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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: leinfelder $'
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* '$Date: 2010-12-03 16:24:18 -0800 (Fri, 03 Dec 2010) $'
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* '$Revision: 5688 $'
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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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var searchTerm = $("#" + divId + "Search").val();
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if (searchTerm.length >= 3) {
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// search
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$("#" + divId).jstree("search", searchTerm);
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// now prune
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prune(divId, "jstree-search");
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// is it an exact match?
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checkExactMatch(divId, searchTerm, "jstree-search");
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}
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});
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// toggle the active domain prune
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$("#" + divId + "Only").click(function() {
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doActiveDomain(divId);
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});
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// actually prune if we should
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doActiveDomain(divId);
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// open first node always
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$("#" + divId).jstree("open_node", $("#" + divId).children("ul").first().children("li").first());
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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 checkExactMatch(divId, searchTerm, matchClass) {
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// get the current search matches
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var matches = $("#" + divId).find("a." + matchClass);
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// get their parent nodes
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matches = $(matches).parents("li");
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// check for exact matches
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var exactMatch = $(matches).filter("#" + searchTerm).first();
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if (exactMatch && exactMatch.length == 1) {
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//alert("exactMatch: " + exactMatch);
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select($(exactMatch).children("a"));
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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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//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 = $(item).parent().attr("id");
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$("#" + $(treeInstance).attr("id") + "Search").val(shortName)
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// refresh the search results
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doSearch($("#searchForm").get(0));
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// refresh the other trees for active domain after this filtering action
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initialize($(parent).children("div"));
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}
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function doSearch(formObj) {
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// set the hidden parameters based on the current state of the form
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checkSearch(formObj);
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// start the busy indicator
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$("#searchResults").busy(
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{
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position : 'left',
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offset : -30,
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hide : true,
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img : "<%=STYLE_SKINS_URL%>/semtools/images/busy.gif"
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});
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//load the results
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$("#searchResults").load(
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"<%=SERVLET_URL%>" + " #content_wrapper",
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$(formObj).serialize(),
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// call back function when loading finishes
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function(response, status, xhr) {
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if (status == "error") {
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var msg = "Sorry but there was an error performing the search: ";
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$("#error").html(msg + xhr.status + " " + xhr.statusText);
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}
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295
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// collapsible search results?
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$(function() {
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$('.accordian').click(function() {
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$(this).next().slideToggle("slow");
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return false;
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300
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}).next().hide();
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});
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// stop the busy indicator
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$("#searchResults").busy("hide");
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});
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306
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return false;
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308
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}
