source: trunk/www/views/scans/view_scan.jsp @ 2918

Last change on this file since 2918 was 2918, checked in by Nicklas Nordborg, 17 years ago

References #348: Take ownership of items

Implemented on all pages in the "View" menu.
  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 11.6 KB
Line 
1<%-- $Id: view_scan.jsp 2918 2006-11-15 11:21:13Z 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  @author Nicklas
25  @version 2.0
26--%>
27<%@ page
28  import="net.sf.basedb.core.SessionControl"
29  import="net.sf.basedb.core.DbControl"
30  import="net.sf.basedb.core.SystemItems"
31  import="net.sf.basedb.core.Item"
32  import="net.sf.basedb.core.ItemContext"
33  import="net.sf.basedb.core.Permission"
34  import="net.sf.basedb.core.AnnotationType"
35  import="net.sf.basedb.core.AnnotationSet"
36  import="net.sf.basedb.core.Scan"
37  import="net.sf.basedb.core.RawBioAssay"
38  import="net.sf.basedb.core.Protocol"
39  import="net.sf.basedb.core.Hardware"
40  import="net.sf.basedb.core.Hybridization"
41  import="net.sf.basedb.core.User"
42  import="net.sf.basedb.core.ItemQuery"
43  import="net.sf.basedb.core.ItemResultList"
44  import="net.sf.basedb.core.Include"
45  import="net.sf.basedb.core.PermissionDeniedException"
46  import="net.sf.basedb.core.PluginDefinition"
47  import="net.sf.basedb.core.plugin.GuiContext"
48  import="net.sf.basedb.core.plugin.Plugin"
49  import="net.sf.basedb.core.query.Orders"
50  import="net.sf.basedb.core.query.Hql"
51  import="net.sf.basedb.clients.web.Base"
52  import="net.sf.basedb.clients.web.PermissionUtil"
53  import="net.sf.basedb.clients.web.util.HTML"
54  import="net.sf.basedb.util.Values"
55  import="java.util.Date"
56  import="java.util.Map"
57  import="java.util.Set"
58  import="java.util.List"
59%>
60<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
61<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
62<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
63<%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
64<%!
65  private static final Item itemType = Item.SCAN;
66  private static final GuiContext guiContext = new GuiContext(itemType, GuiContext.Type.ITEM);
67%>
68<%
69final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
70final String ID = sc.getId();
71final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null);
72final int itemId = cc.getId();
73final String tab = Values.getString(request.getParameter("tab"), "properties");
74final float scale = Base.getScale(sc);
75final DbControl dc = sc.newDbControl();
76try
77{
78  Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
79
80  String title = null;
81  Scan scan = Scan.getById(dc, itemId);
82 
83  final boolean usePermission = scan.hasPermission(Permission.USE);
84  final boolean writePermission = scan.hasPermission(Permission.WRITE);
85  final boolean deletePermission = scan.hasPermission(Permission.DELETE);
86  final boolean sharePermission = scan.hasPermission(Permission.SET_PERMISSION);
87  final boolean setOwnerPermission = scan.hasPermission(Permission.SET_OWNER);
88  final boolean isOwner = scan.isOwner();
89  %>
90
91  <base:page title="<%=title%>">
92  <base:head scripts="table.js,tabcontrol.js" styles="table.css,toolbar.css,headertabcontrol.css,path.css">
93    <script language="JavaScript">
94    function editItem()
95    {
96      Main.viewOrEditItem('<%=ID%>', '<%=itemType.name()%>', <%=itemId%>, true);
97    }
98    function shareItem()
99    {
100      Main.openPopup('index.jsp?ID=<%=ID%>&cmd=ShareItem&item_id=<%=itemId%>', 'ShareScan', 500, 400);
101    }
102    function deleteItem()
103    {
104      location.replace('index.jsp?ID=<%=ID%>&cmd=DeleteItem&item_id=<%=itemId%>');
105    }
106    function restoreItem()
107    {
108      location.replace('index.jsp?ID=<%=ID%>&cmd=RestoreItem&item_id=<%=itemId%>');
109    }
110    function takeOwnership()
111    {
112      if (confirm('Are you sure that you want to take ownership of this item? It can\'t be undone.'))
