source: trunk/www/lims/arraydesigns/features/view_feature.jsp @ 5917

Last change on this file since 5917 was 5917, checked in by Nicklas Nordborg, 10 years ago

References #1655: GUI improvements

Edit dialogs for array lims.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 9.6 KB
Line 
1<%-- $Id: view_feature.jsp 5917 2011-12-19 11:28:45Z nicklas $
2  ------------------------------------------------------------------
3  Copyright (C) 2006 Johan Enell, Jari Häkkinen, Nicklas Nordborg
4  Copyright (C) 2007 Nicklas Nordborg
5
6  This file is part of BASE - BioArray Software Environment.
7  Available at http://base.thep.lu.se/
8
9  BASE is free software; you can redistribute it and/or
10  modify it under the terms of the GNU General Public License
11  as published by the Free Software Foundation; either version 3
12  of the License, or (at your option) any later version.
13
14  BASE is distributed in the hope that it will be useful,
15  but WITHOUT ANY WARRANTY; without even the implied warranty of
16  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
17  GNU General Public License for more details.
18
19  You should have received a copy of the GNU General Public License
20  along with BASE. If not, see <http://www.gnu.org/licenses/>.
21  ------------------------------------------------------------------
22
23  @author Nicklas
24  @version 2.0
25--%>
26<%@ page pageEncoding="UTF-8" session="false"
27  import="net.sf.basedb.core.SessionControl"
28  import="net.sf.basedb.core.DbControl"
29  import="net.sf.basedb.core.SystemItems"
30  import="net.sf.basedb.core.Item"
31  import="net.sf.basedb.core.ItemContext"
32  import="net.sf.basedb.core.Permission"
33  import="net.sf.basedb.core.ExtendedProperties"
34  import="net.sf.basedb.core.ExtendedProperty"
35  import="net.sf.basedb.core.ArrayDesign"
36  import="net.sf.basedb.core.ArrayDesignBlock"
37  import="net.sf.basedb.core.Feature"
38  import="net.sf.basedb.core.ReporterType"
39  import="net.sf.basedb.core.Reporter"
40  import="net.sf.basedb.core.Plate"
41  import="net.sf.basedb.core.Well"
42  import="net.sf.basedb.core.PermissionDeniedException"
43  import="net.sf.basedb.core.PluginDefinition"
44  import="net.sf.basedb.core.data.FeatureData"
45  import="net.sf.basedb.core.data.ReporterData"
46  import="net.sf.basedb.core.plugin.GuiContext"
47  import="net.sf.basedb.core.plugin.Plugin"
48  import="net.sf.basedb.clients.web.Base"
49  import="net.sf.basedb.clients.web.util.HTML"
50  import="net.sf.basedb.util.Values"
51  import="net.sf.basedb.util.formatter.Formatter"
52  import="net.sf.basedb.util.formatter.WellCoordinateFormatter"
53  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
54  import="java.util.Date"
55  import="java.util.Map"
56  import="java.util.Set"
57  import="java.util.List"
58%>
59<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
60<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
61<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
62<%!
