Reconciliation Service for Google Refine.
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elc2013
parent
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/*
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Copyright (c) 2011, Cornell University
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright notice,
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this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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* Neither the name of Cornell University nor the names of its contributors
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may be used to endorse or promote products derived from this software
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without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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package edu.cornell.mannlib.vitro.webapp.controller;
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import java.io.IOException;
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import java.io.PrintWriter;
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import java.io.Writer;
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import java.net.URLEncoder;
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import java.util.ArrayList;
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import java.util.Enumeration;
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import java.util.HashMap;
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import java.util.Iterator;
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import java.util.List;
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import java.util.ListIterator;
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import java.util.Map;
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import javax.servlet.ServletContext;
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import javax.servlet.ServletException;
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import javax.servlet.ServletOutputStream;
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import javax.servlet.http.HttpServletRequest;
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import javax.servlet.http.HttpServletResponse;
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import javax.servlet.http.HttpSession;
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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 org.apache.lucene.analysis.Analyzer;
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import org.apache.lucene.document.Document;
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import org.apache.lucene.document.Field;
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import org.apache.lucene.index.Term;
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import org.apache.lucene.queryParser.ParseException;
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import org.apache.lucene.queryParser.QueryParser;
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import org.apache.lucene.search.BooleanClause;
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import org.apache.lucene.search.BooleanQuery;
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import org.apache.lucene.search.IndexSearcher;
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import org.apache.lucene.search.Query;
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import org.apache.lucene.search.TermQuery;
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import org.apache.lucene.search.TopDocs;
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import org.apache.lucene.search.WildcardQuery;
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import org.json.JSONArray;
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import org.json.JSONException;
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import org.json.JSONObject;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.rdf.model.Literal;
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import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
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import edu.cornell.mannlib.vitro.webapp.beans.Individual;
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import edu.cornell.mannlib.vitro.webapp.beans.VClass;
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import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
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import edu.cornell.mannlib.vitro.webapp.controller.TabEntitiesController.PageRecord;
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import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
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import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
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import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VClassGroupCache;
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import edu.cornell.mannlib.vitro.webapp.edit.n3editing.EditConfiguration;
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import edu.cornell.mannlib.vitro.webapp.edit.n3editing.SelectListGenerator;
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import edu.cornell.mannlib.vitro.webapp.flags.PortalFlag;
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import edu.cornell.mannlib.vitro.webapp.search.SearchException;
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import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
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import edu.cornell.mannlib.vitro.webapp.search.lucene.Entity2LuceneDoc;
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import edu.cornell.mannlib.vitro.webapp.search.lucene.LuceneIndexFactory;
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import edu.cornell.mannlib.vitro.webapp.search.lucene.LuceneSetup;
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import edu.cornell.mannlib.vitro.webapp.search.lucene.Entity2LuceneDoc.VitroLuceneTermNames;
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import edu.cornell.mannlib.vitro.webapp.web.templatemodels.VClassGroupTemplateModel;
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import edu.cornell.mannlib.vitro.webapp.web.templatemodels.VClassTemplateModel;
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import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.IndividualTemplateModel;
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/**
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* This servlet is for servicing JSON requests for Google Refine's
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* Reconciliation Service.
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*
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* @author Eliza Chan (elc2013@med.cornell.edu)
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*
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*/
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public class JSONReconcileServlet extends VitroHttpServlet {
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private static String VIVO_NAMESPACE = "http://vivo.med.cornell.edu/individual/";
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private static String QUERY_PARAMETER_NAME = "term";
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public static final int MAX_QUERY_LENGTH = 500;
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private static final Log log = LogFactory.getLog(JSONReconcileServlet.class.getName());
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@Override
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protected void doPost(HttpServletRequest req, HttpServletResponse resp)
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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)
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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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if (vreq.getParameter("query") != null
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|| vreq.getParameter("queries") != null) {
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JSONObject qJson = getResult(vreq, req, resp);
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System.out.println("result: " + qJson.toString());
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String responseStr = (vreq.getParameter("callback") == null) ? qJson
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.toString() : vreq.getParameter("callback") + "("
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+ qJson.toString() + ")";
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resp.setContentType("application/json");
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ServletOutputStream out = resp.getOutputStream();
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out.print(responseStr);
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} else { // metadata
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JSONObject metaJson = getMetadata(req, resp);
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String callbackStr = (vreq.getParameter("callback") == null) ? ""
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: vreq.getParameter("callback");
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resp.setContentType("application/json");
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ServletOutputStream out = resp.getOutputStream();
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out.print(callbackStr + "(" + metaJson.toString() + ")");
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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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private JSONObject getResult(VitroRequest vreq, HttpServletRequest req,
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HttpServletResponse resp) throws ServletException {
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HashMap<String, JSONObject> searchWithTypeMap = new HashMap<String, JSONObject>();
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HashMap<String, JSONObject> searchNoTypeMap = new HashMap<String, JSONObject>();
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ArrayList<String> queries = new ArrayList<String>();
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Object qObj = vreq.getParameter("queries");
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if (qObj == null) {
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qObj = vreq.getParameter("query");
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}
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if (qObj != null && qObj instanceof String) {
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// e.g.
