Revision 5632
Added by ben leinfelder over 13 years ago
| lib/style/skins/semtools/index.jsp | ||
|---|---|---|
| 1 | 1 |
<%@ page language="java"%> |
| 2 | 2 |
<%@page import="java.util.List"%> |
| 3 |
<%@page import="java.util.ArrayList"%> |
|
| 3 | 4 |
<%@page import="org.ecoinformatics.sms.SMS"%> |
| 4 | 5 |
<%@page import="org.ecoinformatics.sms.ontology.OntologyClass"%> |
| 6 |
|
|
| 5 | 7 |
<% |
| 6 | 8 |
/** |
| 7 | 9 |
* |
| ... | ... | |
| 28 | 30 |
*/ |
| 29 | 31 |
%> |
| 30 | 32 |
<% |
| 33 |
|
|
| 34 |
//harvest parameters |
|
| 35 |
String[] entityParam = request.getParameterValues("entity");
|
|
| 36 |
String[] characteristicParam = request.getParameterValues("characteristic");
|
|
| 37 |
String[] standardParam = request.getParameterValues("standard");
|
|
| 38 |
String[] protocolParam = request.getParameterValues("protocol");
|
|
| 39 |
String[] measurementParam = request.getParameterValues("measurement");
|
|
| 40 |
|
|
| 41 |
List<OntologyClass> activeEntities = new ArrayList<OntologyClass>(); |
|
| 42 |
List<OntologyClass> activeCharacteristics = new ArrayList<OntologyClass>(); |
|
| 43 |
List<OntologyClass> activeStandards = new ArrayList<OntologyClass>(); |
|
| 44 |
List<OntologyClass> activeProtocols = new ArrayList<OntologyClass>(); |
|
| 45 |
List<OntologyClass> activeMeasurements = new ArrayList<OntologyClass>(); |
|
| 46 |
|
|
| 47 |
// Entity |
|
| 48 |
if (entityParam != null) {
|
|
| 49 |
for (String entityString: entityParam) {
|
|
| 50 |
OntologyClass e = new OntologyClass(entityString); |
|
| 51 |
activeEntities.add(e); |
|
| 52 |
} |
|
| 53 |
} |
|
| 54 |
// Characteristic |
|
| 55 |
if (characteristicParam != null) {
|
|
| 56 |
for (String classString: characteristicParam) {
|
|
| 57 |
OntologyClass c = new OntologyClass(classString); |
|
| 58 |
activeCharacteristics.add(c); |
|
| 59 |
} |
|
| 60 |
} |
|
| 61 |
// Standard |
|
| 62 |
if (standardParam != null) {
|
|
| 63 |
for (String classString: standardParam) {
|
|
| 64 |
OntologyClass c = new OntologyClass(classString); |
|
| 65 |
activeStandards.add(c); |
|
| 66 |
} |
|
| 67 |
} |
|
| 68 |
// Protocol |
|
| 69 |
if (protocolParam != null) {
|
|
| 70 |
for (String classString: protocolParam) {
|
|
| 71 |
OntologyClass c = new OntologyClass(classString); |
|
| 72 |
activeProtocols.add(c); |
|
| 73 |
} |
|
| 74 |
} |
|
| 75 |
// Measurement |
|
| 76 |
// TODO: implement measurement expansion |
|
| 77 |
|
|
| 31 | 78 |
// construct the selection fields for existing annotations |
| 32 | 79 |
// Entity |
| 33 | 80 |
StringBuffer entityOptions = new StringBuffer(); |
| 34 |
List<OntologyClass> entities = SMS.getInstance().getAnnotationManager().getActiveEntities(); |
|
| 81 |
List<OntologyClass> entities = SMS.getInstance().getAnnotationManager().getActiveEntities(activeCharacteristics, activeStandards);
|
|
| 35 | 82 |
for (OntologyClass oc: entities) {
|
| 36 | 83 |
entityOptions.append("<option ");
