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<%@ page language="java"%>
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<%
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/**
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*
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* '$RCSfile$'
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* Copyright: 2008 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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* '$Author$'
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* '$Date$'
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* '$Revision$'
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 2 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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%>
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<%@ include file="../../common/common-settings.jsp"%>
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<%@ include file="../../common/configure-check.jsp"%>
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<html>
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<head>
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<title>Semantic search</title>
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<link rel="stylesheet" type="text/css" href="<%=STYLE_SKINS_URL%>/semtools/semtools.css">
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<link rel="stylesheet" type="text/css" href="<%=STYLE_SKINS_URL%>/semtools/jqueryui/css/smoothness/jquery-ui-1.8.6.custom.css">
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<script type="text/javascript"
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src="<%=STYLE_SKINS_URL%>/semtools/search.js"></script>
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<script type="text/javascript">
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// Set defaults for this installation
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//var BP_SEARCH_SERVER = "http://oor-01.cim3.net";
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//var BP_SITE = "Sandbox";
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//var BP_ORG = "OOR";
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</script>
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<!--
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<script language="Javascript" type="text/JavaScript" src="<%=STYLE_SKINS_URL%>/semtools/bioportal/form_complete.js"></script>
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-->
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<script language="javascript" type="text/javascript" src="<%=STYLE_SKINS_URL%>/semtools/jsTree/_lib/jquery.js"></script>
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<script language="javascript" type="text/javascript" src="<%=STYLE_SKINS_URL%>/semtools/jsTree/_lib/jquery.cookie.js"></script>
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<script language="javascript" type="text/javascript" src="<%=STYLE_SKINS_URL%>/semtools/jsTree/jquery.jstree.js"></script>
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<!-- jquery ui -->
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<script language="javascript" type="text/javascript" src="<%=STYLE_SKINS_URL%>/semtools/jqueryui/js/jquery-ui-1.8.6.custom.min.js"></script>
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<script language="javascript" type="text/javascript" src="<%=STYLE_SKINS_URL%>/semtools/jquery/jquery.busy.js"></script>
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<script language="javascript" type="text/javascript" src="<%=STYLE_SKINS_URL%>/semtools/semtools.js"></script>
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<script language="javascript" type="text/javascript" src="<%=STYLE_COMMON_URL%>/branding.js"></script>
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<script language="Javascript" type="text/JavaScript"><!--
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function populateActiveDomain(divId, class) {
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// collect the filtering values we have so far
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// these are hidden input fields in the form for holding the selected values
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var entity = $("#activeEntitiesValue").val() ? $("#activeEntitiesValue").val() : "";
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var characteristic = $("#activeCharacteristicsValue").val() ? $("#activeCharacteristicsValue").val() : "";
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var protocol = $("#activeProtocolsValue").val() ? $("#activeProtocolsValue").val() : "";
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var measurement = $("#activeMeasurementsValue").val() ? $("#activeMeasurementsValue").val() : "";
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// TODO: remember the selected value for this when filtering by active domain
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var selectedNode = $("#" + divId).jstree("get_selected", $("#" + divId));
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var selectedNodeId = $(selectedNode).attr("id");
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//alert(divId + " selected node: " + selectedNodeId);
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// load the tree for the given div, passing in the other filtered values
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$("#" + divId).load(
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"<%=SERVLET_URL%>",
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{
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'action': "getactivedomain",
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'class': class,
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'entity': entity,
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'characteristic': characteristic,
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'protocol': protocol,
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'measurement': measurement
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},
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// call back function when loading finishes
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function(response, status, xhr) {
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//alert("callback for: " + divId + " selected node: " + selectedNodeId);
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// error
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if (status == "error") {
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var msg = "Sorry but there was an error: ";
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$("#error").html(msg + xhr.status + " " + xhr.statusText);
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}
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// make it a js tree
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$(function () {
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$("#" + divId)
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//bind calls here
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.jstree({
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"ui" : {
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"select_limit" : 1,
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"select_multiple_modifier" : "alt",
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"selected_parent_close" : "select_parent"//,
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//"initially_select" : [ selectedNodeId ]
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},
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"themes" : {
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"theme" : "default",
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"dots" : true,
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"icons" : false
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},
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//"core" : { "initially_open" : [ selectedNodeId ] },
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"search" : { "case_insensitive" : true },
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//"cookies" : {
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// "save_opened" : "jstree_open_" + divId,
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// "save_selected" : "jstree_select_" + divId,
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//},
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"plugins" : [
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"themes",
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"html_data",
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"ui",
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//"cookies",
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"search" ]
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});
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});
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// enable searching on it
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$("#" + divId + "Search").keyup(
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function () {
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if ($("#" + divId + "Search").val().length >= 3) {
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// search
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$("#" + divId).jstree("search", $("#" + divId + "Search").val());
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// now prune
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prune(divId, "jstree-search");
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}
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});
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// toggle the active domain prune
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$("#" + divId + "Only").click(function() {
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doActiveDomain(divId);
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});
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// actually prune if we should
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doActiveDomain(divId);
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// open to the node to last selected
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var nodePath = $("#" + divId).jstree("get_path", $(selectedNode));
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if (nodePath) {
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for (var index = 0; index < nodePath.length; index++) {
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$("#" + divId).jstree("open_node", $("#" + nodePath[index]));
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}
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// select the original node
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$("#" + divId).jstree("select_node", $(selectedNode), false);
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$("#" + divId).jstree("refresh", $(selectedNode));
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// TODO: scroll to selected node.
