source: trunk/www/common/annotations/index.jsp @ 7110

Last change on this file since 7110 was 7110, checked in by Nicklas Nordborg, 6 years ago

Fixes #1994: Display information about the item for annotations in the trashcan

See attached image.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 6.0 KB
Line 
1<%-- $Id: index.jsp 7110 2016-03-15 07:35:05Z 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        "&annotation_id="+itemId+
79        "&annotationtype_id=" + at.getId() + "&standalone=1";
80    newDc.close();
81  }
82  else if ("SaveAnnotations".equals(cmd))
83  {
84    final Item itemType = Item.valueOf(request.getParameter("item_type"));
85    newDc = sc.newDbControl();
86    oldDc = sc.newDbControl();
87    ItemContext cc = sc.getCurrentContext(itemType);
88    Annotatable oldItem = (Annotatable)cc.getObject("item");
89    Annotatable newItem = (Annotatable)itemType.getById(newDc, itemId);
90    oldDc.reattachItem((BasicItem)oldItem, false);
91    Base.updateAnnotations(newDc, oldItem, newItem, request);
92    oldDc.close();
93    newDc.commit();
94    cc.removeObject("item");
95    message = "Annotations saved";
96  }
97  else if ("BatchInherit".equals(cmd))
98  {
99    final Item itemType = Item.valueOf(request.getParameter("item_type"));
100    final String subContext = Values.getString(request.getParameter("subcontext"), "");
101    final ItemContext cc = sc.getCurrentContext(itemType, subContext);
102   
103    newDc = sc.newDbControl();
104
105    Set<AnnotatedItem> items = (Set<AnnotatedItem>)cc.getObject("AnnotatedItems");
106    cc.removeObject("AnnotatedItems");
107   
108    RunnableInheritAnnotationsManager manager = new RunnableInheritAnnotationsManager(sc);
109    manager.addAllItems(items);
110   
111    for (Integer atId : Values.getInt(request.getParameter("annotationTypes").split(",")))
112    {
113      AnnotationType at = AnnotationType.getById(newDc, atId);
114      if (at.getDisableInheritance()) continue; // Inheritance has been disabled
115     
116      InheritSpecification spec = new InheritSpecification(at);
117      String action = request.getParameter("action_"+atId);
118     
119      if ("remove".equals(action))
120      {
121        spec.setRemove(true);
122      }
123      else if ("resync".equals(action))
124      {
125        spec.setResyncCloned(true);
126      }
127      else
128      {
129        spec.setClone("clone".equals(action));
130        int subtypeId = Values.getInt(request.getParameter("from_"+atId));
131        boolean noDup = Values.getBoolean(request.getParameter("nodup_"+atId));
132        boolean replaceExisting = Values.getBoolean(request.getParameter("replace_"+atId));
133        if (subtypeId != 0)
134        {
135          spec.setItemSubtype(ItemSubtype.getById(newDc, subtypeId));
136        }
137        spec.setNoDuplicates(noDup);
138        spec.setReplaceExisting(replaceExisting);
139      }
140      manager.addSpecification(spec);
141    }
142    newDc.commit();
143   
144    SimpleProgressReporter progress = new SimpleProgressReporter(null);
145    sc.setSessionSetting("progress.inherit-annotations", progress);
146    manager.setProgressReporter(progress);
147    new Thread(manager).start();
148   
149    redirect = "../../common/progress_reporter.jsp?ID="+ID+
150      "&progress=inherit-annotations&title=Inheriting annotations to " + items.size() + " items";
151
152  }
153  else
154  {
155    throw new WebException("popup", "Invalid command", "The command {1} is not recognised as a valid command.", cmd);
156  }
157}
158finally
159{
160  if (oldDc != null) oldDc.close();
161  if (newDc != null) newDc.close();
162}
163
164if (forward != null)
165{
166  sc.setSessionSetting("alert-message", message);
167  pageContext.forward(forward);
168}
169else if (redirect != null)
170{
171  sc.setSessionSetting("alert-message", message);
172  response.sendRedirect(redirect);
173}
174else if (message == null)
175{
176  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&wait=0");
177}
178else
179{
180  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&message="+HTML.urlEncode(message));
181}
182%>
183
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