63  private static final Item itemType = Item.FEATURE;
64  private static final GuiContext guiContext = new GuiContext(itemType, GuiContext.Type.ITEM);
65%>
66<%
67final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
68final String ID = sc.getId();
69final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null);
70final int itemId = cc.getId();
71final int arrayDesignId = Values.getInt(request.getParameter("arraydesign_id"));
72final float scale = Base.getScale(sc);
73final DbControl dc = sc.newDbControl();
74try
75{
76  Formatter<Date> dateTimeFormatter = FormatterFactory.getDateTimeFormatter(sc);
77  Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
78  WellCoordinateFormatter rowFormatter = new WellCoordinateFormatter(true);
79  WellCoordinateFormatter columnFormatter = new WellCoordinateFormatter(false);
80  Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
81
82  final ArrayDesign design = ArrayDesign.getById(dc, arrayDesignId);
83  FeatureData feature = design.getFeatureById(itemId, true);
84  ReporterData reporter = feature.getReporter();
85
86  ArrayDesignBlock block = Feature.getArrayDesignBlock(dc, feature);
87 
88  Well well = null;
89  boolean readWell = true;
90  try
91  {
92    well = Feature.getWell(dc, feature);
93  }
94  catch (PermissionDeniedException ex)
95  {
96    readWell = false;
97  }
98
99 
100 
101  String title = "Feature of "+HTML.encodeTags(design.getName()) + " at position " + feature.getPosition();
102  %>
103
104  <base:page title="<%=title%>" type="popup">
105  <base:head scripts="tabcontrol.js" styles="tabcontrol.css">
106    <script language="JavaScript">
107    function runPlugin(cmd)
108    {
109      Main.openPopup('index.jsp?ID=<%=ID%>&cmd='+cmd+'&item_id=<%=itemId%>', 'RunPlugin'+cmd, 540, 460);
110    }
111    </script>
112  </base:head>
113  <base:body>
114    <h1><%=title%> <base:help helpid="feature.view.properties" /></h1>
115
116    <t:tabcontrol id="feature" 
117      subclass="content dialogtabcontrol"
118      position="bottom">
119    <t:tab id="feat" title="Feature">
120   
121      <table class="fullform outlined">
122      <tbody class="section">
123        <tr>
124          <th colspan="6">Array design</th>
125        </tr>
126      </tbody>
127      <tbody>
128      <tr>
129        <th>Name</th>
130        <td colspan="5"><%=HTML.encodeTags(design.getName())%></td>
131      </tr>
132      <tr>
133        <th>Platform / Variant</th>
134        <td colspan="5"><base:propertyvalue item="<%=design%>" property="platform" /> / <base:propertyvalue item="<%=design%>" property="variant" /></td>
135      </tr>
136      <tr>
137        <th>Feature identification method</th>
138        <td colspan="5"><%=design.getFeatureIdentificationMethod()%></td>
139      </tr>
140      </tbody>
141     
142      <tbody class="section">
143        <tr>
144          <th colspan="6">Feature / block</th>
145        </tr>
146      </tbody>
147     
148      <tbody>
149      <tr>
150        <th>Feature ID</td>
151        <td><%=HTML.encodeTags(feature.getExternalId())%></td>
152        <th class="leftborder">Reporter</th>
153        <td><%=reporter == null ? "<i>- none -</i>" : HTML.encodeTags(reporter.getName())%></td>
154        <th class="leftborder">Diameter</th>
155        <td><%=block.getFeatureDiameter()%></td>
156      </tr>
157      <tr>
158        <th>Position</th>
159        <td><%=feature.getPosition()%></td>
160        <th class="leftborder">Meta grid X</th>
161        <td><%=block.getMetaGridX()%></td>
162        <th class="leftborder">Meta grid Y</th>
163        <td><%=block.getMetaGridY()%></td>
164      </tr>
165      <tr>
166        <th>Block number</th>
167        <td><%=block.getBlockNumber()%></td>
168        <th class="leftborder">Block size X</th>
169        <td><%=block.getBlockSizeX()%></td>
170        <th class="leftborder">Block size Y</th>
171        <td><%=block.getBlockSizeY()%></td>
172      </tr>
173      <tr>
174        <th>Row</th>
175        <td><%=feature.getRow()%></td>
176        <th class="leftborder">Origin X</th>
177        <td><%=block.getOriginX()%></td>
178        <th class="leftborder">Origin Y</th>
179        <td><%=block.getOriginY()%></td>
180      </tr>
181      <tr>
182        <th>Column</th>
183        <td><%=feature.getColumn()%></td>
184        <th class="leftborder">Spacing X</th>
185        <td><%=block.getSpacingX()%></td>
186        <th class="leftborder">Spacing Y</th>
187        <td><%=block.getSpacingY()%></td>
188      </tr>
189      </tbody>
190     
191      <tbody class="section">