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// This is supposed to be part of jsTree 1.0-rc2 but appears to be broken
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}
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});
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}
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/**
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* Prunes the given tree to inlcude the given matched class
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**/
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function prune(divId, matchClass) {
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// show all nodes (reset)
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$("#" + divId).find("li").show();
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// done if we don't have any thing to prune
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if (!matchClass) {
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return;
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}
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// get all non-matched anchor tags
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var nonmatches = $("#" + divId).find("a").not("." + matchClass);
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// get their parent nodes
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nonmatches = $(nonmatches).parents("li");
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// are there any matches under each parent node?
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$(nonmatches).each(
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function(index) {
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// do any chidren match?
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var childMatches = $(this).find("a." + matchClass);
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if (childMatches && childMatches.length > 0) {
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return true;
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}
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// parent matches?
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var parentMatches = $(this).parents("li").children("a." + matchClass);
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if (parentMatches && parentMatches.length > 0) {
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return true;
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}
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// hide this node if no matches under it
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$(this).hide();
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});
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}
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function doActiveDomain(divId) {
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if ($("#" + divId + "Only").is(":checked")) {
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// prune to active
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prune(divId, "bold");
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} else {
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// reset
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prune(divId, null);
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}
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}
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function initialize(source) {
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// we don't want to reload the source of the filtering request
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// but we do want to reload the other trees for active domains
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// we reload all of them if no source is given - first time the page loads
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if (source) {
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source = $(source).attr("id");
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}
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if (!source) {
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source = "";
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}
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if (source != 'activeEntities') {
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populateActiveDomain('activeEntities', 'org.ecoinformatics.sms.annotation.Entity');
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}
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if (source != 'activeCharacteristics') {
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populateActiveDomain('activeCharacteristics', 'org.ecoinformatics.sms.annotation.Characteristic');
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}
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if (source != 'activeProtocols') {
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populateActiveDomain('activeProtocols', 'org.ecoinformatics.sms.annotation.Protocol');
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}
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if (source != 'activeMeasurements') {
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populateActiveDomain('activeMeasurements', 'org.ecoinformatics.sms.annotation.Measurement');
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}
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}
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function select(item) {
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// get the selected value, stored in the title attribute of the item <a> tag
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var value = $(item).attr("title");
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//alert("value: " + value);
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// get the parent div so we know what kind of class it is meant to filter
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// this is "the first parent of the class 'select'"
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var parent = $(item).parents("div.select:first");
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//alert("parent: " + parent);
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// set the value for the hidden input value
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// the input field of class "value" will hold it, this way we don't need to know the id
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var input = $(parent).children("input.value");
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$(input).val(value);
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| 241 |
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//alert("input: " + input);
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// set it in the search field
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var treeInstance = $(item).parents("div.jstree:first");
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var shortName = $(item).parent().attr("id");
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| 246 |
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$("#" + $(treeInstance).attr("id") + "Search").val(shortName)
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// refresh the search results
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| 249 |
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doSearch($("#searchForm").get(0));
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// refresh the other trees for active domain after this filtering action
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initialize($(parent).children("div"));
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| 253 |
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}
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| 254 |
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function doSearch(formObj) {
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| 255 |
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// set the hidden parameters based on the current state of the form
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| 256 |
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checkSearch(formObj);
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| 257 |
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// start the busy indicator
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$("#searchResults").busy(
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| 260 |
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{
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| 261 |
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position : 'left',
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offset : -30,
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| 263 |
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hide : true,
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| 264 |
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img : "<%=STYLE_SKINS_URL%>/semtools/images/busy.gif"
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| 265 |
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});
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| 266 |
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//load the results
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| 268 |
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$("#searchResults").load(
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| 269 |
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"<%=SERVLET_URL%>" + " #content_wrapper",
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$(formObj).serialize(),
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| 271 |
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// call back function when loading finishes
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| 272 |
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function(response, status, xhr) {
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| 273 |
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if (status == "error") {
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| 274 |
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var msg = "Sorry but there was an error performing the search: ";
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| 275 |
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$("#error").html(msg + xhr.status + " " + xhr.statusText);
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| 276 |
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}
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| 277 |
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// collapsible search results?
