| 1 |
5509
|
leinfelder
|
<%@ page language="java"%>
|
| 2 |
|
|
<%
|
| 3 |
|
|
/**
|
| 4 |
|
|
*
|
| 5 |
|
|
* '$RCSfile$'
|
| 6 |
|
|
* Copyright: 2008 Regents of the University of California and the
|
| 7 |
|
|
* National Center for Ecological Analysis and Synthesis
|
| 8 |
|
|
* '$Author$'
|
| 9 |
|
|
* '$Date$'
|
| 10 |
|
|
* '$Revision$'
|
| 11 |
|
|
*
|
| 12 |
|
|
* This program is free software; you can redistribute it and/or modify
|
| 13 |
|
|
* it under the terms of the GNU General Public License as published by
|
| 14 |
|
|
* the Free Software Foundation; either version 2 of the License, or
|
| 15 |
|
|
* (at your option) any later version.
|
| 16 |
|
|
*
|
| 17 |
|
|
* This program is distributed in the hope that it will be useful,
|
| 18 |
|
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
| 19 |
|
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
| 20 |
|
|
* GNU General Public License for more details.
|
| 21 |
|
|
|
| 22 |
|
|
* You should have received a copy of the GNU General Public License
|
| 23 |
|
|
* along with this program; if not, write to the Free Software
|
| 24 |
|
|
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
| 25 |
|
|
*/
|
| 26 |
5385
|
leinfelder
|
%>
|
| 27 |
5632
|
leinfelder
|
|
| 28 |
5509
|
leinfelder
|
<%@ include file="../../common/common-settings.jsp"%>
|
| 29 |
|
|
<%@ include file="../../common/configure-check.jsp"%>
|
| 30 |
5604
|
leinfelder
|
|
| 31 |
5385
|
leinfelder
|
<html>
|
| 32 |
|
|
<head>
|
| 33 |
5509
|
leinfelder
|
<title>Semantic search</title>
|
| 34 |
|
|
<link rel="stylesheet" type="text/css" href="<%=STYLE_SKINS_URL%>/semtools/semtools.css">
|
| 35 |
|
|
<script type="text/javascript"
|
| 36 |
|
|
src="<%=STYLE_SKINS_URL%>/semtools/search.js"></script>
|
| 37 |
|
|
|
| 38 |
|
|
<script type="text/javascript">
|
| 39 |
|
|
// Set defaults for this installation
|
| 40 |
|
|
//var BP_SEARCH_SERVER = "http://oor-01.cim3.net";
|
| 41 |
|
|
//var BP_SITE = "Sandbox";
|
| 42 |
|
|
//var BP_ORG = "OOR";
|
| 43 |
|
|
</script>
|
| 44 |
5656
|
leinfelder
|
<!--
|
| 45 |
|
|
<script language="Javascript" type="text/JavaScript" src="<%=STYLE_SKINS_URL%>/semtools/bioportal/form_complete.js"></script>
|
| 46 |
|
|
-->
|
| 47 |
|
|
<script language="javascript" type="text/javascript" src="<%=STYLE_SKINS_URL%>/semtools/jsTree/_lib/jquery.js"></script>
|
| 48 |
|
|
<script language="javascript" type="text/javascript" src="<%=STYLE_SKINS_URL%>/semtools/jsTree/_lib/jquery.cookie.js"></script>
|
| 49 |
|
|
<script language="javascript" type="text/javascript" src="<%=STYLE_SKINS_URL%>/semtools/jsTree/jquery.jstree.js"></script>
|
| 50 |
5509
|
leinfelder
|
<script language="javascript" type="text/javascript" src="<%=STYLE_SKINS_URL%>/semtools/semtools.js"></script>
|
| 51 |
|
|
