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

Last change on this file since 2978 was 2978, checked in by Nicklas Nordborg, 15 years ago

Added session="false" to all jsp pages so we no longer generate unneeded cookies

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 11.5 KB
Line 
1<%-- $Id: inherit.jsp 2978 2006-11-30 07:27:42Z nicklas $
2  ------------------------------------------------------------------
3  Copyright (C) Authors contributing to this file.
4
5  This file is part of BASE - BioArray Software Environment.
6  Available at http://base.thep.lu.se/
7
8  BASE is free software; you can redistribute it and/or
9  modify it under the terms of the GNU General Public License
10  as published by the Free Software Foundation; either version 2
11  of the License, or (at your option) any later version.
12
13  BASE is distributed in the hope that it will be useful,
14  but WITHOUT ANY WARRANTY; without even the implied warranty of
15  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
16  GNU General Public License for more details.
17
18  You should have received a copy of the GNU General Public License
19  along with this program; if not, write to the Free Software
20  Foundation, Inc., 59 Temple Place - Suite 330,
21  Boston, MA  02111-1307, USA.
22  ------------------------------------------------------------------
23
24  This page is used to display and modify the attributes of
25  the of a news item
26
27  @author Nicklas
28  @version 2.0
29--%>
30<%@ page session="false"
31  import="net.sf.basedb.core.SessionControl"
32  import="net.sf.basedb.core.DbControl"
33  import="net.sf.basedb.core.Item"
34  import="net.sf.basedb.core.Type"
35  import="net.sf.basedb.core.BasicItem"
36  import="net.sf.basedb.core.Permission"
37  import="net.sf.basedb.core.Annotatable"
38  import="net.sf.basedb.core.AnnotationSet"
39  import="net.sf.basedb.core.Annotation"
40  import="net.sf.basedb.core.ItemQuery"
41  import="net.sf.basedb.core.Include"
42  import="net.sf.basedb.core.Nameable"
43  import="net.sf.basedb.core.ItemResultList"
44  import="net.sf.basedb.core.AnnotationType"
45  import="net.sf.basedb.core.PermissionDeniedException"
46  import="net.sf.basedb.core.query.Orders"
47  import="net.sf.basedb.core.query.Hql"
48  import="net.sf.basedb.util.Tree"
49  import="net.sf.basedb.clients.web.Base"
50  import="net.sf.basedb.clients.web.WebException"
51  import="net.sf.basedb.clients.web.util.HTML"
52  import="net.sf.basedb.util.Values"
53  import="net.sf.basedb.util.formatter.Formatter"
54  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
55  import="java.util.List"
56  import="java.util.Set"
57  import="java.util.HashSet"
58  import="java.util.Map"
59  import="java.util.HashMap"
60%>
61<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
62<%!
63private void loadParents(Set<AnnotationSet> parentAnnotations, Set<Annotatable> parentItems, Annotatable item)
64{
65  Set<Annotatable> parents = item.getAnnotatableParents();
66  if (parents == null) return;
67  for (Annotatable parent : parents)
68  {
69    if (parent != null && parentItems.add(parent))
70    {
71      if (parent.hasPermission(Permission.USE) && parent.isAnnotated())
72      {
73        parentAnnotations.add(parent.getAnnotationSet());
74      }
75      loadParents(parentAnnotations, parentItems, parent);
76    }
77  }
78}
79
80private String generateJoustTree(Set<AnnotationSet> parentAnnotations, Set<Annotation> inheritedAnnotations, Set<AnnotationSet> inheritedSets)
81{
82  StringBuilder sb = new StringBuilder();
83  String itemIcon = "Annotatable";
84  String annotationIcon = "Annotation";
85  String parameterIcon = "Parameter";
86 
87  for (AnnotationSet as : parentAnnotations)
88  {
89    Annotatable item = null;
90    try
91    {
92      item = as.getItem();
93    }
94    catch (PermissionDeniedException ex)
95    {}
96   
97    boolean setInherited = inheritedSets != null && inheritedSets.contains(as);
98
99    String input = "<input type=\"checkbox\""+
100      " name=\"AS"+as.getId()+"\""+
101      (setInherited ? " checked" : "")+
102      " onclick=\"itemOnToggle(event, "+as.getId()+")\""+
103      ">";
104    String name = item == null ? "<i>- denied -</i>" : 
105      HTML.javaScriptEncode(((Nameable)item).getName()) + " (" + item.getType() + ")";
106    sb.append("var item").append(as.getId());
107    sb.append(" = JoustMenu.addMenuItem(-1"); 
108    sb.append(",'").append(itemIcon).append("'");
109    sb.append(",'").append(input).append(name).append("'");
110    sb.append(", 'itemOnClick(event, ").append(as.getId()).append(")'");