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| 278 |
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$(function() {
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| 279 |
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$('.accordian').click(function() {
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| 280 |
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$(this).next().slideToggle("slow");
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| 281 |
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return false;
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| 282 |
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}).next().hide();
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| 283 |
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});
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| 284 |
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| 285 |
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// stop the busy indicator
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| 286 |
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$("#searchResults").busy("hide");
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| 287 |
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});
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| 288 |
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return false;
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}
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| 292 |
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function clearForm() {
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| 293 |
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// clear the form values
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| 294 |
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$('#searchForm').get(0).reset();
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| 295 |
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// clear each of the tree selections
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| 296 |
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$(".jstree").each(function(index) {
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| 297 |
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$(this).jstree("deselect_all");
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| 298 |
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});
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| 299 |
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$("input.value").each(function(index) {
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| 300 |
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$(this).val("");
|
| 301 |
|
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});
|
| 302 |
|
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// reload the trees
|
| 303 |
|
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initialize();
|
| 304 |
|
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// reload the search results
|
| 305 |
|
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//alert($('#searchForm').get(0));
|
| 306 |
|
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doSearch($('#searchForm').get(0));
|
| 307 |
|
|
}
|
| 308 |
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function donothing() {}
|
| 309 |
|
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--></script>
|
| 310 |
|
|
|
| 311 |
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</head>
|
| 312 |
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<body onload="initialize()">
|
| 313 |
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<script language="javascript">
|
| 314 |
|
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insertTemplateOpening("<%=CONTEXT_URL%>");
|
| 315 |
|
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</script>
|
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<div id="content_wrapper">
|
| 318 |
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|
| 319 |
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<h2>Annotation-based search</h2>
|
| 320 |
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| 321 |
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<div id="error">
|
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<!-- error messages here -->
|
| 323 |
|
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</div>
|
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|
|
|
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<!-- set up the tabs -->
|
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<script>
|
| 327 |
|
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$(function() {
|
| 328 |
|
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$("#searchTabs").tabs();
|
| 329 |
|
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$("#searchTabs").tabs("add", "#ecpTab", "Entity, Characteristic, Protocol");
|
| 330 |
|
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$("#searchTabs").tabs("add", "#measurementTab", "Measurement");
|
| 331 |