<script language="javascript" type="text/javascript" src="<%=STYLE_COMMON_URL%>/branding.js"></script>
|
| 52 |
|
|
|
| 53 |
5656
|
leinfelder
|
<script language="Javascript" type="text/JavaScript"><!--
|
| 54 |
5633
|
leinfelder
|
function populateActiveDomain(divId, class) {
|
| 55 |
5656
|
leinfelder
|
// collect the filtering values we have so far
|
| 56 |
|
|
// these are hidden input fields in the form for holding the selected values
|
| 57 |
|
|
var entity = $("#activeEntitiesValue").val() ? $("#activeEntitiesValue").val() : "";
|
| 58 |
|
|
var characteristic = $("#activeCharacteristicsValue").val() ? $("#activeCharacteristicsValue").val() : "";
|
| 59 |
|
|
var protocol = $("#activeProtocolsValue").val() ? $("#activeProtocolsValue").val() : "";
|
| 60 |
|
|
var measurement = $("#activeMeasurementsValue").val() ? $("#activeMeasurementsValue").val() : "";
|
| 61 |
5633
|
leinfelder
|
|
| 62 |
5656
|
leinfelder
|
// TODO: remember the selected value for this when filtering by active domain
|
| 63 |
|
|
var selectedNode = $("#" + divId).jstree("get_selected", $("#" + divId));
|
| 64 |
|
|
var selectedNodeId = $(selectedNode).attr("id");
|
| 65 |
|
|
//alert(divId + " selected node: " + selectedNodeId);
|
| 66 |
|
|
|
| 67 |
|
|
// load the tree for the given div, passing in the other filtered values
|
| 68 |
5633
|
leinfelder
|
$("#" + divId).load(
|
| 69 |
5656
|
leinfelder
|
"<%=SERVLET_URL%>",
|
| 70 |
|
|
{
|
| 71 |
|
|
'action': "getactivedomain",
|
| 72 |
|
|
'class': class,
|
| 73 |
|
|
'entity': entity,
|
| 74 |
|
|
'characteristic': characteristic,
|
| 75 |
|
|
'protocol': protocol,
|
| 76 |
|
|
'measurement': measurement
|
| 77 |
|
|
},
|
| 78 |
|
|
// call back function when loading finishes
|
| 79 |
|
|
function(response, status, xhr) {
|
| 80 |
|
|
//alert("callback for: " + divId + " selected node: " + selectedNodeId);
|
| 81 |
|
|
// error
|
| 82 |
|
|
if (status == "error") {
|
| 83 |
|
|
var msg = "Sorry but there was an error: ";
|
| 84 |
|
|
$("#error").html(msg + xhr.status + " " + xhr.statusText);
|
| 85 |
|
|
}
|
| 86 |
|
|
|
| 87 |
|
|
// make it a js tree
|
| 88 |
|
|
$(function () {
|
| 89 |
|
|
$("#" + divId)
|
| 90 |
5660
|
leinfelder
|
//bind calls here
|
| 91 |
5656
|
leinfelder
|
.jstree({
|
| 92 |
|
|
"ui" : {
|
| 93 |
|
|
"select_limit" : 1,
|
| 94 |
|
|
"select_multiple_modifier" : "alt",
|
| 95 |
|
|
"selected_parent_close" : "select_parent"//,
|
| 96 |
|
|
//"initially_select" : [ selectedNodeId ]
|
| 97 |
5659
|
leinfelder
|
},
|
| 98 |
|
|
"themes" : {
|
| 99 |
|
|
"theme" : "default",
|
| 100 |
|
|
"dots" : true,
|
| 101 |
|
|
"icons" : false
|
| 102 |
|
|
},
|
| 103 |
5656
|
leinfelder
|
//"core" : { "initially_open" : [ selectedNodeId ] },
|
| 104 |
5658
|
leinfelder
|
"search" : { "case_insensitive" : true },
|
| 105 |
