Adding changes and code for terminology annotation support and integration of UMLS vocabulary
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hjkhjk54
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9 changed files with 1005 additions and 1 deletions
286
productMods/edit/forms/terminologyAnnotation.jsp
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286
productMods/edit/forms/terminologyAnnotation.jsp
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<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
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<%-- Custom form for adding terminology annotation
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--%>
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<%@ page import="java.util.List" %>
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<%@ page import="java.util.ArrayList" %>
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<%@ page import="java.util.Arrays" %>
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<%@ page import="java.util.Collections" %>
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<%@ page import="com.hp.hpl.jena.rdf.model.Model" %>
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<%@ page import="com.hp.hpl.jena.vocabulary.XSD" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.beans.Individual" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.beans.DataPropertyComparator" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.EditConfiguration" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.controller.VitroRequest" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.web.MiscWebUtils" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.JavaScript" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.Css" %>
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<%@ page import="org.apache.commons.lang.StringUtils" %>
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<%@ page import="org.json.JSONObject" %>
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<%@ page import="org.apache.commons.logging.Log" %>
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<%@ page import="org.apache.commons.logging.LogFactory" %>
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<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core"%>
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<%@ taglib prefix="v" uri="http://vitro.mannlib.cornell.edu/vitro/tags" %>
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<%!
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public static Log log = LogFactory.getLog("edu.cornell.mannlib.vitro.webapp.jsp.edit.forms.terminologyAnnotation.jsp");
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%>
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<%
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VitroRequest vreq = new VitroRequest(request);
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WebappDaoFactory wdf = vreq.getWebappDaoFactory();
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vreq.setAttribute("defaultNamespace", ""); //empty string triggers default new URI behavior
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vreq.setAttribute("stringDatatypeUriJson", MiscWebUtils.escape(XSD.xstring.toString()));
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%>
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<c:set var="vivoCore" value="http://vivoweb.org/ontology/core#" />
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<c:set var="rdfs" value="<%= VitroVocabulary.RDFS %>" />
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<c:set var="label" value="${rdfs}label" />
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<c:set var="foaf" value="http://xmlns.com/foaf/0.1/" />
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<c:set var="personClassUri" value="${foaf}Person" />
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<%-- Unlike other custom forms, this form does not allow edits of existing authors, so there are no
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SPARQL queries for existing values. --%>
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<v:jsonset var="n3ForTerminology">
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@prefix core: <${vivoCore}> .
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?subject ?predicate ?terminologyContextNode .
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?terminologyContextNode core:referencedTerm ?referencedTerm .
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?terminologyContextNode core:entryTerm ?entryTerm .
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?terminologyContextNode core:termLabel ?termLabel .
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</v:jsonset>
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<c:set var="returnPathAfterSubmit" value="/edit/editRequestDispatch.jsp?subjectUri=${subjectUri}&predicateUri=${predicateUri}" />
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<c:set var="submitSearchUrl" value="/UMLSTermsRetrieval"/>
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<c:url var="UMLSCUIURL" value="http://link.informatics.stonybrook.edu/umls/CUI/" />
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<c:set var="editjson" scope="request">
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{
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"formUrl" : "${formUrl}",
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"editKey" : "${editKey}",
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"urlPatternToReturnTo" : "${returnPathAfterSubmit}",
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"subject" : ["subject", "${subjectUriJson}" ],
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"predicate" : ["predicate", "${predicateUriJson}" ],
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"object" : ["terminologyContextNode", "${objectUriJson}", "URI" ],
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"n3required" : [ "${n3ForTerminology}" ],
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"n3optional" : [ ],
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"newResources" : { "terminologyContextNode" : "${defaultNamespace}" },
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"urisInScope" : { },
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"literalsInScope": { },
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"urisOnForm" : [ "referencedTerm" ],
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"literalsOnForm" : [ "entryTerm", "termLabel" ],
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"filesOnForm" : [ ],
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"sparqlForLiterals" : { },
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"sparqlForUris" : { },
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"sparqlForExistingLiterals" : { },
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"sparqlForExistingUris" : { },
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"fields" : {
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"referencedTerm" : {
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"newResource" : "false",
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"validators" : [ "nonempty" ],
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"optionsType" : "UNDEFINED", //UNSURE WHAT TO KEEP HERE
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"literalOptions" : [ ],
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"predicateUri" : "",
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"objectClassUri" : "",
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"rangeDatatypeUri" : "",
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"rangeLang" : "",
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"assertions" : [ "${n3ForTerminology}" ]
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},
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"entryTerm" : {
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"newResource" : "false",
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"validators" : [ "nonempty" ],
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"optionsType" : "UNDEFINED",
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"literalOptions" : [ ],
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"predicateUri" : "",
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"objectClassUri" : "",
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"rangeDatatypeUri" : "",
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"rangeLang" : "",
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"assertions" : [ "${n3ForTerminology}" ]
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},
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"termLabel" : {
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"newResource" : "false",
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"validators" : [ "nonempty" ],
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"optionsType" : "UNDEFINED",
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"literalOptions" : [ ],
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"predicateUri" : "",
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"objectClassUri" : "",
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"rangeDatatypeUri" : "",
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"rangeLang" : "",
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"assertions" : [ "${n3ForTerminology}" ]
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}
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}
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}
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</c:set>
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<%
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log.debug(request.getAttribute("editjson"));
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EditConfiguration editConfig = EditConfiguration.getConfigFromSession(session,request);
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if (editConfig == null) {
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editConfig = new EditConfiguration((String) request.getAttribute("editjson"));
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EditConfiguration.putConfigInSession(editConfig,session);
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}
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//Specific validators can be included here
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Model model = (Model) application.getAttribute("jenaOntModel");
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String objectUri = (String) request.getAttribute("objectUri");
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//for some reason we are comming from the add new and that is working
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//but we also come from the edit, and that is not working.