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$("#searchTabs").tabs("add", "#optionsTab", "Options");
|
| 332 |
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});
|
| 333 |
|
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</script>
|
| 334 |
|
|
|
| 335 |
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<form method="POST"
|
| 336 |
|
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action="<%=SERVLET_URL%>"
|
| 337 |
|
|
target="_top"
|
| 338 |
|
|
id="searchForm"
|
| 339 |
|
|
name="searchForm"
|
| 340 |
|
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onSubmit="return doSearch(this)">
|
| 341 |
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<input name="query" type="hidden" />
|
| 342 |
|
|
<input name="qformat" value="semtools" type="hidden" />
|
| 343 |
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<input name="includeHeader" value="false" type="hidden" />
|
| 344 |
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<input name="action" value="semquery" type="hidden" />
|
| 345 |
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|
|
| 346 |
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<!-- tabs for the search interface -->
|
| 347 |
|
|
<div id="searchTabs">
|
| 348 |
|
|
<!-- place holder for ui tabs -->
|
| 349 |
|
|
<ul></ul>
|
| 350 |
|
|
|
| 351 |
|
|
<!-- other criteria tabs -->
|
| 352 |
|
|
<div id="ecpTab">
|
| 353 |
|
|
<table>
|
| 354 |
|
|
<tr>
|
| 355 |
|
|
<td>
|
| 356 |
|
|
<table class="subGroup subGroup_border">
|
| 357 |
|
|
|
| 358 |
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<tr>
|
| 359 |
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<th><p>Find observations of</p></th>
|
| 360 |
|
|
</tr>
|
| 361 |
|
|
<tr>
|
| 362 |
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<td>
|
| 363 |
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<input type="text" id="activeEntitiesSearch" />
|
| 364 |
|
|
<input type="checkbox" id="activeEntitiesOnly" title="Show only active concepts" />
|
| 365 |
|
|
<div class="select">
|
| 366 |
|
|
<div id="activeEntities" class="activeTree">
|
| 367 |
|
|
<p>loading...</p>
|
| 368 |
|
|
</div>
|
| 369 |
|
|
<input type="hidden" class="value" name="activeEntitiesValue" id="activeEntitiesValue"/>
|
| 370 |
|
|
<input type="hidden" name="activeEntitiesClass" id="activeEntitiesClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Entity"/>
|
| 371 |
|
|
</div>
|
| 372 |
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</td>
|
| 373 |
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|
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</tr>
|
| 374 |
|
|
</table>
|
| 375 |
|
|
</td>
|
| 376 |
|
|
<td>
|
| 377 |
|
|
<table class="subGroup subGroup_border">
|
| 378 |
|
|
<tr>
|
| 379 |
|
|
<th><p>with measurements of</p></th>
|
| 380 |
|
|
</tr>
|
| 381 |
|
|
<tr>
|
| 382 |
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|
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<td>
|
| 383 |
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|
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|
<input type="text" id="activeCharacteristicsSearch" />
|
| 384 |
|
|
<input type="checkbox" id="activeCharacteristicsOnly" title="Show only active concepts" />
|
| 385 |
|
|
<div class="select">
|
| 386 |
|
|
<div id="activeCharacteristics" class="activeTree">
|
| 387 |
|
|
<p>loading...</p>
|
| 388 |
|
|
</div>
|
| 389 |
|
|
<input type="hidden" class="value" name="activeCharacteristicsValue" id="activeCharacteristicsValue"/>
|
| 390 |
|
|
<input type="hidden" name="activeCharacteristicsClass" id="activeCharacteristicsClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Characteristic"/>
|
| 391 |
|
|
</div>
|
| 392 |
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|
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|
</td>
|
| 393 |
|
|
</tr>
|
| 394 |
|
|
</table>
|
| 395 |
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|
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|
</td>
|
| 396 |
|
|
<td>
|
| 397 |
|
|
<table class="subGroup subGroup_border">
|
| 398 |
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|
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|
<tr>
|
| 399 |
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|
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<th><p>using procedures outlined by</p></th>
|
| 400 |
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|
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|
</tr>
|
| 401 |
|
|
<tr>
|
| 402 |
|
|
<td>
|
| 403 |
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|
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|
<input type="text" id="activeProtocolsSearch" />
|
| 404 |
|
|
<input type="checkbox" id="activeProtocolsOnly" title="Show only active concepts" />
|
| 405 |
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|
leinfelder
|
<div class="select">
|
| 406 |
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|
leinfelder
|
<div id="activeProtocols" class="activeTree">
|
| 407 |
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|