|
|
"plugins" : [ "themes", "html_data", "ui", "cookies", "search" ]
|
| 106 |
5656
|
leinfelder
|
});
|
| 107 |
|
|
});
|
| 108 |
|
|
|
| 109 |
5658
|
leinfelder
|
// enable searching on it
|
| 110 |
|
|
$("#" + divId + "Search").keyup(
|
| 111 |
|
|
function () {
|
| 112 |
|
|
if ($("#" + divId + "Search").val().length >= 3) {
|
| 113 |
|
|
$("#" + divId).jstree("search", $("#" + divId + "Search").val());
|
| 114 |
|
|
}
|
| 115 |
|
|
});
|
| 116 |
|
|
|
| 117 |
5656
|
leinfelder
|
// TODO: try to select the original node after refresh with active domain
|
| 118 |
|
|
//$("#" + divId).jstree("open_node", $(selectedNode));
|
| 119 |
|
|
//$("#" + divId).jstree("select_node", $(selectedNode));
|
| 120 |
|
|
});
|
| 121 |
5633
|
leinfelder
|
}
|
| 122 |
|
|
function initialize(source) {
|
| 123 |
5656
|
leinfelder
|
// we don't want to reload the source of the filtering request
|
| 124 |
|
|
// but we do want to reload the other trees for active domains
|
| 125 |
|
|
// we reload all of them if no source is given - first time the page loads
|
| 126 |
5633
|
leinfelder
|
if (source) {
|
| 127 |
5656
|
leinfelder
|
source = $(source).attr("id");
|
| 128 |
5633
|
leinfelder
|
}
|
| 129 |
|
|
if (!source) {
|
| 130 |
|
|
source = "";
|
| 131 |
|
|
}
|
| 132 |
|
|
if (source != 'activeEntities') {
|
| 133 |
|
|
populateActiveDomain('activeEntities', 'org.ecoinformatics.sms.annotation.Entity');
|
| 134 |
|
|
}
|
| 135 |
|
|
if (source != 'activeCharacteristics') {
|
| 136 |
|
|
populateActiveDomain('activeCharacteristics', 'org.ecoinformatics.sms.annotation.Characteristic');
|
| 137 |
|
|
}
|
| 138 |
|
|
if (source != 'activeProtocols') {
|
| 139 |
|
|
populateActiveDomain('activeProtocols', 'org.ecoinformatics.sms.annotation.Protocol');
|
| 140 |
|
|
}
|
| 141 |
|
|
if (source != 'activeMeasurements') {
|
| 142 |
|
|
populateActiveDomain('activeMeasurements', 'org.ecoinformatics.sms.annotation.Measurement');
|
| 143 |
|
|
}
|
| 144 |
|
|
}
|
| 145 |
5656
|
leinfelder
|
function select(item) {
|
| 146 |
5633
|
leinfelder
|
|
| 147 |
5656
|
leinfelder
|
// get the selected value, stored in the title attribute of the item <a> tag
|
| 148 |
|
|
var value = $(item).attr("title");
|
| 149 |
|
|
//alert("value: " + value);
|
| 150 |
|
|
|
| 151 |
|
|
// get the parent div so we know what kind of class it is meant to filter
|
| 152 |
|
|
// this is "the first parent of the class 'select'"
|
| 153 |
|
|
var parent = $(item).parents("div.select:first");
|
| 154 |
|
|
//alert("parent: " + parent);
|
| 155 |
|
|
|
| 156 |
|
|
// set the value for the hidden input value
|
| 157 |
|
|
// the input field of class "value" will hold it, this way we don't need to know the id
|
| 158 |
|
|
var input = $(parent).children("input.value");
|
| 159 |
|
|
$(input).val(value);
|