113      {
114        location.replace('index.jsp?ID=<%=ID%>&cmd=TakeOwnershipOfItem&item_id=<%=itemId%>');
115      }
116    }
117    function runPlugin(cmd)
118    {
119      Main.openPopup('index.jsp?ID=<%=ID%>&cmd='+cmd+'&item_id=<%=itemId%>', 'RunPlugin'+cmd, 740, 540);
120    }
121    function viewImages()
122    {
123      location.href = 'images/index.jsp?ID=<%=ID%>&cmd=List&scan_id=<%=itemId%>';
124    }
125    function switchTab(tabControlId, tabId)
126    {
127      if (tabId == 'images')
128      {
129        viewImages();
130      }
131      else
132      {
133        TabControl.setActiveTab(tabControlId, tabId);
134      }
135    }
136    function newRawBioAssay()
137    {
138      Main.viewOrEditItem('<%=ID%>', 'RAWBIOASSAY', 0, true, '&scan_id=<%=itemId%>');
139    }
140    </script>
141  </base:head>
142  <base:body>
143    <p>
144    <p:path>
145      <p:pathelement title="Scans" href="<%="index.jsp?ID="+ID%>" />
146      <p:pathelement title="<%=HTML.encodeTags(scan.getName())%>" />
147    </p:path>
148   
149    <t:tabcontrol id="main" active="<%=tab%>" switch="switchTab">
150    <t:tab id="properties" title="Properties">
151
152    <tbl:toolbar
153      >
154      <tbl:button 
155        disabled="<%=writePermission ? false : true%>" 
156        image="<%=writePermission ? "edit.gif" : "edit_disabled.gif"%>" 
157        onclick="editItem()" 
158        title="Edit&hellip;" 
159        tooltip="<%=writePermission ? "Edit this scan" : "You do not have permission to edit this scan"%>" 
160      />
161      <tbl:button 
162        disabled="<%=deletePermission ? false : true%>" 
163        image="<%=deletePermission ? "delete.gif" : "delete_disabled.gif"%>" 
164        onclick="deleteItem()" 
165        title="Delete"
166        visible="<%=!scan.isRemoved()%>"
167        tooltip="<%=deletePermission ? "Delete this scan" : "You do not have permission to delete this scan"%>" 
168      />
169      <tbl:button 
170        disabled="<%=writePermission ? false : true%>" 
171        image="<%=writePermission ? "restore.gif" : "restore_disabled.gif"%>" 
172        onclick="restoreItem()" 
173        title="Restore"
174        visible="<%=scan.isRemoved()%>"
175        tooltip="<%=writePermission ? "Restore this scan" : "You do not have permission to restore this scan"%>" 
176      />
177      <tbl:button 
178        disabled="<%=sharePermission ? false : true%>"
179        image="<%=sharePermission ? "share.gif" : "share_disabled.gif"%>"
180        onclick="shareItem()" 
181        title="Share&hellip;" 
182        tooltip="<%=sharePermission ? "Share this scan to other user, groups and projects" : "You do not have permission to share this scan"%>"
183      />
184      <tbl:button 
185        disabled="<%=setOwnerPermission ? false : true%>"
186        image="<%=setOwnerPermission ? "take_ownership.png" : "take_ownership_disabled.png"%>"
187        onclick="takeOwnership()" 
188        title="Take ownership&hellip;"
189        visible="<%=!isOwner%>"
190        tooltip="<%=setOwnerPermission ? "Take ownership of this item" : "You do not have permission to take ownership of this item"%>"
191      />
192      <tbl:button
193        image="add.png"
194        onclick="newRawBioAssay()"
195        title="New raw bioassay&hellip;"
196        tooltip="Create a new raw bioassay from this scan"
197        visible="<%=sc.hasPermission(Permission.CREATE, Item.RAWBIOASSAY) && usePermission%>"
198      />
199      <tbl:button 
200        image="import.gif" 
201        onclick="runPlugin('ImportItem')" 
202        title="Import&hellip;" 
203        tooltip="Import data" 
204        visible="<%=pluginCount.containsKey(Plugin.MainType.IMPORT)%>"
205      />
206      <tbl:button 
207        image="export.gif" 
208        onclick="runPlugin('ExportItem')" 
209        title="Export&hellip;" 
210        tooltip="Export data" 
211        visible="<%=pluginCount.containsKey(Plugin.MainType.EXPORT)%>"
212      />
213      <tbl:button 
214        image="runplugin.gif" 
215        onclick="runPlugin('RunPlugin')" 
216        title="Run plugin&hellip;" 
217        tooltip="Run a plugin" 
218        visible="<%=pluginCount.containsKey(Plugin.MainType.OTHER)%>"
219      />
220      <tbl:button
221        image="help.gif"
222        onclick="<%="Main.openHelp('" + ID +"', 'scan.view.properties')"%>"
223        title="Help&hellip;"
224        tooltip="Get help about this page"
225      />
226      </tbl:toolbar>
227    <div class="boxedbottom">
228      <div class="itemstatus">Permissions on this item: <i><%=PermissionUtil.getFullPermissionNames(scan)%></i></div>
