source: trunk/www/views/itemlists/index.jsp @ 6770

<%-- $Id$
  ------------------------------------------------------------------
  Copyright (C) 2015 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
--%>
<%@ 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.Type"
  import="net.sf.basedb.core.Include"
  import="net.sf.basedb.core.ItemList"
  import="net.sf.basedb.core.RawDataTypes"
  import="net.sf.basedb.core.ItemSubtype"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.SyncFilter"
  import="net.sf.basedb.core.SyncFilter.SourceItemTransform"
  import="net.sf.basedb.core.ItemResultIterator"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.MultiPermissions"
  import="net.sf.basedb.core.OwnedItem"
  import="net.sf.basedb.core.Listable"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.core.ItemAlreadyExistsException"
  import="net.sf.basedb.core.query.Restrictions"
  import="net.sf.basedb.core.query.Hql"
  import="net.sf.basedb.core.query.Expressions"
  import="net.sf.basedb.util.RemovableUtil"
  import="net.sf.basedb.util.ShareableUtil"
  import="net.sf.basedb.util.OwnableUtil"
  import="net.sf.basedb.util.collections.CollectionTransformer"
  import="net.sf.basedb.util.biomaterial.ListUtil"
  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="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.edit.EditUtil"
  import="net.sf.basedb.clients.web.extensions.edit.OnSaveRenderer"
  import="net.sf.basedb.clients.web.extensions.list.ListColumnExportRenderer"
  import="net.sf.basedb.clients.web.extensions.list.ListColumnUtil"
  import="java.util.Enumeration"
  import="java.util.Set"
  import="java.util.HashSet"
  import="java.util.List"
  import="java.util.ArrayList"
  import="java.util.Collections"
  import="java.util.Arrays"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%!
  private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,memberType,size,description");
  private static final Item itemType = Item.ITEMLIST;
%>
<%
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_lists.jsp?ID="+ID
  +(mode == null ? "" : "&mode="+mode)
  +(callback == null ? "" : "&callback="+callback)
  +(itemId == null ? "" : "&item_id="+itemId);
final String viewPage = "view_list.jsp?ID="+ID;
final String editPage = "edit_list.jsp?ID="+ID;

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 ("NewItem".equals(cmd))
  {
    // Display the edit page for a new item (should be opened in a popup)
    if (!sc.hasPermission(Permission.CREATE, itemType))
    {
      throw new PermissionDeniedException(Permission.CREATE, itemType.toString());
    }
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    cc.setId(0);
    forward = 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();
    ItemList list = (ItemList)cc.getObject("item");
    if (list == null)
    {
      Item memberType = Item.valueOf(request.getParameter("memberType"));
      list = ItemList.getNew(dc, memberType);
      dc.saveItem(list);
      message = "List created";
    }
    else
    {
      dc.reattachItem(list, false);
      message = "List updated";
    }
    JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.item(Item.ITEMLIST), list);
    ExtensionsInvoker invoker = EditUtil.useOnSaveExtensions(jspContext);
    try
    {
      list.setName(Values.getStringOrNull(request.getParameter("name")));
      list.setExternalId(Values.getStringOrNull(request.getParameter("external_id")));
      list.setDescription(Values.getStringOrNull(request.getParameter("description")));
      if (list.getMemberType() == Item.RAWBIOASSAY)
      {
        list.setRawDataType(RawDataTypes.getRawDataType(request.getParameter("rawdatatype")));
      }
      else
      {
        int subtypeId = Values.getInt(request.getParameter("subtype_id"), -1);
        ItemSubtype subtype = null;
        if (subtypeId >= 0) // < 0 = denied or unchanged
        {
          if (subtypeId > 0) subtype = ItemSubtype.getById(dc, subtypeId);
          list.setItemSubtype(subtype);
        }
      }