| 160 |
|
|
//alert("input: " + input);
|
| 161 |
5662
|
leinfelder
|
|
| 162 |
|
|
// set it in the search field
|
| 163 |
|
|
var treeInstance = $(item).parents("div.jstree:first");
|
| 164 |
|
|
var shortName = $(item).parent().attr("id");
|
| 165 |
|
|
$("#" + $(treeInstance).attr("id") + "Search").val(shortName)
|
| 166 |
5656
|
leinfelder
|
|
| 167 |
|
|
// refresh the other trees for active domain after this filtering action
|
| 168 |
|
|
// TODO actually do the active domain filtering when selection is made
|
| 169 |
|
|
//initialize($(parent).children("div"));
|
| 170 |
|
|
}
|
| 171 |
|
|
function donothing() {}
|
| 172 |
|
|
--></script>
|
| 173 |
|
|
|
| 174 |
5385
|
leinfelder
|
</head>
|
| 175 |
5633
|
leinfelder
|
<body onload="initialize()">
|
| 176 |
5509
|
leinfelder
|
<script language="javascript">
|
| 177 |
|
|
insertTemplateOpening("<%=CONTEXT_URL%>");
|
| 178 |
|
|
</script>
|
| 179 |
5385
|
leinfelder
|
|
| 180 |
5574
|
leinfelder
|
<div id="content_wrapper">
|
| 181 |
|
|
|
| 182 |
5533
|
leinfelder
|
<h2>Annotation-based search</h2>
|
| 183 |
5385
|
leinfelder
|
|
| 184 |
5633
|
leinfelder
|
<div id="error">
|
| 185 |
|
|
<!-- error messages here -->
|
| 186 |
|
|
</div>
|
| 187 |
|
|
|
| 188 |
5509
|
leinfelder
|
<form method="POST" action="<%=SERVLET_URL%>" target="_top" id="searchForm" name="searchForm" onSubmit="return checkSearch(this)">
|
| 189 |
|
|
<input name="query" type="hidden" />
|
| 190 |
|
|
<input name="qformat" value="semtools" type="hidden" />
|
| 191 |
5533
|
leinfelder
|
<input name="action" value="semquery" type="hidden" />
|
| 192 |
5509
|
leinfelder
|
|
| 193 |
5602
|
leinfelder
|
<table class="group group_border">
|
| 194 |
5509
|
leinfelder
|
<tr>
|
| 195 |
5632
|
leinfelder
|
<th colspan="3">
|
| 196 |
5602
|
leinfelder
|
<p>
|
| 197 |
|
|
Locate <b>data packages</b> that have been semantically annotated within the observation model by
|
| 198 |
|
|
selecting concepts from
|
| 199 |
|
|
<br/>
|
| 200 |
|
|
(a) existing semantic annotations
|
| 201 |
|
|
<br/>
|
| 202 |
|
|
(b) registered OBOE extension ontologies
|
| 203 |
|
|
</p>
|
| 204 |
|
|
</th>
|
| 205 |
5533
|
leinfelder
|
</tr>
|
| 206 |
5632
|
leinfelder
|
<!-- measurement -->
|
| 207 |
5533
|
leinfelder
|
<tr>
|
| 208 |
5632
|
leinfelder
|
<td colspan="3">
|
| 209 |
|
|
<table class="subGroup subGroup_border onehundred_percent">
|
| 210 |
|
|
<tr>
|
| 211 |
|
|
<th colspan="2">
|
| 212 |
|
|
Measurement
|
| 213 |
|
|
</th>
|
| 214 |
|
|
</tr>
|
| 215 |
|
|
<tr>
|
| 216 |
|
|
<td>a template that defines Entity, Characteristic, Standard, and/or Protocol</td>
|
| 217 |
|
|
</tr>
|
| 218 |
|
|
<tr>
|
| 219 |
|
|
<td>
|
| 220 |
5658
|
leinfelder
|
<input type="text" id="activeMeasurementsSearch" />
|
| 221 |
5656
|
leinfelder
|
<div class="select">