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// {"q0":{"query":"Cathleen","type":"http://xmlns.com/foaf/0.1/Person","type_strict":"should"},
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// "q1":{"query":"Geoffrey","type":"http://xmlns.com/foaf/0.1/Person","type_strict":"should"},
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// "q2":{"query":"Dina","type":"http://xmlns.com/foaf/0.1/Person","type_strict":"should"}}
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String qStr = (String) qObj;
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queries.add(qStr);
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System.out.println();
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System.out.println("strArr: " + qStr + "\n");
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}
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try {
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for (int i = 0; i < queries.size(); i++) {
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String queryStr = (String) queries.get(i);
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JSONObject json = new JSONObject(queryStr);
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if (json.has("query")) { // single query
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if (json.has("type")) {
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searchWithTypeMap.put("query", json);
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} else {
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// user did not specify a type
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searchNoTypeMap.put("query", json);
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}
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} else { // multiple queries
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for (Iterator<String> iter = json.keys(); iter.hasNext();) {
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ArrayList<JSONObject> jsonList = new ArrayList<JSONObject>();
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String key = (String) iter.next();
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Object obj = json.get(key);
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JSONObject jsonLvl2 = (JSONObject) obj;
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if (jsonLvl2.has("query")) {
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if (jsonLvl2.has("type")) {
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searchWithTypeMap.put(key, jsonLvl2);
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} else {
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// user did not specify a type
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// System.out.println("before search: " + jsonLvl2.getString("query"));
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searchNoTypeMap.put(key, jsonLvl2);
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}
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}
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}
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}
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}
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} catch (JSONException ex) {
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System.err.println("JSONReconcileServlet JSONException: " + ex);
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throw new ServletException("JSONReconcileServlet JSONException: "
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+ ex);
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}
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// Run index search
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JSONObject qJson = null;
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if (searchWithTypeMap.size() > 0) {
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qJson = runSearch(searchWithTypeMap, vreq);
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} else {
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qJson = runSearch(searchNoTypeMap, vreq);
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}
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return qJson;
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}
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/**
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* Returns a default JSON response.
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*
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* @param req
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* @param resp
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* @return
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* @throws ServletException
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*/
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private JSONObject getMetadata(HttpServletRequest req,
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HttpServletResponse resp) throws ServletException {
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JSONObject json = new JSONObject();
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try {
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json.put("name", "VIVO Reconciliation Service");
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json.put("identifierSpace", this.VIVO_NAMESPACE);
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json.put("schemaSpace", this.VIVO_NAMESPACE);
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JSONObject viewJson = new JSONObject();
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StringBuffer urlBuf = new StringBuffer();
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urlBuf.append("http://" + req.getServerName());
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if (req.getServerPort() == 8080) {
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urlBuf.append(":" + req.getServerPort());
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}
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if (req.getContextPath() != null) {
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urlBuf.append(req.getContextPath());
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}
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viewJson.put("url", urlBuf.toString() + "/individual?uri={{id}}");
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json.put("view", viewJson);
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HashMap<String, String> typeMap = new HashMap<String, String>();
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typeMap.put("http://vivoweb.org/ontology/core#Course", "Course");
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typeMap.put("http://vivoweb.org/ontology/core#Grant", "Grant");
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typeMap.put("http://vivoweb.org/ontology/core#GeographicRegion",
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"Location");
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typeMap.put("http://xmlns.com/foaf/0.1/Organization",
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"Organization");
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typeMap.put("http://xmlns.com/foaf/0.1/Person", "Person");
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typeMap.put("http://purl.org/ontology/bibo/Article", "Publication");
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JSONArray defaultTypesJsonArr = new JSONArray();
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for (Map.Entry<String, String> entry : typeMap.entrySet()) {
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String id = entry.getKey();
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String name = entry.getValue();
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JSONObject defaultTypesJson = new JSONObject();
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defaultTypesJson.put("id", id);
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defaultTypesJson.put("name", name);
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defaultTypesJsonArr.put(defaultTypesJson);
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}
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json.put("defaultTypes", defaultTypesJsonArr);
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} catch (JSONException ex) {
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throw new ServletException(
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"JSONReconcileServlet: Could not create metadata: " + ex);
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}
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return json;
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}
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private JSONObject runSearch(HashMap<String, JSONObject> currMap,
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VitroRequest vreq) throws ServletException {
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JSONObject qJson = new JSONObject();
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try {
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PortalFlag portalFlag = vreq.getPortalFlag();
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Analyzer analyzer = getAnalyzer(getServletContext());
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IndexSearcher searcherForRequest = LuceneIndexFactory
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.getIndexSearcher(getServletContext());
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for (Map.Entry<String, JSONObject> entry : currMap.entrySet()) {
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JSONObject resultAllJson = new JSONObject();
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String key = entry.getKey();
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JSONObject json = (JSONObject) entry.getValue();
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String queryVal = json.getString("query");
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// continue with properties list
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String searchType = null;
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int limit = 3; // default
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String typeStrict = "should"; // default
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ArrayList<String[]> propertiesList = new ArrayList<String[]>();
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if (json.has("type")) {
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searchType = json.getString("type");
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}
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if (json.has("limit")) {
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limit = json.getInt("limit");
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}
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if (json.has("type_strict")) { // Not sure what this variable
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// represents. Skip for now.