      // Annotations tab
      Base.updateAnnotations(dc, list, list, request);

      if (!list.isInDatabase())
      {
        // Add individual items from selected from a list page
        String source = request.getParameter("source");
        if (source != null)
        {
          String subContext = Values.getString(request.getParameter("subContext"), "");
          boolean useSyncFilter = false;
          ItemContext filterContext = sc.getCurrentContext(list.getMemberType(), subContext);
          ItemQuery<? extends Listable> query = (ItemQuery<? extends Listable>)filterContext.getQuery();
          if ("all".equals(source))
          {
            useSyncFilter = Values.getBoolean(request.getParameter("syncFilter"));
            query.setFirstResult(0);
            query.setMaxResults(-1);
            if (useSyncFilter)
            {
              SyncFilter sf = list.newSyncFilter(dc);
              sf.setName("Origin");
              sf.setSyncContext(filterContext, SourceItemTransform.NONE);
              dc.saveItem(sf);
            }
          }
          else if ("selected".equals(source))
          {
            query.setFirstResult(0);
            query.setMaxResults(-1);
            Integer[] itemIds = Values.getInt(request.getParameter("items").split(","));
            query.restrict(
              Restrictions.in(
                Hql.property("id"),
                Expressions.parameter("selectedItems")
              )
            );
            query.setParameter("selectedItems", Arrays.asList(itemIds), Type.INT);      
          }
          // else -- no modifications to the query mean that we only get the current page
          
          if (!useSyncFilter) list.add(query.iterate(dc));
        }
        
        message = "List created with " + list.getSize() + " item(s)";
      }

      
      // OnSave extensions
      invoker.render(OnSaveRenderer.ON_SAVE);
      dc.commit();
      invoker.render(OnSaveRenderer.ON_COMMIT);
    }
    catch (Exception ex)
    {
      invoker.render(OnSaveRenderer.onRollback(ex));
      throw ex;
    }
    finally
    {
      cc.removeObject("item");
    }
  }
  /*
  else if ("ReSyncFilter".equals(cmd))
  {
    dc = sc.newDbControl();
    ItemList list = ItemList.getById(dc, Values.getInt(itemId));
    list.resyncFilter(dc, ItemList.SynchronizeOption.FULL);
    dc.commit();
    forward = viewPage;
  }
  */
  else if ("DeleteItem".equals(cmd))
  {
    // Delete a single item and then return to the view page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    RemovableUtil.setRemoved(dc, itemType, Collections.singleton(cc.getId()), true);
    dc.commit();
    redirect = viewPage;
  }
  else if ("DeleteItems".equals(cmd))
  {
    // Delete all selected items on the list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    int numTotal = cc.getSelected().size();
    int numRemoved = RemovableUtil.setRemoved(dc, itemType, cc.getSelected(), true);
    dc.commit();
    if (numTotal != numRemoved)
    {
      message = (numRemoved == 0 ? "No" : "Only "+numRemoved+" of "+numTotal) + " items could be deleted, because you have no DELETE permission";
    }
    redirect = listPage;
  }
  else if ("RestoreItem".equals(cmd))
  {
    // Restore a single item and then return to the view page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    RemovableUtil.setRemoved(dc, itemType, Collections.singleton(cc.getId()), false);
    dc.commit();
    redirect = viewPage;
  }
  else if ("RestoreItems".equals(cmd))
  {
    // Restore all selected items on the list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    int numTotal = cc.getSelected().size();
    int numRemoved = RemovableUtil.setRemoved(dc, itemType, cc.getSelected(), false);
    dc.commit();
    if (numTotal != numRemoved)
    {
      message = (numRemoved == 0 ? "No" : "Only "+numRemoved+" of "+numTotal) + " items could be restored, because you have no WRITE permission";
    }
    redirect = listPage;
  }
  else if ("ShareItem".equals(cmd))
  {
    // Display a popup window for sharing a single item
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    MultiPermissions permissions = ShareableUtil.getMultiPermissions(dc, itemType, Collections.singleton(cc.getId()));
    dc.close();
    cc.setObject("MultiPermissions", permissions);
    redirect = "../../common/share/share.jsp?ID="+ID+"&item_type="+itemType.name();
  }
  else if ("ShareItems".equals(cmd))
  {
    // Display a popup window for sharing all selected items on the list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    MultiPermissions permissions = ShareableUtil.getMultiPermissions(dc, itemType, cc.getSelected());
    dc.close();
    cc.setObject("MultiPermissions", permissions);
    redirect = "../../common/share/share.jsp?ID="+ID+"&item_type="+itemType.name();
  }
  else if ("SetOwnerOfItem".equals(cmd))
  {
    // Change owner of items selected on a list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    OwnedItem item = (OwnedItem)itemType.getById(dc, cc.getId());
    cc.setObject("OwnedItems", Collections.singleton(item));
    redirect = "../../common/ownership/ownership.jsp?ID="+ID+"&item_type="+itemType.name();
  }
  else if ("SetOwnerOfItems".equals(cmd))
  {
    // Change owner of items selected on a list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    Set<OwnedItem> items = new HashSet<OwnedItem>();
    for (Integer id : cc.getSelected())
    {
      if (id != null) items.add((OwnedItem)itemType.getById(dc, id));
    }
    dc.close();
    cc.setObject("OwnedItems", items);
    redirect = "../../common/ownership/ownership.jsp?ID="+ID+"&item_type="+itemType.name();
  }
  else if ("ExportItems".equals(cmd))
  {
    // Run an export plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<ItemList> query = ItemList.getQuery();
    dc = sc.newDbControl();
    cc.configureQuery(dc, 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+item+lists";
  }
  else if ("ExportItem".equals(cmd))
  {
    // Run an export plugin in single-item context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+item+list";
  }
  else if ("ImportItems".equals(cmd))
  {
    // Run an import plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<ItemList> query = ItemList.getQuery();
    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/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+item+lists";
  }
  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+item+list";
  }
  else if ("RunListPlugin".equals(cmd))
  {
    // Run another plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<ItemList> query = ItemList.getQuery();
    dc = sc.newDbControl();
    cc.configureQuery(dc, query, true);
    dc.close();
    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 ("MergeItem".equals(cmd))
  {
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, defaultContext);
    dc = sc.newDbControl();
    ItemList itemList = (ItemList)cc.getObject("item");
    dc.reattachItem(itemList, false);
    
