source: trunk/www/common/annotations/index.jsp @ 6729

Last change on this file since 6729 was 6729, checked in by Nicklas Nordborg, 7 years ago

References #1910 and #1908.

Batch inherit annotations has been updated to not allow selection of annotation type that has been disabled for inheritance.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 5.8 KB
Line 
1<%-- $Id: index.jsp 6729 2015-02-13 08:44:56Z nicklas $
2  ------------------------------------------------------------------
3  Copyright (C) 2006 Nicklas Nordborg
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 3
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 BASE. If not, see <http://www.gnu.org/licenses/>.
20  ------------------------------------------------------------------
21
22  @author Nicklas
23  @version 2.0
24--%>
25<%@ page pageEncoding="UTF-8" session="false"
26  import="net.sf.basedb.core.SessionControl"
27  import="net.sf.basedb.core.DbControl"
28  import="net.sf.basedb.core.Item"
29  import="net.sf.basedb.core.ItemContext"
30  import="net.sf.basedb.core.BasicItem"
31  import="net.sf.basedb.core.AnnotatedItem"
32  import="net.sf.basedb.core.Annotation"
33  import="net.sf.basedb.core.AnnotationType"
34  import="net.sf.basedb.core.Annotatable"
35  import="net.sf.basedb.core.ItemSubtype"
36  import="net.sf.basedb.core.BaseException"
37  import="net.sf.basedb.core.SimpleProgressReporter"
38  import="net.sf.basedb.core.snapshot.SnapshotManager"
39  import="net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager"
40  import="net.sf.basedb.util.annotations.InheritAnnotationsManager"
41  import="net.sf.basedb.util.annotations.InheritSpecification"
42  import="net.sf.basedb.clients.web.Base"
43  import="net.sf.basedb.clients.web.WebException"
44  import="net.sf.basedb.util.Values"
45  import="net.sf.basedb.clients.web.util.HTML"
46  import="java.util.Set"
47  import="java.util.List"
48  import="java.util.ArrayList"
49 
50 
51%>
52<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
53<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
54
55<%
56final String root = request.getContextPath()+"/";
57final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
58final String ID = sc.getId();
59final String cmd = request.getParameter("cmd");
60final int itemId = Values.getInt(request.getParameter("item_id"));
61
62DbControl newDc = null;
63DbControl oldDc = null;
64String forward = null;
65String message = null;
66String redirect = null;
67try
68{
69  if ("EditItem".equals(cmd))
70  {
71    newDc = sc.newDbControl();
72    Annotation a = Annotation.getById(newDc, itemId);
73    AnnotationType at = a.getAnnotationType();
74    Annotatable item = a.getAnnotationSet().getItem();
75   
76    redirect = "annotate.jsp?ID=" + ID + "&item_id=" + item.getId() + 
77        "&item_type=" + item.getType().name() + 
78        "&annotationtype_id=" + at.getId() + "&standalone=1";
79    newDc.close();
80  }
81  else if ("SaveAnnotations".equals(cmd))
82  {
83    final Item itemType = Item.valueOf(request.getParameter("item_type"));
84    newDc = sc.newDbControl();
85    oldDc = sc.newDbControl();
86    ItemContext cc = sc.getCurrentContext(itemType);
87    Annotatable oldItem = (Annotatable)cc.getObject("item");
88    Annotatable newItem = (Annotatable)itemType.getById(newDc, itemId);
89    oldDc.reattachItem((BasicItem)oldItem, false);
90    Base.updateAnnotations(newDc, oldItem, newItem, request);
91    oldDc.close();
92    newDc.commit();
93    cc.removeObject("item");
94    message = "Annotations saved";
95  }
96  else if ("BatchInherit".equals(cmd))
97  {
98    final Item itemType = Item.valueOf(request.getParameter("item_type"));
99    final String subContext = Values.getString(request.getParameter("subcontext"), "");
100    final ItemContext cc = sc.getCurrentContext(itemType, subContext);
101   
102    newDc = sc.newDbControl();
103
104    Set<AnnotatedItem> items = (Set<AnnotatedItem>)cc.getObject("AnnotatedItems");
105    cc.removeObject("AnnotatedItems");
106   
107    RunnableInheritAnnotationsManager manager = new RunnableInheritAnnotationsManager(sc);
108    manager.addAllItems(items);
109   
110    for (Integer atId : Values.getInt(request.getParameter("annotationTypes").split(",")))
111    {
112      AnnotationType at = AnnotationType.getById(newDc, atId);
113      if (at.getDisableInheritance()) continue; // Inheritance has been disabled
114     
115      InheritSpecification spec = new InheritSpecification(at);
116      String action = request.getParameter("action_"+atId);
117     
118      if ("remove".equals(action))
119      {
120        spec.setRemove(true);
121      }
122      else
123      {
124        int subtypeId = Values.getInt(request.getParameter("from_"+atId));
125        boolean noDup = Values.getBoolean(request.getParameter("nodup_"+atId));
126        boolean replaceExisting = Values.getBoolean(request.getParameter("replace_"+atId));
127        if (subtypeId != 0)
128        {
129          spec.setItemSubtype(ItemSubtype.getById(newDc, subtypeId));
130        }
131        spec.setNoDuplicates(noDup);
132        spec.setReplaceExisting(replaceExisting);
133      }
134      manager.addSpecification(spec);
135    }
136    newDc.commit();
137   
138    SimpleProgressReporter progress = new SimpleProgressReporter(null);
139    sc.setSessionSetting("progress.inherit-annotations", progress);
140    manager.setProgressReporter(progress);
141    new Thread(manager).start();
142   
143    redirect = "../../common/progress_reporter.jsp?ID="+ID+
144      "&progress=inherit-annotations&title=Inheriting annotations to " + items.size() + " items";
145
146  }
147  else
148  {
149    throw new WebException("popup", "Invalid command", "The command {1} is not recognised as a valid command.", cmd);
150  }
151}
152finally
153{
154  if (oldDc != null) oldDc.close();
155  if (newDc != null) newDc.close();
156}
157
158if (forward != null)
159{
160  sc.setSessionSetting("alert-message", message);
161  pageContext.forward(forward);
162}
163else if (redirect != null)
164{
165  sc.setSessionSetting("alert-message", message);
166  response.sendRedirect(redirect);
167}
168else if (message == null)
169{
170  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&wait=0");
171}
172else
173{
174  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&message="+HTML.urlEncode(message));
175}
176%>
177
Note: See TracBrowser for help on using the repository browser.