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310
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function clearForm() {
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// clear the form values
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$('#searchForm').get(0).reset();
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313
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// clear each of the tree selections
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314
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$(".jstree").each(function(index) {
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$(this).jstree("deselect_all");
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});
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317
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$("input.value").each(function(index) {
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$(this).val("");
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});
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// reload the trees
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321
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initialize();
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322
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// reload the search results
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323
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//alert($('#searchForm').get(0));
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324
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doSearch($('#searchForm').get(0));
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325
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}
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326
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/**
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327
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* Perform this when the page first loads
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328
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*/
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329
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function pageLoad() {
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initialize();
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331
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doSearch($('#searchForm').get(0));
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}
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333
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function donothing() {}
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334
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--></script>
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335
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336
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</head>
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337
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<body onload="pageLoad()">
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338
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<script language="javascript">
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insertTemplateOpening("<%=CONTEXT_URL%>");
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340
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</script>
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341
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342
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<div id="content_wrapper">
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343
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344
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<h2>Annotation-based search</h2>
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345
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346
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<div id="error">
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347
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<!-- error messages here -->
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348
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</div>
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349
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350
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<!-- set up the tabs -->
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<script>
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352
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$(function() {
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353
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$("#searchTabs").tabs();
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354
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$("#searchTabs").tabs("add", "#ecpTab", "Entity, Characteristic, Protocol");
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$("#searchTabs").tabs("add", "#measurementTab", "Measurement");
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$("#searchTabs").tabs("add", "#optionsTab", "Options");
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});
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</script>
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359
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360
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<form method="POST"
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361
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action="<%=SERVLET_URL%>"
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362
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target="_top"
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363
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id="searchForm"
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name="searchForm"
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365
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onSubmit="return doSearch(this)">
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366
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<input name="query" type="hidden" />
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367
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<input name="qformat" value="semtools" type="hidden" />
|
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368
|
<input name="includeHeader" value="false" type="hidden" />
|