111    sb.append(", '', 'AS").append(as.getId()).append("', true);\n");
112
113    List<Annotation> annotations = as.getAnnotations().list(as.getDbControl());
114    SessionControl sc = as.getSessionControl();
115    for (Annotation a : annotations)
116    {
117      Formatter formatter = FormatterFactory.getTypeFormatter(sc, a.getValueType());
118      boolean inherited = inheritedAnnotations != null && inheritedAnnotations.contains(a);
119      AnnotationType at = null;
120      String annotationName = "<i>- denied -</i>";
121      boolean isParameter = false;
122      try
123      {
124        at = a.getAnnotationType();
125        annotationName = at.getName();
126        isParameter = at.isProtocolParameter();
127      }
128      catch (PermissionDeniedException ex)
129      {}
130      String values = Values.getString(a.getValues(), ", ", true, formatter);
131      name = HTML.javaScriptEncode(annotationName +
132        " [" + Values.trimString(values, 20)+"]");
133      input = "<input type=\"checkbox\""+
134        " name=\"A"+a.getId()+"\""+
135        (inherited || setInherited ? " checked" : "")+
136        (setInherited ? " disabled" : "")+
137        " onclick=\"annotationOnToggle(event, "+a.getId()+")\""+
138        ">";
139      sb.append("JoustMenu.addChildItem(item" + as.getId());
140      sb.append(",'").append(isParameter ? parameterIcon : annotationIcon).append("'");
141      sb.append(",'").append(input).append(name).append("'");
142      sb.append(", 'annotationOnClick(event, ").append(a.getId()).append(")'");
143      sb.append(", '', 'A").append(a.getId()).append("');\n");
144      sb.append("annotationValues['A").append(a.getId()).append("'] = ");
145      sb.append("'").append(HTML.javaScriptEncode(values)).append("';\n");
146    }
147  }
148  return sb.toString();
149}
150%>
151<%
152final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
153final String ID = sc.getId();
154final float scale = Base.getScale(sc);
155final Item itemType = Item.valueOf(request.getParameter("item_type"));
156final int itemId = Values.getInt(request.getParameter("item_id"));
157
158final DbControl dc = sc.newDbControl();
159ItemResultList<AnnotationType> annotationTypes = null;
160try
161{
162  final Annotatable item = itemId == 0 ? null : (Annotatable)itemType.getById(dc, itemId);
163  Set<AnnotationSet> parentAnnotations = new HashSet<AnnotationSet>();
164  Set<Annotatable> parentItems = new HashSet<Annotatable>();
165
166  if (item != null)
167  {
168    // Get all annotated parents and their annotation sets
169    loadParents(parentAnnotations, parentItems, item);
170  }
171 
172  // Parent items may have been submitted by caller
173  String[] parents = request.getParameterValues("parents");
174  // Each parameter is ITEMTYPE:ID:ID:...
175  if (parents != null)
176  {
177    for (String parent : parents)
178    {
179      String[] temp = parent.split(":");
180      Item parentType = Item.valueOf(temp[0]);
181      for (int i = 1; i < temp.length; ++i)
182      {
183        int parentId = Values.getInt(temp[i], -1);
184        if (parentId != -1) 
185        {
186          Annotatable parentItem = (Annotatable)parentType.getById(dc, parentId);
187          if (parentItems.add(parentItem))
188          {
189            // This is a new parent
190            if (parentItem.hasPermission(Permission.USE) && parentItem.isAnnotated()) 
191            {
192              parentAnnotations.add(parentItem.getAnnotationSet());
193            }
194            loadParents(parentAnnotations, parentItems, parentItem);
195          }
196        }
197      }
198    }
199  }
200 
201  // Get the currently inherited annotations
202  final AnnotationSet as = item != null && item.isAnnotated() ? item.getAnnotationSet() : null;
203  Set<Annotation> inheritedAnnotations = null;
204  Set<AnnotationSet> inheritedSets = null;
205  if (as != null)
206  {
207    ItemQuery<Annotation> inheritedQuery = as.getInheritedAnnotations();
208    inheritedQuery.order(Orders.asc(Hql.property("annotationSet")));
209    inheritedQuery.order(Orders.asc(Hql.property("annotationType.name")));
210    inheritedAnnotations = new HashSet<Annotation>(inheritedQuery.list(dc));
211    for (Annotation a : inheritedAnnotations)
212    {
213      AnnotationSet from = a.getAnnotationSet();
214      if (!parentAnnotations.contains(from) && from.hasPermission(Permission.USE))
215      {
216        parentAnnotations.add(from);
217      }
218    }
219   
220    ItemQuery<AnnotationSet> setQuery = as.getInheritedAnnotationSets();
