source: trunk/www/common/annotations/inherit.jsp @ 2978

<%-- $Id: inherit.jsp 2978 2006-11-30 07:27:42Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) Authors contributing to this file.

  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 2
  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 this program; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place - Suite 330,
  Boston, MA  02111-1307, USA.
  ------------------------------------------------------------------

  This page is used to display and modify the attributes of
  the of a news item

  @author Nicklas
  @version 2.0
--%>
<%@ page 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.BasicItem"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.Annotatable"
  import="net.sf.basedb.core.AnnotationSet"
  import="net.sf.basedb.core.Annotation"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.Include"
  import="net.sf.basedb.core.Nameable"
  import="net.sf.basedb.core.ItemResultList"
  import="net.sf.basedb.core.AnnotationType"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.core.query.Orders"
  import="net.sf.basedb.core.query.Hql"
  import="net.sf.basedb.util.Tree"
  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.Formatter"
  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
  import="java.util.List"
  import="java.util.Set"
  import="java.util.HashSet"
  import="java.util.Map"
  import="java.util.HashMap"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%!
private void loadParents(Set<AnnotationSet> parentAnnotations, Set<Annotatable> parentItems, Annotatable item)
{
  Set<Annotatable> parents = item.getAnnotatableParents();
  if (parents == null) return;
  for (Annotatable parent : parents)
  {
    if (parent != null && parentItems.add(parent))
    {
      if (parent.hasPermission(Permission.USE) && parent.isAnnotated())
      {
        parentAnnotations.add(parent.getAnnotationSet());
      }
      loadParents(parentAnnotations, parentItems, parent);
    }
  }
}

private String generateJoustTree(Set<AnnotationSet> parentAnnotations, Set<Annotation> inheritedAnnotations, Set<AnnotationSet> inheritedSets)
{
  StringBuilder sb = new StringBuilder();
  String itemIcon = "Annotatable";
  String annotationIcon = "Annotation";
  String parameterIcon = "Parameter";
  
  for (AnnotationSet as : parentAnnotations)
  {
    Annotatable item = null;
    try
    {
      item = as.getItem();
    }
    catch (PermissionDeniedException ex)
    {}
    
    boolean setInherited = inheritedSets != null && inheritedSets.contains(as);

    String input = "<input type=\"checkbox\""+
      " name=\"AS"+as.getId()+"\""+
      (setInherited ? " checked" : "")+
      " onclick=\"itemOnToggle(event, "+as.getId()+")\""+
      ">";
    String name = item == null ? "<i>- denied -</i>" : 
      HTML.javaScriptEncode(((Nameable)item).getName()) + " (" + item.getType() + ")";
    sb.append("var item").append(as.getId());
    sb.append(" = JoustMenu.addMenuItem(-1"); 
    sb.append(",'").append(itemIcon).append("'");
    sb.append(",'").append(input).append(name).append("'");
    sb.append(", 'itemOnClick(event, ").append(as.getId()).append(")'");
    sb.append(", '', 'AS").append(as.getId()).append("', true);\n");

