source: trunk/www/common/annotations/index.jsp @ 6694

<%-- $Id: index.jsp 6694 2015-01-26 14:41:25Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2006 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.BasicItem"
  import="net.sf.basedb.core.AnnotatedItem"
  import="net.sf.basedb.core.Annotation"
  import="net.sf.basedb.core.AnnotationType"
  import="net.sf.basedb.core.Annotatable"
  import="net.sf.basedb.core.ItemSubtype"
  import="net.sf.basedb.core.BaseException"
  import="net.sf.basedb.core.SimpleProgressReporter"
  import="net.sf.basedb.core.snapshot.SnapshotManager"
  import="net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager"
  import="net.sf.basedb.util.annotations.InheritAnnotationsManager"
  import="net.sf.basedb.util.annotations.InheritSpecification"
  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="java.util.Set"
  import="java.util.List"
  import="java.util.ArrayList"
  
  
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>

<%
final String root = request.getContextPath()+"/";
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final String ID = sc.getId();
final String cmd = request.getParameter("cmd");
final int itemId = Values.getInt(request.getParameter("item_id"));

DbControl newDc = null;
DbControl oldDc = null;
String forward = null;
String message = null;
String redirect = null;
try
{
  if ("EditItem".equals(cmd))
  {
    newDc = sc.newDbControl();
    Annotation a = Annotation.getById(newDc, itemId);
    AnnotationType at = a.getAnnotationType();
    Annotatable item = a.getAnnotationSet().getItem();
    
    redirect = "annotate.jsp?ID=" + ID + "&item_id=" + item.getId() + 
        "&item_type=" + item.getType().name() + 
        "&annotationtype_id=" + at.getId() + "&standalone=1";
    newDc.close();
  }
  else if ("SaveAnnotations".equals(cmd))
  {
    final Item itemType = Item.valueOf(request.getParameter("item_type"));
    newDc = sc.newDbControl();
    oldDc = sc.newDbControl();
    ItemContext cc = sc.getCurrentContext(itemType);
    Annotatable oldItem = (Annotatable)cc.getObject("item");
    Annotatable newItem = (Annotatable)itemType.getById(newDc, itemId);
    oldDc.reattachItem((BasicItem)oldItem, false);
    Base.updateAnnotations(newDc, oldItem, newItem, request);
    oldDc.close();
    newDc.commit();
    cc.removeObject("item");
    message = "Annotations saved";
  }
  else if ("BatchInherit".equals(cmd))
  {
    final Item itemType = Item.valueOf(request.getParameter("item_type"));
    final String subContext = Values.getString(request.getParameter("subcontext"), "");
    final ItemContext cc = sc.getCurrentContext(itemType, subContext);
    
    newDc = sc.newDbControl();

    Set<AnnotatedItem> items = (Set<AnnotatedItem>)cc.getObject("AnnotatedItems");
    cc.removeObject("AnnotatedItems");
    
    RunnableInheritAnnotationsManager manager = new RunnableInheritAnnotationsManager(sc);
    manager.addAllItems(items);
    
    for (Integer atId : Values.getInt(request.getParameter("annotationTypes").split(",")))
    {
      AnnotationType at = AnnotationType.getById(newDc, atId);
      InheritSpecification spec = new InheritSpecification(at);
      String action = request.getParameter("action_"+atId);
      
      if ("remove".equals(action))
      {
        spec.setRemove(true);
      }
      else
      {
        int subtypeId = Values.getInt(request.getParameter("from_"+atId));
        boolean noDup = Values.getBoolean(request.getParameter("nodup_"+atId));
        boolean replaceExisting = Values.getBoolean(request.getParameter("replace_"+atId));
        if (subtypeId != 0)
        {
          spec.setItemSubtype(ItemSubtype.getById(newDc, subtypeId));
        }
        spec.setNoDuplicates(noDup);
        spec.setReplaceExisting(replaceExisting);
      }
      manager.addSpecification(spec);
      
      //System.out.println("at:" + atId + "; " + action + "; from=" + from + "; noDup="+noDup + "; replace="+replaceExisting);
    }
    newDc.commit();
    
    SimpleProgressReporter progress = new SimpleProgressReporter(null);
    sc.setSessionSetting("progress.inherit-annotations", progress);
    manager.setProgressReporter(progress);
    new Thread(manager).start();
    
    redirect = "../../common/progress_reporter.jsp?ID="+ID+
      "&progress=inherit-annotations&title=Inheriting annotations to " + items.size() + " items";

  }
  else
  {
    throw new WebException("popup", "Invalid command", "The command {1} is not recognised as a valid command.", cmd);
  }
}
finally
{
  if (oldDc != null) oldDc.close();
  if (newDc != null) newDc.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));
}
%>