|
1
|
<%@ page language="java"%>
|
|
2
|
<%@page import="java.util.List"%>
|
|
3
|
<%@page import="org.ecoinformatics.sms.SMS"%>
|
|
4
|
<%@page import="org.ecoinformatics.sms.ontology.OntologyClass"%>
|
|
5
|
<%
|
|
6
|
/**
|
|
7
|
*
|
|
8
|
* '$RCSfile$'
|
|
9
|
* Copyright: 2008 Regents of the University of California and the
|
|
10
|
* National Center for Ecological Analysis and Synthesis
|
|
11
|
* '$Author: leinfelder $'
|
|
12
|
* '$Date: 2010-10-07 13:33:15 -0700 (Thu, 07 Oct 2010) $'
|
|
13
|
* '$Revision: 5604 $'
|
|
14
|
*
|
|
15
|
* This program is free software; you can redistribute it and/or modify
|
|
16
|
* it under the terms of the GNU General Public License as published by
|
|
17
|
* the Free Software Foundation; either version 2 of the License, or
|
|
18
|
* (at your option) any later version.
|
|
19
|
*
|
|
20
|
* This program is distributed in the hope that it will be useful,
|
|
21
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
22
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
23
|
* GNU General Public License for more details.
|
|
24
|
|
|
25
|
* You should have received a copy of the GNU General Public License
|
|
26
|
* along with this program; if not, write to the Free Software
|
|
27
|
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
|
28
|
*/
|
|
29
|
%>
|
|
30
|
<%
|
|
31
|
// construct the selection fields for existing annotations
|
|
32
|
// Entity
|
|
33
|
StringBuffer entityOptions = new StringBuffer();
|
|
34
|
List<OntologyClass> entities = SMS.getInstance().getAnnotationManager().getActiveEntities();
|
|
35
|
for (OntologyClass oc: entities) {
|
|
36
|
entityOptions.append("<option ");
|
|
37
|
entityOptions.append("title='");
|
|
38
|
entityOptions.append(oc.getURI());
|
|
39
|
entityOptions.append("' ");
|
|
40
|
entityOptions.append("value='");
|
|
41
|
entityOptions.append(oc.getURI());
|
|
42
|
entityOptions.append("'");
|
|
43
|
entityOptions.append(">");
|
|
44
|
entityOptions.append(oc.getName());
|
|
45
|
entityOptions.append("</option>");
|
|
46
|
}
|
|
47
|
// Characteristic
|
|
48
|
StringBuffer characteristicOptions = new StringBuffer();
|
|
49
|
List<OntologyClass> characteristics = SMS.getInstance().getAnnotationManager().getActiveCharacteristics();
|
|
50
|
for (OntologyClass oc: characteristics) {
|
|
51
|
characteristicOptions.append("<option ");
|
|
52
|
characteristicOptions.append("title='");
|
|
53
|
characteristicOptions.append(oc.getURI());
|
|
54
|
characteristicOptions.append("' ");
|
|
55
|
characteristicOptions.append("value='");
|
|
56
|
characteristicOptions.append(oc.getURI());
|
|
57
|
characteristicOptions.append("'");
|
|
58
|
characteristicOptions.append(">");
|
|
59
|
characteristicOptions.append(oc.getName());
|
|
60
|
characteristicOptions.append("</option>");
|
|
61
|
}
|
|
62
|
// Standard
|
|
63
|
StringBuffer standardOptions = new StringBuffer();
|
|
64
|
List<OntologyClass> standards = SMS.getInstance().getAnnotationManager().getActiveStandards();
|
|
65
|
for (OntologyClass oc: standards) {
|
|
66
|
standardOptions.append("<option ");
|
|
67
|
standardOptions.append("title='");
|
|
68
|
standardOptions.append(oc.getURI());
|
|
69
|
standardOptions.append("' ");
|
|
70
|
standardOptions.append("value='");
|
|
71
|
standardOptions.append(oc.getURI());
|
|
72
|
standardOptions.append("'");
|
|
73
|
standardOptions.append(">");
|
|
74
|
standardOptions.append(oc.getName());
|
|
75
|
standardOptions.append("</option>");
|
|
76
|