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editConfig.setObject(""); //this will force the edit config to always be an add, never an update
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editConfig.prepareForNonUpdate(model); // we're only adding new, not editing existing
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String subjectUri = vreq.getParameter("subjectUri");
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String predicateUri = vreq.getParameter("predicateUri");
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String vivoCore = "http://vivoweb.org/ontology/core#";
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//Individual infoResource = vreq.getWebappDaoFactory().getIndividualDao().getIndividualByURI(subjectUri);
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Individual subject = ((Individual) request.getAttribute("subject"));
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vreq.setAttribute("subjectName", subject.getName());
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//Get existing terminology annotations
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List<Individual> terminologyAnnotationNodes = subject.getRelatedIndividuals(predicateUri);
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List<String> customJs = new ArrayList<String>(Arrays.asList(JavaScript.JQUERY_UI.path(),
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JavaScript.CUSTOM_FORM_UTILS.path(),
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"/js/browserUtils.js",
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"/edit/forms/js/addTerminology.js"
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));
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request.setAttribute("customJs", customJs);
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//no custom css we know of yet
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List<String> customCss = new ArrayList<String>(Arrays.asList(Css.JQUERY_UI.path(),
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Css.CUSTOM_FORM.path(),
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"/edit/forms/css/addTerminology.css"
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));
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request.setAttribute("customCss", customCss);
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%>
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<c:set var="title" value="<em>${subjectName}</em>"/>
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<jsp:include page="${preForm}" />
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<%-- DO NOT CHANGE IDS, CLASSES, OR HTML STRUCTURE ON THIS PAGE WITHOUT UNDERSTANDING THE IMPACT ON THE JAVASCRIPT! --%>
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<h2>${title}</h2>
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<%@ include file="unsupportedBrowserMessage.jsp" %>
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<div class="noIE67">
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<h3>Manage Terminology Annotations</h3>
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<ul id="existingTerms" >
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<%
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int existingTermsCount = terminologyAnnotationNodes.size();
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%>
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<script type="text/javascript">
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var existingTermsData = [];
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</script>
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<%
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String termLabelUri = vivoCore + "termLabel";
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for ( Individual termNode : terminologyAnnotationNodes ) {
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request.setAttribute("termNodeUri", termNode.getURI());
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//Get label and type only as mirroring authorship where labels but no links for individuals incoldued
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DataPropertyStatement termLabelStatement = termNode.getDataPropertyStatement(termLabelUri);
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String termLabel = termLabelStatement.getData();
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request.setAttribute("termLabel", termLabel);
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//Possible to get referenced term using object property statement?
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%>
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<li class="existingTerm">
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<%-- span.author will be used in the next phase, when we display a message that the author has been
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removed. That text will replace the a.authorName, which will be removed. --%>
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<span class="term">
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<%-- This span is here to assign a width to. We can't assign directly to the a.authorName,
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for the case when it's followed by an em tag - we want the width to apply to the whole thing. --%>
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<span class="termWrapper">
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<span class="termLabel">
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${termLabel}</span>
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</span>
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<c:url var="deleteTermHref" value="/edit/primitiveDelete" />
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<a href="${deleteTermHref}" class="remove">Remove</a>
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</span>
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</li>
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<script type="text/javascript">
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existingTermsData.push({
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"termNodeUri": "${termNodeUri}",
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"termLabel": "${termLabel}"
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});
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</script>
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<%
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}
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%>
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</ul>
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<% if (existingTermsCount == 0) { %>
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<p>There are currently no terms specified.</p>
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<% } %>
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<div id="showAddForm">
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<v:input type="submit" value="Add Term" id="showAddFormButton" name="showAddFormButton" cancel="true" cancelLabel="Return" cancelUrl="/individual" />
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</div>
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<form id="addTerminologyForm" class="customForm" action="<c:url value="/edit/processTerminologyAnnotation"/>" >
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<h3>Search UMLS Terms</h3>
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<p class="inline"><v:input type="text" id="searchTerm" label="Search UMLS" cssClass="acSelector" size="35" />
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<input type="button" id="searchButton" name="searchButton" value="Search"/>
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</p>
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<input type="hidden" id="entryTerm" name="entryTerm" value="" /> <!-- Field value populated by JavaScript -->
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<input type="hidden" id="referencedTerm" name="referencedTerm" value=""/> <!-- Field value populated by JavaScript -->
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<input type="hidden" id="termLabel" name="termLabel" value="" /> <!-- Field value populated by JavaScript -->
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<input type="hidden" id="termType" name="termType" value="" /> <!-- Field value populated by JavaScript -->
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<div id="selectedTerm" name="selectedTerm" class="acSelection">
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<%-- RY maybe make this a label and input field. See what looks best. --%>
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<p class="inline">
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</p>
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<!-- Field value populated by JavaScript -->
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</div>
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<p class="submit"><v:input type="submit" id="submit" name="submit" value="Add Term" cancel="true" /></p>
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</form>
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</div>
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<script type="text/javascript">
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var customFormData = {
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dataServiceUrl: '${submitSearchUrl}',
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UMLSCUIURL: '${UMLSCUIURL}'
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};
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</script>
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<jsp:include page="${postForm}"/>
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