|
| 37 | 84 |
entityOptions.append("title='");
|
| ... | ... | |
| 46 | 93 |
} |
| 47 | 94 |
// Characteristic |
| 48 | 95 |
StringBuffer characteristicOptions = new StringBuffer(); |
| 49 |
List<OntologyClass> characteristics = SMS.getInstance().getAnnotationManager().getActiveCharacteristics(); |
|
| 96 |
List<OntologyClass> characteristics = SMS.getInstance().getAnnotationManager().getActiveCharacteristics(activeEntities, activeStandards);
|
|
| 50 | 97 |
for (OntologyClass oc: characteristics) {
|
| 51 | 98 |
characteristicOptions.append("<option ");
|
| 52 | 99 |
characteristicOptions.append("title='");
|
| ... | ... | |
| 61 | 108 |
} |
| 62 | 109 |
// Standard |
| 63 | 110 |
StringBuffer standardOptions = new StringBuffer(); |
| 64 |
List<OntologyClass> standards = SMS.getInstance().getAnnotationManager().getActiveStandards(); |
|
| 111 |
List<OntologyClass> standards = SMS.getInstance().getAnnotationManager().getActiveStandards(activeEntities, activeCharacteristics);
|
|
| 65 | 112 |
for (OntologyClass oc: standards) {
|
| 66 | 113 |
standardOptions.append("<option ");
|
| 67 | 114 |
standardOptions.append("title='");
|
| ... | ... | |
| 74 | 121 |
standardOptions.append(oc.getName()); |
| 75 | 122 |
standardOptions.append("</option>");
|
| 76 | 123 |
} |
| 77 |
// Protocol |
|
| 124 |
// Protocol TODO: filtering
|
|
| 78 | 125 |
StringBuffer protocolOptions = new StringBuffer(); |
| 79 | 126 |
List<OntologyClass> protocols = SMS.getInstance().getAnnotationManager().getActiveProtocols(); |
| 80 | 127 |
for (OntologyClass oc: protocols) {
|
| ... | ... | |
| 89 | 136 |
protocolOptions.append(oc.getName()); |
| 90 | 137 |
protocolOptions.append("</option>");
|
| 91 | 138 |
} |
| 92 |
// Measurement |
|
| 139 |
// Measurement TODO: filtering
|
|
| 93 | 140 |
StringBuffer measurementOptions = new StringBuffer(); |
| 94 | 141 |
List<OntologyClass> measurements = SMS.getInstance().getAnnotationManager().getActiveMeasurements(); |
| 95 | 142 |
for (OntologyClass oc: measurements) {
|
| ... | ... | |
| 146 | 193 |
|
| 147 | 194 |
<table class="group group_border"> |
| 148 | 195 |
<tr> |
| 149 |
<th colspan="5">
|
|
| 196 |
<th colspan="3">
|
|
| 150 | 197 |
<p> |
| 151 | 198 |
Locate <b>data packages</b> that have been semantically annotated within the observation model by |
| 152 | 199 |
selecting concepts from |
| ... | ... | |
| 157 | 204 |
</p> |
| 158 | 205 |
</th> |
| 159 | 206 |
</tr> |
| 207 |
<!-- measurement --> |
|
| 160 | 208 |
<tr> |
| 209 |
<td colspan="3"> |
|
| 210 |
<table class="subGroup subGroup_border onehundred_percent"> |
|
| 211 |
<tr> |
|
| 212 |
<th colspan="2"> |
|
| 213 |
Measurement |
|
| 214 |
</th> |
|
| 215 |
</tr> |
|
| 216 |
<tr> |
|
| 217 |
<td>a template that defines Entity, Characteristic, Standard, and/or Protocol</td> |
|
| 218 |
</tr> |
|
| 219 |
<tr> |
|
| 220 |
<td> |
|
| 221 |
<select name="dynamicValue" id="dynamicValue" multiple="multiple" size="5" style="width: 100%"> |