}
|
|
77
|
// Protocol
|
|
78
|
StringBuffer protocolOptions = new StringBuffer();
|
|
79
|
List<OntologyClass> protocols = SMS.getInstance().getAnnotationManager().getActiveProtocols();
|
|
80
|
for (OntologyClass oc: protocols) {
|
|
81
|
protocolOptions.append("<option ");
|
|
82
|
protocolOptions.append("title='");
|
|
83
|
protocolOptions.append(oc.getURI());
|
|
84
|
protocolOptions.append("' ");
|
|
85
|
protocolOptions.append("value='");
|
|
86
|
protocolOptions.append(oc.getURI());
|
|
87
|
protocolOptions.append("'");
|
|
88
|
protocolOptions.append(">");
|
|
89
|
protocolOptions.append(oc.getName());
|
|
90
|
protocolOptions.append("</option>");
|
|
91
|
}
|
|
92
|
// Measurement
|
|
93
|
StringBuffer measurementOptions = new StringBuffer();
|
|
94
|
List<OntologyClass> measurements = SMS.getInstance().getAnnotationManager().getActiveMeasurements();
|
|
95
|
for (OntologyClass oc: measurements) {
|
|
96
|
measurementOptions.append("<option ");
|
|
97
|
measurementOptions.append("title='");
|
|
98
|
measurementOptions.append(oc.getURI());
|
|
99
|
measurementOptions.append("' ");
|
|
100
|
measurementOptions.append("value='");
|
|
101
|
measurementOptions.append(oc.getURI());
|
|
102
|
measurementOptions.append("'");
|
|
103
|
measurementOptions.append(">");
|
|
104
|
measurementOptions.append(oc.getName());
|
|
105
|
measurementOptions.append("</option>");
|
|
106
|
}
|
|
107
|
%>
|
|
108
|
|
|
109
|
<%@ include file="../../common/common-settings.jsp"%>
|
|
110
|
<%@ include file="../../common/configure-check.jsp"%>
|
|
111
|
|
|
112
|
<html>
|
|
113
|
<head>
|
|
114
|
<title>Semantic search</title>
|
|
115
|
<link rel="stylesheet" type="text/css" href="<%=STYLE_SKINS_URL%>/semtools/semtools.css">
|
|
116
|
<script type="text/javascript"
|
|
117
|
src="<%=STYLE_SKINS_URL%>/semtools/search.js"></script>
|
|
118
|
|
|
119
|
<script type="text/javascript">
|
|
120
|
// Set defaults for this installation
|
|
121
|
//var BP_SEARCH_SERVER = "http://oor-01.cim3.net";
|
|
122
|
//var BP_SITE = "Sandbox";
|
|
123
|
//var BP_ORG = "OOR";
|
|
124
|
</script>
|
|
125
|
<script language="Javascript" type="text/JavaScript"
|
|
126
|
src="<%=STYLE_SKINS_URL%>/semtools/bioportal/form_complete.js">
|
|
127
|
</script>
|
|
128
|
|
|
129
|
<script language="javascript" type="text/javascript" src="<%=STYLE_SKINS_URL%>/semtools/semtools.js"></script>
|
|
130
|
<script language="javascript" type="text/javascript" src="<%=STYLE_COMMON_URL%>/branding.js"></script>
|
|
131
|
|
|
132
|
</head>
|
|
133
|
<body>
|
|
134
|
<script language="javascript">
|
|
135
|
insertTemplateOpening("<%=CONTEXT_URL%>");
|
|
136
|
</script>
|
|
137
|
|
|
138
|
<div id="content_wrapper">
|
|
139
|
|
|
140
|
<h2>Annotation-based search</h2>
|
|
141
|
|
|
142
|
<form method="POST" action="<%=SERVLET_URL%>" target="_top" id="searchForm" name="searchForm" onSubmit="return checkSearch(this)">
|
|
143
|
<input name="query" type="hidden" />
|
|
144
|
<input name="qformat" value="semtools" type="hidden" />
|
|
145
|
<input name="action" value="semquery" type="hidden" />
|
|
146
|
|
|
147
|
<table class="group group_border">
|
|
148
|
<tr>
|
|
149
|
<th colspan="5">
|
|
150
|
<p>
|
|
151
|
Locate <b>data packages</b> that have been semantically annotated within the observation model by
|
|
152
|
selecting concepts from
|
|
153
|
<br/>
|
|
154
|
(a) existing semantic annotations
|
|
155
|
<br/>
|
|
156
|
(b) registered OBOE extension ontologies
|
|
157
|
</p>
|
|