|
| 222 |
5660
|
leinfelder
|
<div id="activeMeasurements" style="width: 100%; height: 100px; overflow: auto">
|
| 223 |
5656
|
leinfelder
|
<p>loading...</p>
|
| 224 |
|
|
</div>
|
| 225 |
|
|
<input type="hidden" class="value" name="activeMeasurementsValue" id="activeMeasurementsValue"/>
|
| 226 |
|
|
<input type="hidden" name="activeMeasurementsClass" id="activeMeasurementsClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Measurement"/>
|
| 227 |
|
|
</div>
|
| 228 |
5632
|
leinfelder
|
</td>
|
| 229 |
|
|
</tr>
|
| 230 |
|
|
</table>
|
| 231 |
|
|
</td>
|
| 232 |
|
|
</tr>
|
| 233 |
|
|
<tr>
|
| 234 |
5533
|
leinfelder
|
<td>
|
| 235 |
5602
|
leinfelder
|
<table class="subGroup subGroup_border">
|
| 236 |
|
|
<tr>
|
| 237 |
|
|
<th colspan="1">
|
| 238 |
|
|
Entity
|
| 239 |
|
|
</th>
|
| 240 |
|
|
</tr>
|
| 241 |
|
|
<tr>
|
| 242 |
|
|
<td>Find observations of</td>
|
| 243 |
|
|
</tr>
|
| 244 |
|
|
<tr>
|
| 245 |
|
|
<td>
|
| 246 |
5658
|
leinfelder
|
<input type="text" id="activeEntitiesSearch" />
|
| 247 |
5656
|
leinfelder
|
<div class="select">
|
| 248 |
5660
|
leinfelder
|
<div id="activeEntities" style="width: 216px; height: 100px; overflow: auto">
|
| 249 |
5656
|
leinfelder
|
<p>loading...</p>
|
| 250 |
|
|
</div>
|
| 251 |
|
|
<input type="hidden" class="value" name="activeEntitiesValue" id="activeEntitiesValue"/>
|
| 252 |
|
|
<input type="hidden" name="activeEntitiesClass" id="activeEntitiesClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Entity"/>
|
| 253 |
|
|
</div>
|
| 254 |
5602
|
leinfelder
|
</td>
|
| 255 |
|
|
</tr>
|
| 256 |
|
|
</table>
|
| 257 |
5533
|
leinfelder
|
</td>
|
| 258 |
|
|
<td>
|
| 259 |
5602
|
leinfelder
|
<table class="subGroup subGroup_border">
|
| 260 |
|
|
<tr>
|
| 261 |
|
|
<th colspan="1">
|
| 262 |
|
|
Characteristic
|
| 263 |
|
|
</th>
|
| 264 |
|
|
</tr>
|
| 265 |
|
|
<tr>
|
| 266 |
5632
|
leinfelder
|
<td>with measurements of</td>
|
| 267 |
5602
|
leinfelder
|
</tr>
|
| 268 |
|
|
<tr>
|
| 269 |
|
|
<td>
|
| 270 |
5658
|
leinfelder
|
<input type="text" id="activeCharacteristicsSearch" />
|
| 271 |
5656
|
leinfelder
|
<div class="select">
|
| 272 |
5660
|
leinfelder
|
<div id="activeCharacteristics" style="width: 216px; height: 100px; overflow: auto">
|
| 273 |
5656
|
leinfelder
|
<p>loading...</p>
|
| 274 |
|
|
</div>
|
| 275 |
|
|
<input type="hidden" class="value" name="activeCharacteristicsValue" id="activeCharacteristicsValue"/>
|
| 276 |
|
|
<input type="hidden" name="activeCharacteristicsClass" id="activeCharacteristicsClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Characteristic"/>
|
| 277 |
|
|
</div>
|
| 278 |
5602
|
leinfelder
|
</td>
|
| 279 |
|
|
</tr>
|
| 280 |
|
|
</table>
|
| 281 |
5533
|
leinfelder
|
</td>
|
| 282 |
|
|
<td>
|
| 283 |
5602
|
leinfelder
|