|
| 222 |
<%=measurementOptions %> |
|
| 223 |
</select> |
|
| 224 |
<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Measurement"/> |
|
| 225 |
</td> |
|
| 226 |
</tr> |
|
| 227 |
<tr> |
|
| 228 |
<td colspan="1"> |
|
| 229 |
<input type="text" name="dynamicValue" id="dynamicValue" class="bp_form_complete-all-uri" size="60" /> |
|
| 230 |
<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Measurement"/> |
|
| 231 |
</td> |
|
| 232 |
</tr> |
|
| 233 |
</table> |
|
| 234 |
</td> |
|
| 235 |
</tr> |
|
| 236 |
<tr> |
|
| 161 | 237 |
<td> |
| 162 | 238 |
<table class="subGroup subGroup_border"> |
| 163 | 239 |
<tr> |
| ... | ... | |
| 194 | 270 |
</th> |
| 195 | 271 |
</tr> |
| 196 | 272 |
<tr> |
| 197 |
<td>where measurements of</td>
|
|
| 273 |
<td>with measurements of</td>
|
|
| 198 | 274 |
</tr> |
| 199 | 275 |
<tr> |
| 200 | 276 |
<td> |
| ... | ... | |
| 212 | 288 |
</tr> |
| 213 | 289 |
</table> |
| 214 | 290 |
</td> |
| 291 |
<!-- removing Standard |
|
| 215 | 292 |
<td> |
| 216 | 293 |
<table class="subGroup subGroup_border"> |
| 217 | 294 |
<tr> |
| ... | ... | |
| 238 | 315 |
</tr> |
| 239 | 316 |
</table> |
| 240 | 317 |
</td> |
| 318 |
--> |
|
| 241 | 319 |
<td> |
| 242 | 320 |
<table class="subGroup subGroup_border"> |
| 243 | 321 |
<tr> |
| ... | ... | |
| 246 | 324 |
</th> |
| 247 | 325 |
</tr> |
| 248 | 326 |
<tr> |
| 249 |
<td>following procedures outlined by</td>
|
|
| 327 |
<td>using procedures outlined by</td>
|
|
| 250 | 328 |
</tr> |
| 251 | 329 |
<tr> |
| 252 | 330 |
<td> |
| ... | ... | |
| 264 | 342 |
</tr> |
| 265 | 343 |
</table> |
| 266 | 344 |
</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 | 345 |
</tr> |
| 294 | 346 |
<tr> |
| 295 |
<td colspan="5">Match All? <input type="checkbox" name="matchAll" checked="checked"/></td>
|
|
| 347 |
<td colspan="3">Match All? <input type="checkbox" name="matchAll" checked="checked"/></td>
|
|
| 296 | 348 |
</tr> |
| 297 | 349 |
<tr> |
| 298 |
<td colspan="5">From same Observation? <input type="checkbox" name="strict"/></td>
|
|
| 350 |
<td colspan="3">From same Observation? <input type="checkbox" name="strict"/></td>
|
|
| 299 | 351 |
</tr> |
| 300 | 352 |
<tr> |
| 301 |
<td colspan="5"><input type="submit" value="Search"/></td>
|
|
| 353 |
<td colspan="3"><input type="submit" value="Search"/></td>
|
|
| 302 | 354 |
</tr> |
| 303 | 355 |
</table> |
| 304 | 356 |
<!-- |
| ... | ... | |
| 309 | 361 |
--> |
| 310 | 362 |
</form> |
| 311 | 363 |
|
| 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 | 364 |
<!-- Included default search/login --> |
| 344 | 365 |
<% if ( PropertyService.getProperty("spatial.runSpatialOption").equals("true") ) { %>
|
| 345 | 366 |
<script language="javascript"> |
Also available in: Unified diff
starting to filter by active domains. still request-based, but would like to make asynchronous calls when populating the fields.