    List<Annotation> annotations = as.getAnnotations().list(as.getDbControl());
    SessionControl sc = as.getSessionControl();
    for (Annotation a : annotations)
    {
      Formatter formatter = FormatterFactory.getTypeFormatter(sc, a.getValueType());
      boolean inherited = inheritedAnnotations != null && inheritedAnnotations.contains(a);
      AnnotationType at = null;
      String annotationName = "<i>- denied -</i>";
      boolean isParameter = false;
      try
      {
        at = a.getAnnotationType();
        annotationName = at.getName();
        isParameter = at.isProtocolParameter();
      }
      catch (PermissionDeniedException ex)
      {}
      String values = Values.getString(a.getValues(), ", ", true, formatter);
      name = HTML.javaScriptEncode(annotationName +
        " [" + Values.trimString(values, 20)+"]");
      input = "<input type=\"checkbox\""+
        " name=\"A"+a.getId()+"\""+
        (inherited || setInherited ? " checked" : "")+
        (setInherited ? " disabled" : "")+
        " onclick=\"annotationOnToggle(event, "+a.getId()+")\""+
        ">";
      sb.append("JoustMenu.addChildItem(item" + as.getId());
      sb.append(",'").append(isParameter ? parameterIcon : annotationIcon).append("'");
      sb.append(",'").append(input).append(name).append("'");
      sb.append(", 'annotationOnClick(event, ").append(a.getId()).append(")'");
      sb.append(", '', 'A").append(a.getId()).append("');\n");
      sb.append("annotationValues['A").append(a.getId()).append("'] = ");
      sb.append("'").append(HTML.javaScriptEncode(values)).append("';\n");
    }
  }
  return sb.toString();
}
%>
<%
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final String ID = sc.getId();
final float scale = Base.getScale(sc);
final Item itemType = Item.valueOf(request.getParameter("item_type"));
final int itemId = Values.getInt(request.getParameter("item_id"));

final DbControl dc = sc.newDbControl();
ItemResultList<AnnotationType> annotationTypes = null;
try
{
  final Annotatable item = itemId == 0 ? null : (Annotatable)itemType.getById(dc, itemId);
  Set<AnnotationSet> parentAnnotations = new HashSet<AnnotationSet>();
  Set<Annotatable> parentItems = new HashSet<Annotatable>();

  if (item != null)
  {
    // Get all annotated parents and their annotation sets
    loadParents(parentAnnotations, parentItems, item);
  }
  
  // Parent items may have been submitted by caller
  String[] parents = request.getParameterValues("parents");
  // Each parameter is ITEMTYPE:ID:ID:...
  if (parents != null)
  {
    for (String parent : parents)
    {
      String[] temp = parent.split(":");
      Item parentType = Item.valueOf(temp[0]);
      for (int i = 1; i < temp.length; ++i)
      {
        int parentId = Values.getInt(temp[i], -1);
        if (parentId != -1) 
        {
          Annotatable parentItem = (Annotatable)parentType.getById(dc, parentId);
          if (parentItems.add(parentItem))
          {
            // This is a new parent
            if (parentItem.hasPermission(Permission.USE) && parentItem.isAnnotated()) 
            {
              parentAnnotations.add(parentItem.getAnnotationSet());
            }
            loadParents(parentAnnotations, parentItems, parentItem);
          }
        }
      }
    }
  }
  
  // Get the currently inherited annotations
  final AnnotationSet as = item != null && item.isAnnotated() ? item.getAnnotationSet() : null;
  Set<Annotation> inheritedAnnotations = null;
  Set<AnnotationSet> inheritedSets = null;
  if (as != null)
  {
    ItemQuery<Annotation> inheritedQuery = as.getInheritedAnnotations();
    inheritedQuery.order(Orders.asc(Hql.property("annotationSet")));
    inheritedQuery.order(Orders.asc(Hql.property("annotationType.name")));
    inheritedAnnotations = new HashSet<Annotation>(inheritedQuery.list(dc));
    for (Annotation a : inheritedAnnotations)
    {
      AnnotationSet from = a.getAnnotationSet();
      if (!parentAnnotations.contains(from) && from.hasPermission(Permission.USE))
      {
        parentAnnotations.add(from);
      }
    }
    