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|
<p>loading...</p>
|
| 408 |
|
|
</div>
|
| 409 |
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|
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|
<input type="hidden" class="value" name="activeProtocolsValue" id="activeProtocolsValue" />
|
| 410 |
|
|
<input type="hidden" name="activeProtocolsClass" id="activeProtocolsClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Protocol"/>
|
| 411 |
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|
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|
</div>
|
| 412 |
|
|
</td>
|
| 413 |
|
|
</tr>
|
| 414 |
|
|
</table>
|
| 415 |
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|
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|
</td>
|
| 416 |
|
|
</tr>
|
| 417 |
|
|
</table>
|
| 418 |
|
|
</div>
|
| 419 |
|
|
|
| 420 |
|
|
<!-- measurement -->
|
| 421 |
|
|
<div id="measurementTab">
|
| 422 |
|
|
<table class="subGroup subGroup_border onehundred_percent">
|
| 423 |
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|
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|
|
| 424 |
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|
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|
<tr>
|
| 425 |
|
|
<th><p>a template that defines Entity, Characteristic, Standard, and/or Protocol</p></th>
|
| 426 |
|
|
</tr>
|
| 427 |
|
|
|
| 428 |
|
|
<tr>
|
| 429 |
|
|
<td>
|
| 430 |
|
|
<input type="text" id="activeMeasurementsSearch" />
|
| 431 |
|
|
Only active? <input type="checkbox" id="activeMeasurementsOnly" title="Show only active concepts"/>
|
| 432 |
|
|
<div class="select">
|
| 433 |
|
|
<div id="activeMeasurements" class="activeTree" style="width: 100%">
|
| 434 |
|
|
<p>loading...</p>
|
| 435 |
|
|
</div>
|
| 436 |
|
|
<input type="hidden" class="value" name="activeMeasurementsValue" id="activeMeasurementsValue"/>
|
| 437 |
|
|
<input type="hidden" name="activeMeasurementsClass" id="activeMeasurementsClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Measurement"/>
|
| 438 |
|
|
</div>
|
| 439 |
|
|
</td>
|
| 440 |
|
|
</tr>
|
| 441 |
|
|
</table>
|
| 442 |
|
|
</div>
|
| 443 |
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|
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|
|
| 444 |
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|
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|
<!-- query options -->
|
| 445 |
|
|
<div id="optionsTab">
|
| 446 |
|
|
<table class="group group_border">
|
| 447 |
|
|
<tr>
|
| 448 |
|
|
<th colspan="2">
|
| 449 |
|
|
<p>
|
| 450 |
|
|
Locate <b>data packages</b> that have been semantically annotated within the observation model by
|
| 451 |
|
|
selecting concepts from OBOE extension ontologies
|
| 452 |
|
|
</p>
|
| 453 |
|
|
</th>
|
| 454 |
|
|
</tr>
|
| 455 |
|
|
|
| 456 |
|
|
<tr>
|
| 457 |
|
|
|
| 458 |
|
|
<td colspan="1">Match All? <input type="checkbox" name="matchAll" checked="checked"/></td>
|
| 459 |
|
|
|
| 460 |
|
|
<td colspan="1">From same Observation? <input type="checkbox" name="strict"/></td>
|
| 461 |
|
|
</tr>
|
| 462 |
|
|
|
| 463 |
|
|
</table>
|
| 464 |
|
|
</div>
|
| 465 |
|
|
|
| 466 |
|
|
</div>
|
| 467 |
|
|
|
| 468 |
|
|
<br/>
|
| 469 |
|
|
|
| 470 |
|
|
<!-- search results here -->
|
| 471 |
|
|
<table class="subGroup subGroup_border onehundred_percent">
|
| 472 |
5632
|
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|
<tr>
|
| 473 |
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|
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|
<th>
|
| 474 |
|
|
Search Results
|
| 475 |
5668
|
leinfelder
|
<input type="reset" value="Clear" onclick="clearForm()"/>
|
| 476 |
5672
|
leinfelder
|
</th>
|
| 477 |
5509
|
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|
</tr>
|
| 478 |
|
|
<tr>
|
| 479 |
5672
|
leinfelder
|
<td>
|
| 480 |
|
|
<div id="searchResults">
|
| 481 |
|
|
No query has been specified
|
| 482 |
|
|
</div>
|
| 483 |
|
|
</td>
|
| 484 |
5509
|
leinfelder
|
</tr>
|
| 485 |
5672
|
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|
</table>
|
| 486 |
|
|
|
| 487 |
5509
|
leinfelder
|
</form>
|
| 488 |
|
|
|
| 489 |
5665
|
leinfelder
|
|
| 490 |
5672
|
leinfelder
|
|
| 491 |
5509
|
leinfelder
|
<!-- Included default search/login -->
|
| 492 |
|
|
<% if ( PropertyService.getProperty("spatial.runSpatialOption").equals("true") ) { %>
|
| 493 |
|
|
<script language="javascript">
|
| 494 |
|
|
insertMap("<%=CONTEXT_URL%>");
|
| 495 |
|
|
</script>
|
| 496 |
|
|
<br/>
|
| 497 |
|
|
<% } %>
|
| 498 |
|
|
|
| 499 |
|
|
<script language="javascript">
|
| 500 |
|
|
insertSearchBox("<%=CONTEXT_URL%>");
|
| 501 |
|
|
insertLoginBox("<%=CONTEXT_URL%>");
|
| 502 |
|
|
</script>
|
| 503 |
|
|
|
| 504 |
5574
|
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|
</div>
|
| 505 |
|
|
|
| 506 |
5509
|
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|
<script language="javascript">
|
| 507 |
|
|
insertTemplateClosing("<%=CONTEXT_URL%>");
|
| 508 |
|
|
</script>
|
| 509 |
|
|
|
| 510 |
5385
|
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|
</body>
|
| 511 |
|
|
</html>
|