Adding changes and code for terminology annotation support and integration of UMLS vocabulary
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9 changed files with 1005 additions and 1 deletions
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.vitro.webapp.servlet;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.net.URL;
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import java.net.URLEncoder;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.List;
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import java.util.ArrayList;
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import javax.servlet.ServletOutputStream;
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import javax.servlet.ServletException;
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import javax.servlet.http.HttpServletRequest;
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import javax.servlet.http.HttpServletResponse;
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import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.EditConfiguration;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
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import edu.cornell.mannlib.vitro.webapp.beans.Individual;
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import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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import freemarker.ext.beans.BeansWrapper;
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import freemarker.template.DefaultObjectWrapper;
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import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.Field;
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import javax.servlet.RequestDispatcher;
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public class ProcessTerminologyController extends VitroHttpServlet {
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private static final long serialVersionUID = 1L;
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private static final Log log = LogFactory.getLog(ProcessTerminologyController.class);
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private static final String submissionUrl = "/edit/processRdfForm2.jsp";
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@Override
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protected void doPost(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
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super.doPost(req, resp);
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}
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@Override
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protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
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super.doGet(req, resp);
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VitroRequest vreq = new VitroRequest(req);
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try{
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EditConfiguration editConfig = EditConfiguration.getConfigFromSession(req.getSession(), req);
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//For query parameters, check whether CUI
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String[] termsArray = new String[1];
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String referencedTerms = vreq.getParameter("referencedTerm");
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if(referencedTerms.indexOf(",") != -1) {
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termsArray = referencedTerms.split(",");
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}
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int numberTerms = termsArray.length;
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//if multiple values then need to process this differently by adding additional
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//fields, assertions, etc. as well as changing the URL slightly
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String url = "/edit/processRdfForm2.jsp?" + vreq.getQueryString();
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if(numberTerms > 1) {
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//Add new resources, i.e. the additional terminology context nodes
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addNewResources(editConfig, vreq, numberTerms);
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//Add N3Required
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addN3Required(editConfig,vreq, numberTerms);
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//Add URIs on Form and Add Literals On Form
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addLiteralsAndUrisOnForm(editConfig, vreq, numberTerms);
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//Add fields
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addFields(editConfig, vreq, numberTerms);
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//Generate new url which will map input fields to value
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url = generateUrl(editConfig, vreq);
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}
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RequestDispatcher dispatcher = req.getRequestDispatcher(url);
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dispatcher.forward(req, resp);
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} catch(Exception ex) {
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log.error("error occurred in servlet", ex);
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}
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}
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private String generateUrl(EditConfiguration editConfig, VitroRequest vreq) {
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//Get original url and query string
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String newUrl = "/edit/processRdfForm2.jsp?" + vreq.getQueryString();
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//Iterate through the terms and include appropriate values
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Map <String,String[]> queryParameters = null;
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queryParameters = vreq.getParameterMap();
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//Use same query parameters to forward
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String termParam = vreq.getParameter("referencedTerm");
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String labelParam = vreq.getParameter("termLabel");
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String typeParam = vreq.getParameter("termType");
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if(!labelParam.contains(",")){
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log.error("Multiple labels are not being sent back, this is an error");
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}
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if(!typeParam.contains(",")) {
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log.error("Multiple types are not being sent back, this is an error");
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}
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String[] termsArray = termParam.split(",");
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String[] termLabels = labelParam.split(",");
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String[] termTypes = typeParam.split(",");
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String entryTerm = vreq.getParameter("entryTerm");
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int numberParameters = termsArray.length;
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int index;
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String referencedBase = "referencedTerm";
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String labelBase = "termLabel";
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String termBase = "termType";
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//Should already include entry term so no need to include here
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//newUrl += "&entryTerm=" + URLEncoder.encode(entryTerm);
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//Add entry
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for(index = 1; index <= numberParameters; index++) {
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String referencedInputName = referencedBase + index;
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String termLabelInputName = labelBase + index;
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String termTypeInputName =termBase + index;
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//array is set to start at 0, not 1
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String referencedTerm = termsArray[index - 1];
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String termLabel = termLabels[index - 1];
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String termType = termTypes[index - 1];
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newUrl += "&" + referencedInputName + "=" + URLEncoder.encode(referencedTerm);
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newUrl += "&" + termLabelInputName + "=" + URLEncoder.encode(termLabel);
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newUrl += "&" + termTypeInputName + "=" + URLEncoder.encode(termType);
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}
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return newUrl;
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}
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private void addNewResources(EditConfiguration editConfig, VitroRequest vreq, int numberTerms) {
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Map<String, String> newResources = new HashMap<String, String>();
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//Based on number of terms, add new
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int n;
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String defaultNamespace = "";
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String base = "terminologyContextNode";
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for(n = 1; n <= numberTerms; n++) {
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String newNode = base + n;
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newResources.put(newNode, defaultNamespace);
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}
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//TODO: Check if below is required as this is a reference
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editConfig.setNewResources(newResources);
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}
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/*
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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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private void addFields(EditConfiguration editConfig, VitroRequest vreq, int numberTerms) {
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Map<String, Field> fieldMap = new HashMap<String, Field>();
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int index;
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String referencedBase = "referencedTerm";
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String entryBase = "entryTerm";
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String labelBase = "termLabel";
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//Entry only needs to be added once
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fieldMap.put(entryBase, generateField(editConfig));
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//First one already included so add new ones here
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for(index = 1; index <= numberTerms; index++) {
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int suffix = index;
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String referencedTerm = referencedBase + suffix;
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String label = labelBase + suffix;