    ItemQuery<AnnotationSet> setQuery = as.getInheritedAnnotationSets();
    inheritedSets = new HashSet<AnnotationSet>(setQuery.list(dc));
    for (AnnotationSet ias : inheritedSets)
    {
      if (!parentAnnotations.contains(ias) && ias.hasPermission(Permission.USE))
      {
        parentAnnotations.add(ias);
      }
    }
  }
  %>
  <base:page type="popup" title="Inherit annotations">
  <base:head  scripts="annotations.js,parameters.js,newjoust.js,linkitems.js" styles="parameters.css,newjoust.css">
  <script language="JavaScript">
  var annotationValues = new Array();
  function init()
  {
    <%
    if (parentAnnotations.size() > 0)
    {
      %>
      IconStore.init();
      var path = getRoot() + 'images/joust/';
      IconStore.addIcon('Annotatable', path + 'annotatable.gif', 18, 16);
      IconStore.addIcon('Annotation', path + 'annotation.gif', 18, 16);
      IconStore.addIcon('Parameter', path + 'parameter.gif', 18, 16);
      <%=generateJoustTree(parentAnnotations, inheritedAnnotations, inheritedSets)%>
      JoustMenu.alwaysSendOnClickToSelected = true;
      JoustMenu.draw('joust');
      <%
    }
    %>
  }
  function itemOnClick(event, annotationSetId)
  {
    var frm = document.forms['annotations'];
    frm['AS'+annotationSetId].checked = !frm['AS'+annotationSetId].checked;
    itemOnToggle(event, annotationSetId);
  }
  
  function itemOnToggle(event, annotationSetId)
  {
    //alert('itemOnClick: '+annotationSetId);
    var frm = document.forms['annotations'];

    var linkedItem = Link.getItem('AS', annotationSetId);
    if (!linkedItem)
    {
      linkedItem = new Item('AS', annotationSetId);
    }
    var checked = frm['AS'+annotationSetId].checked;
    linkedItem.action += checked ? 1 : -1;

    frm['AS'+annotationSetId].checked = checked;
    var menuItem = JoustMenu.menuItems['AS'+annotationSetId];
    var childIndex = menuItem.firstChildIndex;
    while (childIndex != -1)
    {
      var childMenuItem = JoustMenu.menuItems[childIndex];
      frm[childMenuItem.externalId].checked = checked;
      frm[childMenuItem.externalId].disabled = checked;
      childIndex = childMenuItem.nextItemIndex;
      
      var annotationId = childMenuItem.externalId.substr(1);
      annotationItem = Link.getItem('A', annotationId);
      if (!annotationItem) annotationItem = new Item('A', annotationId);
      annotationItem.action = -1;
    }
    event.cancelBubble = true;
  }
  
  function annotationOnClick(event, annotationId)
  {
    var frm = document.forms['annotations'];
    var annotation = frm['A'+annotationId];
    if (!annotation.disabled)
    {
      annotation.checked = !annotation.checked;
      annotationOnToggle(event, annotationId);
    }
    document.getElementById('annotationValues').innerHTML = annotationValues['A'+annotationId];
  }
  
  function annotationOnToggle(event, annotationId)
  {
    //alert('itemOnClick: '+annotationSetId);
    var frm = document.forms['annotations'];

    var linkedItem = Link.getItem('A', annotationId);
    if (!linkedItem)
    {
      linkedItem = new Item('A', annotationId);
    }
    var checked = frm['A'+annotationId].checked;
    linkedItem.action = checked ? 1 : -1;
    
    frm['A'+annotationId].checked = checked;
    event.cancelBubble = true;
  }

  </script>
  </base:head>
  <base:body onload="init()" style="background: #E0E0E0;">

  <form name="annotations">
  <table class="form" cellspacing="2" border="0" cellpadding="0" width="100%">
  <tr valign="top">
  <td width="50%">
    <div id="joust" class="joust parameterlist" 
      style="height: <%=(int)(scale*320)%>px;">
      <%
      if (parentAnnotations.size() == 0) 
      {
        %>
        <div class="error">There are no parent items with annotations.</div>
        <%
      }
      %>
    </div>
    <base:icon image="joust/annotation.gif" /> = Annotation
    <base:icon image="joust/parameter.gif" /> = Protocol parameter
  </td>
  <td width="50%">
    <b>Annotation/parameter values</b>
    <div id="annotationValues">
    </div>
  </td>
  </tr>
  </table>
      
  </form>
  </base:body>
  </base:page>
  <%
}
finally
{
  if (dc != null) dc.close();
}
%>