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369
|
<input name="action" value="semquery" type="hidden" />
|
|
370
|
|
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371
|
<!-- tabs for the search interface -->
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372
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<div id="searchTabs">
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373
|
<!-- place holder for ui tabs -->
|
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374
|
<ul></ul>
|
|
375
|
|
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376
|
<!-- other criteria tabs -->
|
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377
|
<div id="ecpTab">
|
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378
|
<table>
|
|
379
|
<tr>
|
|
380
|
<td>
|
|
381
|
<table class="subGroup subGroup_border">
|
|
382
|
|
|
383
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<tr>
|
|
384
|
<th><p>Find observations of</p></th>
|
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385
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</tr>
|
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386
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<tr>
|
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387
|
<td>
|
|
388
|
<input type="text" id="activeEntitiesSearch" />
|
|
389
|
<input type="checkbox" id="activeEntitiesOnly" title="Show only active concepts" />
|
|
390
|
<div class="select">
|
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391
|
<div id="activeEntities" class="activeTree">
|
|
392
|
<p>loading...</p>
|
|
393
|
</div>
|
|
394
|
<input type="hidden" class="value" name="activeEntitiesValue" id="activeEntitiesValue"/>
|
|
395
|
<input type="hidden" name="activeEntitiesClass" id="activeEntitiesClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Entity"/>
|
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396
|
</div>
|
|
397
|
</td>
|
|
398
|
</tr>
|
|
399
|
</table>
|
|
400
|
</td>
|
|
401
|
<td>
|
|
402
|
<table class="subGroup subGroup_border">
|
|
403
|
<tr>
|
|
404
|
<th><p>with measurements of</p></th>
|
|
405
|
</tr>
|
|
406
|
<tr>
|
|
407
|
<td>
|
|
408
|
<input type="text" id="activeCharacteristicsSearch" />
|
|
409
|
<input type="checkbox" id="activeCharacteristicsOnly" title="Show only active concepts" />
|
|
410
|
<div class="select">
|
|
411
|
<div id="activeCharacteristics" class="activeTree">
|
|
412
|
<p>loading...</p>
|
|
413
|
</div>
|
|
414
|
<input type="hidden" class="value" name="activeCharacteristicsValue" id="activeCharacteristicsValue"/>
|
|
415
|
<input type="hidden" name="activeCharacteristicsClass" id="activeCharacteristicsClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Characteristic"/>
|
|
416
|
</div>
|
|
417
|
</td>
|
|
418
|
</tr>
|
|
419
|
</table>
|
|
420
|
</td>
|
|
421
|
<td>
|
|
422
|
<table class="subGroup subGroup_border">
|
|
423
|
<tr>
|
|
424
|
<th><p>using procedures outlined by</p></th>
|
|
425
|
</tr>
|
|
426
|
<tr>
|
|
427
|
<td>
|
|
428
|
<input type="text" id="activeProtocolsSearch" />
|
|
429
|
<input type="checkbox" id="activeProtocolsOnly" title="Show only active concepts" />
|
|
430
|
<div class="select">
|
|
431
|
<div id="activeProtocols" class="activeTree">
|
|
432
|
<p>loading...</p>
|
|
433
|
</div>
|
|
434
|
<input type="hidden" class="value" name="activeProtocolsValue" id="activeProtocolsValue" />
|
|
435
|
<input type="hidden" name="activeProtocolsClass" id="activeProtocolsClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Protocol"/>
|
|
436
|
</div>
|
|
437
|
</td>
|
|
438
|
</tr>
|
|
439
|
</table>
|
|
440
|
</td>
|
|
441
|
</tr>
|
|
442
|
</table>
|
|
443
|
</div>
|
|
444
|
|
|
445
|
<!-- measurement -->
|
|
446
|
<div id="measurementTab">
|
|
447
|
<table class="subGroup subGroup_border onehundred_percent">
|
|
448
|
|
|
449
|
<tr>
|
|
450
|
<th><p>a template that defines Entity, Characteristic, Standard, and/or Protocol</p></th>
|
|
451
|
</tr>
|
|
452
|
|
|
453
|
<tr>
|
|
454
|
<td>
|
|
455
|
<input type="text" id="activeMeasurementsSearch" />
|
|
456
|
Only active? <input type="checkbox" id="activeMeasurementsOnly" title="Show only active concepts"/>
|
|
457
|
<div class="select">
|
|
458
|
<div id="activeMeasurements" class="activeTree" style="width: 100%">
|
|
459
|
<p>loading...</p>
|
|
460
|
</div>
|
|
461
|
<input type="hidden" class="value" name="activeMeasurementsValue" id="activeMeasurementsValue"/>
|
|
462
|
<input type="hidden" name="activeMeasurementsClass" id="activeMeasurementsClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Measurement"/>
|
|
463
|
</div>
|
|
464
|
</td>
|
|
465
|
</tr>
|
|
466
|
</table>
|
|
467
|
</div>
|
|
468
|
|
|
469
|
<!-- query options -->
|
|
470
|
<div id="optionsTab">
|
|
471
|
<table class="group group_border">
|
|
472
|
<tr>
|
|
473
|
<th colspan="2">
|
|
474
|
<p>
|
|
475
|
Locate <b>data packages</b> that have been semantically annotated within the observation model by
|
|
476
|
selecting concepts from OBOE extension ontologies
|
|
477
|
</p>
|
|
478
|
</th>
|
|
479
|
</tr>
|
|
480
|
|
|
481
|
<tr>
|
|
482
|
|
|
483
|
<td colspan="1">Match All? <input type="checkbox" name="matchAll" checked="checked"/></td>
|
|
484
|
|
|
485
|
<td colspan="1">From same Observation? <input type="checkbox" name="strict"/></td>
|
|
486
|
</tr>
|
|
487
|
|
|
488
|
</table>
|
|
489
|
</div>
|
|
490
|
|
|
491
|
</div>
|
|
492
|
|
|
493
|
<br/>
|
|
494
|
|
|
495
|
<!-- search results here -->
|
|
496
|
<table class="subGroup subGroup_border onehundred_percent">
|
|
497
|
<tr>
|
|
498
|
<th>
|
|
499
|
Search Results
|
|
500
|
<input type="reset" value="Clear" onclick="clearForm()"/>
|
|
501
|
</th>
|
|
502
|
</tr>
|
|
503
|
<tr>
|
|
504
|
<td>
|
|
505
|
<div id="searchResults">
|
|
506
|
No query has been specified
|
|
507
|
</div>
|
|
508
|
</td>
|
|
509
|
</tr>
|
|
510
|
</table>
|
|
511
|
|
|
512
|
</form>
|
|
513
|
|
|
514
|
|
|
515
|
|
|
516
|
<!-- Included default search/login -->
|
|
517
|
<% if ( PropertyService.getProperty("spatial.runSpatialOption").equals("true") ) { %>
|
|
518
|
<script language="javascript">
|
|
519
|
insertMap("<%=CONTEXT_URL%>");
|
|
520
|
</script>
|
|
521
|
<br/>
|
|
522
|
<% } %>
|
|
523
|
|
|
524
|
<script language="javascript">
|
|
525
|
insertSearchBox("<%=CONTEXT_URL%>");
|
|
526
|
insertLoginBox("<%=CONTEXT_URL%>");
|
|
527
|
</script>
|
|
528
|
|
|
529
|
</div>
|
|
530
|
|
|
531
|
<script language="javascript">
|
|
532
|
insertTemplateClosing("<%=CONTEXT_URL%>");
|
|
533
|
</script>
|
|
534
|
|
|
535
|
</body>
|
|
536
|
</html>
|