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//need to add termType
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//Generate Field for each
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fieldMap.put(referencedTerm, generateField(editConfig));
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fieldMap.put(label, generateField(editConfig));
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//termType would also go in here
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}
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editConfig.setFields(fieldMap);
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}
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/*
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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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private Field generateField(EditConfiguration editConfig) {
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List<String> n3Required = editConfig.getN3Required();
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Field field = new Field();
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field.setNewResource(false);
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List<String> validators = new ArrayList<String>();
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validators.add("nonempty");
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field.setValidators(validators);
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field.setOptionsType("UNDEFINED");
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field.setLiteralOptions(new ArrayList<List<String>>());
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field.setPredicateUri("");
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field.setObjectClassUri("");
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field.setRangeDatatypeUri("");
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field.setRangeLang("");
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field.setAssertions(n3Required);
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return field;
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}
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//Original uris and literals included:
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/*
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* "urisOnForm" : [ "referencedTerm" ],
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"literalsOnForm" : [ "entryTerm", "termLabel" ],
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*/
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private void addLiteralsAndUrisOnForm(EditConfiguration editConfig,
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VitroRequest vreq, int numberTerms) {
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List<String> urisOnForm = new ArrayList<String>();
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List<String> literalsOnForm = new ArrayList<String>();
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int index;
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String referencedBase = "referencedTerm";
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String entryBase = "entryTerm";
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String labelBase = "termLabel";
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//entry term needs to be added only once
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literalsOnForm.add(entryBase);
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//First one already included so add new ones here
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for(index = 1; index <= numberTerms; index++) {
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int suffix = index;
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String referencedTerm = referencedBase + suffix;
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String label = labelBase + suffix;
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urisOnForm.add(referencedTerm);
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literalsOnForm.add(label);
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}
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editConfig.setUrisOnform(urisOnForm);
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editConfig.setLiteralsOnForm(literalsOnForm);
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}
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//original n3 required is of this format
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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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*/
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private void addN3Required(EditConfiguration editConfig, VitroRequest vreq, int numberTerms) {
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//List<String> n3Required = editConfig.getN3Required();
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List<String> n3Required = new ArrayList<String>();
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int index;
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String nodeBase = "?terminologyContextNode";
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String referencedBase = "?referencedTerm";
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//there's only one entry term in this case
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String entryBase = "?entryTerm";
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String labelBase = "?termLabel";
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String prefixStr = "@prefix core: <http://vivoweb.org/ontology/core#> .";
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//First one already included so add new ones here
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for(index = 1; index <= numberTerms; index++) {
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int suffix = index;
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String node = nodeBase + suffix;
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String referencedTerm = referencedBase + suffix;
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String label = labelBase + suffix;
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String n3String = prefixStr;
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n3String += "?subject ?predicate " + node + " . " +
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node + " core:entryTerm " + entryBase + " . " +
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node + " core:termLabel " + label + " . " +
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node + " core:referencedTerm " + referencedTerm + " . ";
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n3Required.add(n3String);
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}
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editConfig.setN3Required(n3Required);
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}
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}
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.vitro.webapp.servlet;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.net.URL;
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import java.net.URLEncoder;
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import java.util.HashMap;
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import java.util.Map;
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import javax.servlet.ServletOutputStream;
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import javax.servlet.ServletException;
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import javax.servlet.http.HttpServletRequest;
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import javax.servlet.http.HttpServletResponse;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
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import edu.cornell.mannlib.vitro.webapp.beans.Individual;
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import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServlet;
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import edu.cornell.mannlib.vitro.webapp.controller.freemarker.IndividualController;
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import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ExceptionResponseValues;
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import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
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import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
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import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.IndividualTemplateModel;
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import freemarker.ext.beans.BeansWrapper;
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import freemarker.template.DefaultObjectWrapper;
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public class UMLSTerminologyAnnotation extends VitroHttpServlet {
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private static final long serialVersionUID = 1L;
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private static final Log log = LogFactory.getLog(UMLSTerminologyAnnotation.class);
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private static final String submissionUrl = "http://link.informatics.stonybrook.edu/MeaningLookup/MlServiceServlet?";
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@Override
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protected void doPost(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
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super.doPost(req, resp);
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}
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@Override
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protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
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super.doGet(req, resp);
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VitroRequest vreq = new VitroRequest(req);
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try{
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//Get parameter
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String entryText = vreq.getParameter("searchTerm");
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System.out.println("Entry text is " + entryText);
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//TODO: Find a non-deprecated mechanism to do so
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String dataUrl = submissionUrl + "textToProcess=" + URLEncoder.encode(entryText) + "&format=json";
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try{
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ServletOutputStream sos = resp.getOutputStream();
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resp.setCharacterEncoding("UTF-8");
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resp.setContentType("application/json;charset=UTF-8");
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URL rss = new URL(dataUrl);
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BufferedReader in = new BufferedReader(new InputStreamReader(rss.openStream()));
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String inputLine;
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while((inputLine = in.readLine()) != null) {
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sos.println(inputLine);
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}
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in.close();
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} catch(Exception ex) {
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log.error("error occurred in servlet", ex);
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}
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}catch(Exception ex){
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log.warn(ex,ex);
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}
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}
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}
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