("export.formatter.&children(name)", new NameableFormatter());
      cc.setObject("export.formatter.&creationEvent.sources(bioMaterial.name)", new BioMaterialEventSourceFormatter());
      cc.setObject("export.formatter.&childCreationEvents(event.physicalBioAssay.name)", new NameableFormatter());
      cc.setObject("export.formatter.&childCreationEvents(event.bioMaterial.name)", new NameableFormatter());
      cc.setObject("export.formatter.parentType", new ItemTypeFormatter());
      
      String restrictionParameter = "extract";

      // Physical bioassays
      ItemQuery<PhysicalBioAssay> bioAssayQuery = PhysicalBioAssay.getQuery();
      bioAssayQuery.join(Hql.innerJoin("creationEvent", "ce"));
      bioAssayQuery.join(Hql.innerJoin("ce", "sources", "src"));
      bioAssayQuery.restrict(Restrictions.eq(Hql.property("src", "bioMaterial"), Expressions.parameter(restrictionParameter)));
      bioAssayQuery.order(Orders.asc(Hql.property("name")));
      bioAssayQuery.include(cc.getInclude());
      cc.setObject("export.dataloader.&childCreationEvents(event.physicalBioAssay.name)", new ItemQueryLoader(bioAssayQuery, restrictionParameter));

      // Child extracts
      ItemQuery<Extract> childExtractsQuery = Extract.getQuery();
      childExtractsQuery.join(Hql.innerJoin("creationEvent", "ce"));
      childExtractsQuery.join(Hql.innerJoin("ce", "sources", "src"));
      childExtractsQuery.restrict(Restrictions.eq(Hql.property("src", "bioMaterial"), Expressions.parameter(restrictionParameter)));
      childExtractsQuery.order(Orders.asc(Hql.property("name")));
      childExtractsQuery.include(cc.getInclude());
      cc.setObject("export.dataloader.&childCreationEvents(event.bioMaterial.name)", new ItemQueryLoader(childExtractsQuery, restrictionParameter));
      
      // Parent items
      cc.setObject("export.dataloader.&creationEvent.sources(bioMaterial.name)", new ParentBioMaterialEventSourceLoader());
    }
  }
%>
<%
final int listId = Values.getInt(request.getParameter("list_id"));
final String subContext = "listmembers."+listId;

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 listPage = "list_members.jsp?ID="+ID
  +"&list_id="+listId
  +(mode == null ? "" : "&mode="+mode)
  +(callback == null ? "" : "&callback="+callback);

String forward = null;
String redirect = null;
String message = null;
DbControl dc = null;
try
{
  dc = sc.newDbControl();
  final ItemList list = ItemList.getById(dc, listId);
  final Item itemType = list.getMemberType();
  
  if (cmd == null || "List".equals(cmd))
  {
    // Display the list page without updatinging the current context
    Base.getAndSetCurrentContext(sc, itemType, subContext, (PageContext)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, 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, subContext, pageContext, defaultContext);
    registerExportUtils(cc);
    final ItemQuery<? extends Listable> query = list.getMembers();
    dc = sc.newDbControl();
    cc.configureQuery(dc, query, true);
    cc.setQuery(query);
    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&subcontext="+subContext+"&title=Export+list+members";
  }
  else if ("ImportItems".equals(cmd))
  {
    // Run an import plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, subContext, pageContext, defaultContext);
    final ItemQuery<? extends Listable> query = list.getMembers();
    cc.configureQuery(dc, query, true);
    cc.setQuery(query);
    dc.close();
    redirect = "../../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&subcontext="+subContext+"&title=Import+list+members";
  }
  else if ("RunListPlugin".equals(cmd))
  {
    // Run another plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, subContext, pageContext, defaultContext);
    final ItemQuery<? extends BasicItem> query = list.getMembers();
    cc.configureQuery(dc, query, true);
    cc.setQuery(query);
    dc.close();
    redirect = "../../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&subcontext="+subContext+"&main_type=OTHER&title=Run+plugin";
  }
  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));
}
%>