229      <%
230      if (scan.isRemoved() || scan.isShared())
231      {
232        %>
233        <div class="itemstatus">
234          <base:icon image="deleted.gif" 
235            visible="<%=scan.isRemoved()%>"> This item has been flagged for deletion<br></base:icon>
236          <base:icon image="shared.gif" 
237            visible="<%=scan.isShared()%>"> This item is shared to other user, groups and/or projects</base:icon>
238        </div>
239        <%
240      }
241      %>
242      <table class="form" cellspacing=0>
243      <tr>
244        <td class="prompt">Name</td>
245        <td><%=HTML.encodeTags(scan.getName())%></td>
246      </tr>
247      <tr>
248        <td class="prompt">Hybridization</td>
249        <td><base:propertyvalue item="<%=scan%>" property="hybridization" /></td>
250      </tr>
251      <tr>
252        <td class="prompt">Scanner</td>
253        <td><base:propertyvalue item="<%=scan%>" property="scanner" /></td>
254      </tr>
255      <tr>
256        <td class="prompt">Protocol</td>
257        <td><base:propertyvalue item="<%=scan%>" property="protocol" /></td>
258      </tr>
259      <tr>
260        <td class="prompt">Owner</td>
261        <td><base:propertyvalue item="<%=scan%>" property="owner" /></td>
262      </tr>
263      <tr>
264        <td class="prompt">Description</td>
265        <td><%=HTML.niceFormat(scan.getDescription())%></td>
266      </tr>
267      </table>
268 
269      <%
270      ItemQuery<RawBioAssay> rawQuery = scan.getRawBioAssays();
271      rawQuery.include(Include.MINE, Include.SHARED, Include.OTHERS, Include.IN_PROJECT);
272      rawQuery.order(Orders.asc(Hql.property("name")));
273      ItemResultList<RawBioAssay> raw = rawQuery.list(dc);
274      if (raw.size() == 0)
275      {
276        %>
277        <h4>Raw bioassays</h4>
278        No raw bioassays has been created from this scan
279        (or, you don't have permission to view them).
280        <%
281      }
282      else
283      {
284        %>
285        <h4 class="docked">Raw bioassays</h4>
286        <tbl:table
287          id="rawBioAssays"
288          clazz="itemlist"
289          columns="all"
290          >
291        <tbl:columndef 
292          id="name"
293          title="Name"
294        />
295        <tbl:columndef
296          id="type"
297          title="Type"
298        />
299        <tbl:columndef
300          id="software"
301          title="Software"
302        />
303        <tbl:columndef
304          id="data"
305          title="Data"
306        />
307        <tbl:columndef
308          id="arrayDesign"
309          title="Array design"
310        />
311        <tbl:columndef 
312          id="description"
313          title="Description"
314        />
315        <tbl:data>
316          <tbl:columns>
317          </tbl:columns>
318          <tbl:rows>
319          <%
320          for (RawBioAssay item : raw)
321          {
322            %>
323            <tbl:row>
324              <tbl:cell column="name"><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
325              <tbl:cell column="type"><%=HTML.encodeTags(item.getRawDataType().getName())%></tbl:cell>
326              <tbl:cell column="software"><base:propertyvalue item="<%=item%>" property="software" /></tbl:cell>
327              <tbl:cell column="data"><%=item.hasData() ? "yes (" + item.getSpots() + " spots)" : "no"%></tbl:cell>
328              <tbl:cell column="arrayDesign"><base:propertyvalue item="<%=item%>" property="arrayDesign" /></tbl:cell>
329              <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
330            </tbl:row>
331            <%
332          }
333          %>
334          </tbl:rows>
335        </tbl:data>
336        </tbl:table>
337        <%
338      }
339      %>
340 
341    </div>
342      </t:tab>
343     
344      <t:tab id="annotations" title="Annotations &amp; parameters" 
345        tooltip="View annotation values and protocol parameters">
346        <div class="boxed">
347        <jsp:include page="../../common/annotations/list_annotations.jsp">
348          <jsp:param name="item_type" value="<%=itemType.name()%>" />
349          <jsp:param name="item_id" value="<%=itemId%>" />
350          <jsp:param name="ID" value="<%=ID%>" />
351        </jsp:include>
352        </div>
353      </t:tab>
354     
355      <t:tab id="images" title="Images" />
356      </t:tabcontrol>
357
358
359  </base:body>
360  </base:page>
361  <%
362}
363finally
364{
365  if (dc != null) dc.close();
366}
367
368%>
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