<table class="subGroup subGroup_border">
|
| 284 |
|
|
<tr>
|
| 285 |
|
|
<th colspan="1">
|
| 286 |
|
|
Protocol
|
| 287 |
|
|
</th>
|
| 288 |
|
|
</tr>
|
| 289 |
|
|
<tr>
|
| 290 |
5632
|
leinfelder
|
<td>using procedures outlined by</td>
|
| 291 |
5602
|
leinfelder
|
</tr>
|
| 292 |
|
|
<tr>
|
| 293 |
|
|
<td>
|
| 294 |
5658
|
leinfelder
|
<input type="text" id="activeProtocolsSearch" />
|
| 295 |
5656
|
leinfelder
|
<div class="select">
|
| 296 |
5660
|
leinfelder
|
<div id="activeProtocols" style="width: 216px; height: 100px; overflow: auto">
|
| 297 |
5656
|
leinfelder
|
<p>loading...</p>
|
| 298 |
|
|
</div>
|
| 299 |
|
|
<input type="hidden" class="value" name="activeProtocolsValue" id="activeProtocolsValue" />
|
| 300 |
|
|
<input type="hidden" name="activeProtocolsClass" id="activeProtocolsClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Protocol"/>
|
| 301 |
|
|
</div>
|
| 302 |
5602
|
leinfelder
|
</td>
|
| 303 |
|
|
</tr>
|
| 304 |
|
|
</table>
|
| 305 |
5533
|
leinfelder
|
</td>
|
| 306 |
|
|
</tr>
|
| 307 |
|
|
<tr>
|
| 308 |
5632
|
leinfelder
|
<td colspan="3">Match All? <input type="checkbox" name="matchAll" checked="checked"/></td>
|
| 309 |
5509
|
leinfelder
|
</tr>
|
| 310 |
|
|
<tr>
|
| 311 |
5632
|
leinfelder
|
<td colspan="3">From same Observation? <input type="checkbox" name="strict"/></td>
|
| 312 |
5509
|
leinfelder
|
</tr>
|
| 313 |
|
|
<tr>
|
| 314 |
5633
|
leinfelder
|
<td colspan="3">
|
| 315 |
|
|
<input type="submit" value="Search"/>
|
| 316 |
|
|
<input type="reset" value="Clear" onclick="$('#searchForm').get(0).reset(); initialize()"/>
|
| 317 |
|
|
</td>
|
| 318 |
5509
|
leinfelder
|
</tr>
|
| 319 |
5602
|
leinfelder
|
</table>
|
| 320 |
|
|
<!--
|
| 321 |
5509
|
leinfelder
|
<tr>
|
| 322 |
5602
|
leinfelder
|
<td>Entity: (SBC only)</td>
|
| 323 |
|
|
<td><input type="text" name="entity" class="bp_form_complete-1523-uri" size="100" /></td>
|
| 324 |
5509
|
leinfelder
|
</tr>
|
| 325 |
5602
|
leinfelder
|
-->
|
| 326 |
5509
|
leinfelder
|
</form>
|
| 327 |
|
|
|
| 328 |
|
|
<!-- Included default search/login -->
|
| 329 |
|
|
<% if ( PropertyService.getProperty("spatial.runSpatialOption").equals("true") ) { %>
|
| 330 |
|
|
<script language="javascript">
|
| 331 |
|
|
insertMap("<%=CONTEXT_URL%>");
|
| 332 |
|
|
</script>
|
| 333 |
|
|
<br/>
|
| 334 |
|
|
<% } %>
|
| 335 |
|
|
|
| 336 |
|
|
<script language="javascript">
|
| 337 |
|
|
insertSearchBox("<%=CONTEXT_URL%>");
|
| 338 |
|
|
insertLoginBox("<%=CONTEXT_URL%>");
|
| 339 |
|
|
</script>
|
| 340 |
|
|
|
| 341 |
5574
|
leinfelder
|
</div>
|
| 342 |
|
|
|
| 343 |
5509
|
leinfelder
|
<script language="javascript">
|
| 344 |
|
|
insertTemplateClosing("<%=CONTEXT_URL%>");
|
| 345 |
|
|
</script>
|
| 346 |
|
|
|
| 347 |
5385
|
leinfelder
|
</body>
|
| 348 |
|
|
</html>
|