158
|
</th>
|
|
159
|
</tr>
|
|
160
|
<tr>
|
|
161
|
<td>
|
|
162
|
<table class="subGroup subGroup_border">
|
|
163
|
<tr>
|
|
164
|
<th colspan="1">
|
|
165
|
Entity
|
|
166
|
</th>
|
|
167
|
</tr>
|
|
168
|
<tr>
|
|
169
|
<td>Find observations of</td>
|
|
170
|
</tr>
|
|
171
|
<tr>
|
|
172
|
<td>
|
|
173
|
(a)
|
|
174
|
<select name="dynamicValue" id="dynamicValue" multiple="multiple" size="5" style="width: 216px">
|
|
175
|
<%=entityOptions %>
|
|
176
|
</select>
|
|
177
|
<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Entity"/>
|
|
178
|
</td>
|
|
179
|
</tr>
|
|
180
|
<tr>
|
|
181
|
<td colspan="1">
|
|
182
|
(b)
|
|
183
|
<input type="text" name="dynamicValue" id="dynamicValue" class="bp_form_complete-all-uri" size="30" />
|
|
184
|
<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Entity"/>
|
|
185
|
</td>
|
|
186
|
</tr>
|
|
187
|
</table>
|
|
188
|
</td>
|
|
189
|
<td>
|
|
190
|
<table class="subGroup subGroup_border">
|
|
191
|
<tr>
|
|
192
|
<th colspan="1">
|
|
193
|
Characteristic
|
|
194
|
</th>
|
|
195
|
</tr>
|
|
196
|
<tr>
|
|
197
|
<td>where measurements of</td>
|
|
198
|
</tr>
|
|
199
|
<tr>
|
|
200
|
<td>
|
|
201
|
<select name="dynamicValue" id="dynamicValue" multiple="multiple" size="5" style="width: 216px">
|
|
202
|
<%=characteristicOptions %>
|
|
203
|
</select>
|
|
204
|
<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Characteristic"/>
|
|
205
|
</td>
|
|
206
|
</tr>
|
|
207
|
<tr>
|
|
208
|
<td colspan="1">
|
|
209
|
<input type="text" name="dynamicValue" id="dynamicValue" class="bp_form_complete-all-uri" size="30" />
|
|
210
|
<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Characteristic"/>
|
|
211
|
</td>
|
|
212
|
</tr>
|
|
213
|
</table>
|
|
214
|
</td>
|
|
215
|
<td>
|
|
216
|
<table class="subGroup subGroup_border">
|
|
217
|
<tr>
|
|
218
|
<th colspan="1">
|
|
219
|
Standard
|
|
220
|
</th>
|
|
221
|
</tr>
|
|
222
|
<tr>
|
|
223
|
<td>were recorded in units of</td>
|
|
224
|
</tr>
|
|
225
|
<tr>
|
|
226
|
<td>
|
|
227
|
<select name="dynamicValue" id="dynamicValue" multiple="multiple" size="5" style="width: 216px">
|
|
228
|
<%=standardOptions %>
|
|
229
|
</select>
|
|
230
|
<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Standard"/>
|
|
231
|
</td>
|
|
232
|
</tr>
|
|
233
|
<tr>
|
|
234
|
<td colspan="1">
|
|
235
|
<input type="text" name="dynamicValue" id="dynamicValue" class="bp_form_complete-all-uri" size="30" />
|
|
236
|
<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Standard"/>
|
|
237
|
</td>
|
|
238
|
</tr>
|
|
239
|
</table>
|
|
240
|
</td>
|
|
241
|
<td>
|
|
242
|
<table class="subGroup subGroup_border">
|
|
243
|
<tr>
|
|
244
|
<th colspan="1">
|
|
245
|
Protocol
|
|
246
|
</th>
|
|
247
|
</tr>
|
|
248
|
<tr>
|
|
249
|
<td>following procedures outlined by</td>
|
|
250
|
</tr>
|
|
251
|
<tr>
|
|
252
|
<td>
|
|
253
|
<select name="dynamicValue" id="dynamicValue" multiple="multiple" size="5" style="width: 216px">
|
|
254
|
<%=protocolOptions %>
|
|
255
|
</select>
|
|
256
|
<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Protocol"/>
|
|
257
|
</td>
|
|
258
|
</tr>
|
|
259
|
<tr>
|
|
260
|
<td colspan="1">
|
|
261
|
<input type="text" name="dynamicValue" id="dynamicValue" class="bp_form_complete-all-uri" size="30" />
|
|
262
|
<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Protocol"/>
|
|
263
|
</td>
|
|
264
|
</tr>
|
|
265
|
</table>
|
|
266
|
</td>
|
|
267
|
<td>
|
|
268
|
<table class="subGroup subGroup_border">
|
|
269
|
<tr>