221    inheritedSets = new HashSet<AnnotationSet>(setQuery.list(dc));
222    for (AnnotationSet ias : inheritedSets)
223    {
224      if (!parentAnnotations.contains(ias) && ias.hasPermission(Permission.USE))
225      {
226        parentAnnotations.add(ias);
227      }
228    }
229  }
230  %>
231  <base:page type="popup" title="Inherit annotations">
232  <base:head  scripts="annotations.js,parameters.js,newjoust.js,linkitems.js" styles="parameters.css,newjoust.css">
233  <script language="JavaScript">
234  var annotationValues = new Array();
235  function init()
236  {
237    <%
238    if (parentAnnotations.size() > 0)
239    {
240      %>
241      IconStore.init();
242      var path = getRoot() + 'images/joust/';
243      IconStore.addIcon('Annotatable', path + 'annotatable.gif', 18, 16);
244      IconStore.addIcon('Annotation', path + 'annotation.gif', 18, 16);
245      IconStore.addIcon('Parameter', path + 'parameter.gif', 18, 16);
246      <%=generateJoustTree(parentAnnotations, inheritedAnnotations, inheritedSets)%>
247      JoustMenu.alwaysSendOnClickToSelected = true;
248      JoustMenu.draw('joust');
249      <%
250    }
251    %>
252  }
253  function itemOnClick(event, annotationSetId)
254  {
255    var frm = document.forms['annotations'];
256    frm['AS'+annotationSetId].checked = !frm['AS'+annotationSetId].checked;
257    itemOnToggle(event, annotationSetId);
258  }
259 
260  function itemOnToggle(event, annotationSetId)
261  {
262    //alert('itemOnClick: '+annotationSetId);
263    var frm = document.forms['annotations'];
264
265    var linkedItem = Link.getItem('AS', annotationSetId);
266    if (!linkedItem)
267    {
268      linkedItem = new Item('AS', annotationSetId);
269    }
270    var checked = frm['AS'+annotationSetId].checked;
271    linkedItem.action += checked ? 1 : -1;
272
273    frm['AS'+annotationSetId].checked = checked;
274    var menuItem = JoustMenu.menuItems['AS'+annotationSetId];
275    var childIndex = menuItem.firstChildIndex;
276    while (childIndex != -1)
277    {
278      var childMenuItem = JoustMenu.menuItems[childIndex];
279      frm[childMenuItem.externalId].checked = checked;
280      frm[childMenuItem.externalId].disabled = checked;
281      childIndex = childMenuItem.nextItemIndex;
282     
283      var annotationId = childMenuItem.externalId.substr(1);
284      annotationItem = Link.getItem('A', annotationId);
285      if (!annotationItem) annotationItem = new Item('A', annotationId);
286      annotationItem.action = -1;
287    }
288    event.cancelBubble = true;
289  }
290 
291  function annotationOnClick(event, annotationId)
292  {
293    var frm = document.forms['annotations'];
294    var annotation = frm['A'+annotationId];
295    if (!annotation.disabled)
296    {
297      annotation.checked = !annotation.checked;
298      annotationOnToggle(event, annotationId);
299    }
300    document.getElementById('annotationValues').innerHTML = annotationValues['A'+annotationId];
301  }
302 
303  function annotationOnToggle(event, annotationId)
304  {
305    //alert('itemOnClick: '+annotationSetId);
306    var frm = document.forms['annotations'];
307
308    var linkedItem = Link.getItem('A', annotationId);
309    if (!linkedItem)
310    {
311      linkedItem = new Item('A', annotationId);
312    }
313    var checked = frm['A'+annotationId].checked;
314    linkedItem.action = checked ? 1 : -1;
315   
316    frm['A'+annotationId].checked = checked;
317    event.cancelBubble = true;
318  }
319
320  </script>
321  </base:head>
322  <base:body onload="init()" style="background: #E0E0E0;">
323
324  <form name="annotations">
325  <table class="form" cellspacing="2" border="0" cellpadding="0" width="100%">
326  <tr valign="top">
327  <td width="50%">
328    <div id="joust" class="joust parameterlist" 
329      style="height: <%=(int)(scale*320)%>px;">
330      <%
331      if (parentAnnotations.size() == 0) 
332      {
333        %>
334        <div class="error">There are no parent items with annotations.</div>
335        <%
336      }
337      %>
338    </div>
339    <base:icon image="joust/annotation.gif" /> = Annotation
340    <base:icon image="joust/parameter.gif" /> = Protocol parameter
341  </td>
342  <td width="50%">
343    <b>Annotation/parameter values</b>
344    <div id="annotationValues">
345    </div>
346  </td>
347  </tr>
348  </table>
349     
350  </form>
351  </base:body>
352  </base:page>
353  <%
354}
355finally
356{
357  if (dc != null) dc.close();
358}
359%>
360
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