    String mergeType = request.getParameter("mergeType");
    String sourceMerge = request.getParameter("sourceMerge");
    
    String[] sourceListIds = Values.getString(request.getParameter("+ITEMLIST")).split(",");
    List<ItemList> sourceLists = new ArrayList<ItemList>(sourceListIds.length);
    for (int i = 0; i < sourceListIds.length; ++i)
    {
      int listId = Values.getInt(sourceListIds[i], -1);
      if (listId != -1) sourceLists.add(ItemList.getById(dc, listId));
    }
    
    int numAdded = 0;
    int numRemoved = 0;
    if ("union".equals(mergeType))
    {
      if ("union".equals(sourceMerge))
      {
        numAdded = itemList.addUnion(sourceLists);
      }
      else if ("intersection".equals(sourceMerge))
      {
        numAdded = itemList.addIntersection(sourceLists);
      }
      message = numAdded + " items added to this list";
    }
    else if ("intersection".equals(mergeType))
    {
      if ("union".equals(sourceMerge))
      {
        numRemoved = itemList.retainUnion(sourceLists);
      }
      else if ("intersection".equals(sourceMerge))
      {
        numRemoved = itemList.retainIntersection(sourceLists);
      }
      message = numRemoved + " items removed from this list";
    }
    else if ("complement".equals(mergeType))
    {
      if ("union".equals(sourceMerge))
      {
        numRemoved = itemList.removeUnion(sourceLists);
      }
      else if ("intersection".equals(sourceMerge))
      {
        numRemoved = itemList.removeIntersection(sourceLists);
      }
      message = numRemoved + " items removed from this list";
    }
    dc.commit();
  } 
  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));
}
%>