|
|
270
|
<th colspan="2">
|
|
271
|
Measurement
|
|
272
|
</th>
|
|
273
|
</tr>
|
|
274
|
<tr>
|
|
275
|
<td>typically defined as</td>
|
|
276
|
</tr>
|
|
277
|
<tr>
|
|
278
|
<td>
|
|
279
|
<select name="dynamicValue" id="dynamicValue" multiple="multiple" size="5" style="width: 216px">
|
|
280
|
<%=measurementOptions %>
|
|
281
|
</select>
|
|
282
|
<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Measurement"/>
|
|
283
|
</td>
|
|
284
|
</tr>
|
|
285
|
<tr>
|
|
286
|
<td colspan="1">
|
|
287
|
<input type="text" name="dynamicValue" id="dynamicValue" class="bp_form_complete-all-uri" size="30" />
|
|
288
|
<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Measurement"/>
|
|
289
|
</td>
|
|
290
|
</tr>
|
|
291
|
</table>
|
|
292
|
</td>
|
|
293
|
</tr>
|
|
294
|
<tr>
|
|
295
|
<td colspan="5">Match All? <input type="checkbox" name="matchAll" checked="checked"/></td>
|
|
296
|
</tr>
|
|
297
|
<tr>
|
|
298
|
<td colspan="5">From same Observation? <input type="checkbox" name="strict"/></td>
|
|
299
|
</tr>
|
|
300
|
<tr>
|
|
301
|
<td colspan="5"><input type="submit" value="Search"/></td>
|
|
302
|
</tr>
|
|
303
|
</table>
|
|
304
|
<!--
|
|
305
|
<tr>
|
|
306
|
<td>Entity: (SBC only)</td>
|
|
307
|
<td><input type="text" name="entity" class="bp_form_complete-1523-uri" size="100" /></td>
|
|
308
|
</tr>
|
|
309
|
-->
|
|
310
|
</form>
|
|
311
|
|
|
312
|
<!--
|
|
313
|
<h2>Ontology search</h2>
|
|
314
|
<div id="bp_quick_jump"></div>
|
|
315
|
<script type="text/javascript">
|
|
316
|
var BP_ontology_id = "all";
|
|
317
|
</script>
|
|
318
|
<script src="<%=STYLE_SKINS_URL%>/semtools/bioportal/quick_jump.js" type="text/javascript" charset="utf-8">
|
|
319
|
</script>
|
|
320
|
|
|
321
|
<h2>Tree browser</h2>
|
|
322
|
|
|
323
|
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"
|
|
324
|
id="OntologyTree" width="300" height="100%"
|
|
325
|
codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab">
|
|
326
|
<param name="movie" value="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" />
|
|
327
|
<param name="quality" value="high" />
|
|
328
|
<param name="bgcolor" value="#ffffff" />
|
|
329
|
<param name="allowScriptAccess" value="always" />
|
|
330
|
<param name="flashVars" value="ontology=1523&alerterrors=false&canchangeontology=false&virtual=true" />
|
|
331
|
<embed src="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" quality="high" bgcolor="#ffffff"
|
|
332
|
width="300" height="100%" name="OntologyTree" align="middle"
|
|
333
|
play="true"
|
|
334
|
loop="false"
|
|
335
|
allowScriptAccess="always"
|
|
336
|
type="application/x-shockwave-flash"
|
|
337
|
flashVars="ontology=1523&alerterrors=false&canchangeontology=false&virtual=true"
|
|
338
|
pluginspage="http://www.adobe.com/go/getflashplayer">
|
|
339
|
</embed>
|
|
340
|
</object>
|
|
341
|
-->
|
|
342
|
|
|
343
|
<!-- Included default search/login -->
|
|
344
|
<% if ( PropertyService.getProperty("spatial.runSpatialOption").equals("true") ) { %>
|
|
345
|
<script language="javascript">
|
|
346
|
insertMap("<%=CONTEXT_URL%>");
|
|
347
|
</script>
|
|
348
|
<br/>
|
|
349
|
<% } %>
|
|
350
|
|
|
351
|
<script language="javascript">
|
|
352
|
insertSearchBox("<%=CONTEXT_URL%>");
|
|
353
|
insertLoginBox("<%=CONTEXT_URL%>");
|
|
354
|
</script>
|
|
355
|
|
|
356
|
</div>
|
|
357
|
|
|
358
|
<script language="javascript">
|
|
359
|
insertTemplateClosing("<%=CONTEXT_URL%>");
|
|
360
|
</script>
|
|
361
|
|
|
362
|
</body>
|
|
363
|
</html>
|