192        <tr>
193          <th colspan="6">Plage / well</th>
194        </tr>
195      </tbody>
196     
197      <tbody>
198        <%
199        if (!readWell)
200        {
201          %>
202          <tr>
203            <th>Plate</th>
204            <td colspan="5"><i>- denied -</i></td>
205          </tr>
206          <%
207        }
208        else if (well == null)
209        {
210          %>
211          <tr>
212            <th>Plate</th>
213            <td colspan="5"><i>- none -</i></td>
214          </tr>
215          <%
216        }
217        else
218        {
219          Plate plate = well.getPlate();
220          %>
221          <tr>
222            <th>Plate</th>
223            <td colspan="5"><%=HTML.encodeTags(plate.getName())%></td>
224          </tr>
225          <tr>
226            <th>Well</th>
227            <td colspan="5"><%=rowFormatter.format(well.getRow())%><%=columnFormatter.format(well.getColumn())%></td>
228          </tr>
229          <%
230        }
231        %>
232        <tr class="dynamic">
233          <th></th>
234          <td colspan="5"></td>
235        </tr>
236      </tbody>
237      </table>
238     
239    </t:tab>
240   
241    <%
242    if (reporter != null)
243    {
244      boolean readCurrentReporterType = true;
245      ReporterType currentReporterType = null;
246      try
247      {
248        currentReporterType = Reporter.getReporterType(dc, reporter);
249      }
250      catch (PermissionDeniedException ex)
251      {
252        readCurrentReporterType = false;
253      }
254      %>
255      <t:tab id="reporter" title="Reporter" >
256        <table class="fullform outlined">
257        <tbody class="section">
258          <tr>
259            <th colspan="4">Common reporter properties</th>
260          </tr>
261        </tbody>
262        <tbody>
263       
264        <tr>
265          <th>Name</th>
266          <td><%=HTML.encodeTags(reporter.getName())%></td>
267          <th class="leftborder">External ID</th>
268          <td><%=HTML.encodeTags(reporter.getExternalId())%></td>
269        </tr>
270        <tr>
271          <th>Gene symbol</td>
272          <td><%=HTML.encodeTags(reporter.getSymbol())%></td>
273          <th class="leftborder">Type</th>
274          <td><%=Base.getEncodedName(currentReporterType, !readCurrentReporterType)%></td>
275        </tr>
276        <tr>
277          <th>Last update</th>
278          <td><%=dateFormatter.format(reporter.getLastUpdate())%></td>
279          <th class="leftborder">from/by</th>
280          <td><%=reporter.getLastSource() %></td>
281        </tr>
282        <tr>
283          <th>Description</th>
284          <td colspan="3"><%=HTML.niceFormat(reporter.getDescription())%></td>
285        </tr>
286        </tbody>
287       
288        <tbody class="section">
289          <tr>
290            <th colspan="4">Extended reporter properties</th>
291          </tr>
292        </tbody>
293        <tbody>
294          <%
295            List<ExtendedProperty> reporterProperties = ExtendedProperties.getProperties("ReporterData");
296            if (reporterProperties != null)
297            {
298              boolean needsTr = true;
299              for (ExtendedProperty ep : reporterProperties)
300              {
301                String name = ep.getName();
302                Formatter f = FormatterFactory.getExtendedPropertyFormatter(sc, ep);
303                String value = f.format(reporter.getExtended(name));
304                %>
305                  <%=needsTr ? "<tr><th>" : "<th class=\"leftborder\">" %>
306                  <%=HTML.encodeTags(ep.getTitle())%></td>
307                  <td><%=value%></td>
308                  <%=needsTr ? "" : "</tr>"%>
309                <%
310                needsTr = !needsTr;
311              }
312              %>
313              <%=needsTr ? "" : "<th class=\"leftborder\"></th><td></td></tr>"%>
314              <%
315            }
316            %>
317          <tr class="dynamic">
318            <th></th>
319            <td></td>
320            <th class="leftborder"></th>
321            <td></td>
322          </tr>
323        </tbody>
324        </table>
325      </t:tab>
326      <%
327    }
328    %>
329    </t:tabcontrol>
330
331    <base:buttongroup subclass="dialogbuttons">
332      <base:button onclick="window.close()" title="Close" />
333    </base:buttongroup>
334   
335  </base:body>
336  </base:page>
337  <%
338}
339finally
340{
341  if (dc != null) dc.close();
342}
343
344%>
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