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typeStrict = json.getString("type_strict");
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}
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if (json.has("properties")) {
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JSONArray properties = json.getJSONArray("properties");
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for (int i = 0; i < properties.length(); i++) {
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String[] pvPair = new String[2];
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JSONObject jsonProperty = properties.getJSONObject(i);
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String pid = jsonProperty.getString("pid");
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String v = jsonProperty.getString("v");
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pvPair[0] = pid;
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pvPair[1] = v;
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propertiesList.add(pvPair);
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}
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}
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// begin search
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// System.out.println("queryVal: " + queryVal);
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JSONArray resultJsonArr = new JSONArray();
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Query query = getReconcileQuery(vreq, portalFlag, analyzer,
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queryVal, searchType, propertiesList);
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TopDocs topDocs = searcherForRequest.search(query, null, limit);
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if (topDocs != null && topDocs.scoreDocs != null) {
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int hitsLength = topDocs.scoreDocs.length;
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//System.out.println("hitsLength: " + hitsLength);
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if (hitsLength > 0) {
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for (int i = 0; i < topDocs.scoreDocs.length; i++) {
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JSONObject resultJson = new JSONObject();
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float score = topDocs.scoreDocs[i].score;
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resultJson.put("score", score);
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Document doc = searcherForRequest
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.doc(topDocs.scoreDocs[i].doc);
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String uri = doc.get(Entity2LuceneDoc.term.URI);
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IndividualDao iDao = vreq.getWebappDaoFactory()
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.getIndividualDao();
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Individual ind = iDao.getIndividualByURI(uri);
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if (ind != null) {
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String name = ind.getName();
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resultJson.put("id", uri);
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resultJson.put("name", name);
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}
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List fields = doc.getFields();
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JSONArray typesJsonArr = new JSONArray();
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for (int j = 0; j < fields.size(); j++) {
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Field field = (Field) fields.get(j);
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String fieldName = field.name();
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if ("type".equals(fieldName)) {
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// e.g.
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// http://vivoweb.org/ontology/core#FacultyMember
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||||||
|
String type = field.stringValue();
|
||||||
|
int lastIndex2 = type.lastIndexOf('/') + 1;
|
||||||
|
String typeName = type
|
||||||
|
.substring(lastIndex2);
|
||||||
|
typeName = typeName.replace("#", ":");
|
||||||
|
JSONObject typesJson = new JSONObject();
|
||||||
|
typesJson.put("id", type);
|
||||||
|
typesJson.put("name", typeName);
|
||||||
|
typesJsonArr.put(typesJson);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
resultJson.put("type", typesJsonArr);
|
||||||
|
resultJson.put("match", "false");
|
||||||
|
resultJsonArr.put(resultJson);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
resultAllJson.put("result", resultJsonArr);
|
||||||
|
qJson.put(key, resultAllJson);
|
||||||
|
}
|
||||||
|
|
||||||
|
} catch (JSONException ex) {
|
||||||
|
System.err.println("JSONReconcileServlet JSONException: " + ex);
|
||||||
|
throw new ServletException("JSONReconcileServlet JSONException: "
|
||||||
|
+ ex);
|
||||||
|
} catch (SearchException ex) {
|
||||||
|
System.err.println("JSONReconcileServlet SearchException: " + ex);
|
||||||
|
throw new ServletException("JSONReconcileServlet SearchException: "
|
||||||
|
+ ex);
|
||||||
|
} catch (IOException ex) {
|
||||||
|
System.err.println("JSONReconcileServlet IOException: " + ex);
|
||||||
|
throw new ServletException("JSONReconcileServlet IOException: "
|
||||||
|
+ ex);
|
||||||
|
}
|
||||||
|
|
||||||
|
return qJson;
|
||||||
|
}
|
||||||
|
|
||||||
|
private Analyzer getAnalyzer(ServletContext servletContext)
|
||||||
|
throws SearchException {
|
||||||
|
Object obj = servletContext.getAttribute(LuceneSetup.ANALYZER);
|
||||||
|
if (obj == null || !(obj instanceof Analyzer))
|
||||||
|
throw new SearchException("Could not get anlyzer");
|
||||||
|
else
|
||||||
|
return (Analyzer) obj;
|
||||||
|
}
|
||||||
|
|
||||||
|
private Query makeReconcileNameQuery(String querystr, Analyzer analyzer, HttpServletRequest request) {
|
||||||
|
|
||||||
|
/* Original code
|
||||||
|
String tokenizeParam = (String) request.getParameter("tokenize");
|
||||||
|
boolean tokenize = "true".equals(tokenizeParam);
|
||||||
|
|
||||||
|
// Note: Stemming is only relevant if we are tokenizing: an untokenized name
|
||||||
|
// query will not be stemmed. So we don't look at the stem parameter until we get to
|
||||||
|
// makeTokenizedNameQuery().
