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<%@ page language="java"%>
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<%@page import="org.ecoinformatics.sms.ontology.bioportal.OntologyService,org.ecoinformatics.sms.ontology.bioportal.OntologyBean,java.util.List"%>
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<%@page import="org.ecoinformatics.sms.SMS,org.ecoinformatics.sms.ontology.Ontology"%>
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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: 2010-09-23 11:56:26 -0700 (Thu, 23 Sep 2010) $'
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* '$Revision: 5587 $'
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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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<%
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// construct the drop down and the lookup key for the available ontologies
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StringBuffer dropDown = new StringBuffer();
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List<OntologyBean> beans = OntologyService.getInstance().getOntologyBeans();
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for (OntologyBean bean: beans) {
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dropDown.append("<option value='");
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dropDown.append(bean.getId());
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dropDown.append("'>");
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dropDown.append(bean.getDisplayLabel());
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dropDown.append("</option>");
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}
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%>
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<%
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//show the currently registered ontologies in metacat's plugin
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StringBuffer registeredDropDown = new StringBuffer();
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List<String> ontologies = SMS.getInstance().getOntologyManager().getOntologyIds();
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for (String uri: ontologies) {
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Ontology ontology = SMS.getInstance().getOntologyManager().getOntology(uri);
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String label = SMS.getInstance().getOntologyManager().getOntologyLabel(ontology);
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registeredDropDown.append("<option value='");
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registeredDropDown.append(uri);
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registeredDropDown.append("'>");
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registeredDropDown.append(label);
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registeredDropDown.append("</option>");
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}
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%>
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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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<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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<script language="Javascript" type="text/JavaScript"
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src="<%=STYLE_SKINS_URL%>/semtools/bioportal/form_complete.js">
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</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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</head>
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<body>
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<script language="javascript">
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insertTemplateOpening("<%=CONTEXT_URL%>");
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</script>
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<div id="content_wrapper">
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<h2>Ontology Management (Metacat)</h2>
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<p>Ontologies should be registered in Metacat before they can be used in Annotation-based searches.</p>
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<h3>Currently Registered Ontologies</h3>
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<form method="POST" action="<%=SERVLET_URL%>" target="_top" id="existingRegistrationForm" name="existingRegistrationForm" ">
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<input name="qformat" value="semtools" type="hidden" />
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<table>
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<tr>
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<td>Action:</td>
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<td>
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<select name="action" id="action" disabled="disabled">
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<option value="registerOntology">Register Ontology</option>
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<option value="unregisterOntology" selected="selected">Unregister Ontology</option>
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</select>
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</td>
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</tr>
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<tr>
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<td>Ontology:</td>
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<td>
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<select name='id' id='id'>
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<%=registeredDropDown.toString()%>
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</select>
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</td>
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</tr>
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<tr>
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<td colspan="2"><input type="submit" value="Submit"/></td>
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</tr>
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</table>
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</form>
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<h3>Available BioPortal Ontologies</h3>
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<form method="POST" action="<%=SERVLET_URL%>" target="_top" id="bioportalRegistrationForm" name="bioportalRegistrationForm" ">
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<input name="qformat" value="semtools" type="hidden" />
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<table>
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<tr>
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<td>Action:</td>
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<td>
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<select name="action" id="action">
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<option value="registerOntology">Register Ontology</option>
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<option value="unregisterOntology">Unregister Ontology</option>
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</select>
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</td>
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</tr>
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<tr>
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<td>Ontology:</td>
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<td>
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<select name='id' id='id'>
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<%=dropDown.toString()%>
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</select>
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</td>
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</tr>
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<tr>
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<td colspan="2"><input type="submit" value="Submit"/></td>
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</tr>
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</table>
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</form>
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<h3>Other Ontologies</h3>
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<form method="POST" action="<%=SERVLET_URL%>" target="_top" id="registrationForm" name="registrationForm" ">
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<input name="qformat" value="semtools" type="hidden" />
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<table>
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<tr>
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<td>Action:</td>
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<td>
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<select name="action" id="action">
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<option value="registerOntology">Register Ontology</option>
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<option value="unregisterOntology">Unregister Ontology</option>
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</select>
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</td>
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</tr>
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<tr>
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<td>URI:</td>
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<td><input type="text" name="uri" id="uri" size="100" /></td>
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</tr>
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<tr>
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<td>URL:</td>
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<td><input type="text" name="url" id="url" size="100" /></td>
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</tr>
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<tr>
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<td colspan="2"><input type="submit" value="Submit"/></td>
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</tr>
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</table>
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</form>
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<h2>Ontology search (BioPortal)</h2>
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<p>Not sure which BioPortal ontology to use?</p>
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<p>Explore ontologies in BioPortal before registering them with Metacat. Use this search interface to find appropriate ontologies.</p>
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<div id="bp_quick_jump"></div>
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<script type="text/javascript">
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var BP_ontology_id = "all";
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</script>
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<script src="<%=STYLE_SKINS_URL%>/semtools/bioportal/quick_jump.js" type="text/javascript" charset="utf-8">
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</script>
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<h2>Tree browser (BioPortal)</h2>
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<p>Explore existing ontologies in BioPortal</p>
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<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"
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id="OntologyTree" width="300" height="100%"
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codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab">
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<param name="movie" value="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" />
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<param name="quality" value="high" />
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<param name="bgcolor" value="#ffffff" />
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<param name="allowScriptAccess" value="always" />
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<param name="flashVars" value="ontology=1523&alerterrors=false&canchangeontology=true&virtual=true" />
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<embed src="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" quality="high" bgcolor="#ffffff"
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width="300" height="100%" name="OntologyTree" align="middle"
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play="true"
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loop="false"
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allowScriptAccess="always"
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type="application/x-shockwave-flash"
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flashVars="ontology=1523&alerterrors=false&canchangeontology=true&virtual=true"
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pluginspage="http://www.adobe.com/go/getflashplayer">
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</embed>
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</object>
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<!-- Included default search/login -->
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<% if ( PropertyService.getProperty("spatial.runSpatialOption").equals("true") ) { %>
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<script language="javascript">
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insertMap("<%=CONTEXT_URL%>");
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</script>
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<br/>
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<% } %>
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<script language="javascript">
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insertSearchBox("<%=CONTEXT_URL%>");
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insertLoginBox("<%=CONTEXT_URL%>");
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</script>
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</div>
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<script language="javascript">
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insertTemplateClosing("<%=CONTEXT_URL%>");
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</script>
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</body>
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</html>
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