|
||||||
|
if (tokenize) {
|
||||||
|
return makeTokenizedNameQuery(querystr, analyzer, request);
|
||||||
|
} else {
|
||||||
|
return makeUntokenizedNameQuery(querystr);
|
||||||
|
}
|
||||||
|
*/
|
||||||
|
|
||||||
|
// modified code for reconciliation service
|
||||||
|
request.setAttribute("stem", true);
|
||||||
|
return makeTokenizedNameQuery(querystr, analyzer, request);
|
||||||
|
}
|
||||||
|
|
||||||
|
private Query makeTokenizedNameQuery(String querystr, Analyzer analyzer, HttpServletRequest request) {
|
||||||
|
|
||||||
|
String stemParam = (String) request.getParameter("stem");
|
||||||
|
boolean stem = "true".equals(stemParam);
|
||||||
|
String termName = stem ? VitroLuceneTermNames.NAME : VitroLuceneTermNames.NAMEUNSTEMMED;
|
||||||
|
|
||||||
|
BooleanQuery boolQuery = new BooleanQuery();
|
||||||
|
|
||||||
|
// Use the query parser to analyze the search term the same way the indexed text was analyzed.
|
||||||
|
// For example, text is lowercased, and function words are stripped out.
|
||||||
|
QueryParser parser = getQueryParser(termName, analyzer);
|
||||||
|
|
||||||
|
// The wildcard query doesn't play well with stemming. Query term name:tales* doesn't match
|
||||||
|
// "tales", which is indexed as "tale", while query term name:tales does. Obviously we need
|
||||||
|
// the wildcard for name:tal*, so the only way to get them all to match is use a disjunction
|
||||||
|
// of wildcard and non-wildcard queries. The query will look have only an implicit disjunction
|
||||||
|
// operator: e.g., +(name:tales name:tales*)
|
||||||
|
try {
|
||||||
|
log.debug("Adding non-wildcard query for " + querystr);
|
||||||
|
Query query = parser.parse(querystr);
|
||||||
|
boolQuery.add(query, BooleanClause.Occur.SHOULD);
|
||||||
|
|
||||||
|
// Prevent ParseException here when adding * after a space.
|
||||||
|
// If there's a space at the end, we don't need the wildcard query.
|
||||||
|
if (! querystr.endsWith(" ")) {
|
||||||
|
log.debug("Adding wildcard query for " + querystr);
|
||||||
|
Query wildcardQuery = parser.parse(querystr + "*");
|
||||||
|
boolQuery.add(wildcardQuery, BooleanClause.Occur.SHOULD);
|
||||||
|
}
|
||||||
|
|
||||||
|
log.debug("Name query is: " + boolQuery.toString());
|
||||||
|
} catch (ParseException e) {
|
||||||
|
log.warn(e, e);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
return boolQuery;
|
||||||
|
}
|
||||||
|
|
||||||
|
private Query makeUntokenizedNameQuery(String querystr) {
|
||||||
|
|
||||||
|
querystr = querystr.toLowerCase();
|
||||||
|
String termName = VitroLuceneTermNames.NAMELOWERCASE;
|
||||||
|
BooleanQuery query = new BooleanQuery();
|
||||||
|
log.debug("Adding wildcard query on unanalyzed name");
|
||||||
|
query.add(
|
||||||
|
new WildcardQuery(new Term(termName, querystr + "*")),
|
||||||
|
BooleanClause.Occur.MUST);
|
||||||
|
|
||||||
|
return query;
|
||||||
|
}
|
||||||
|
|
||||||
|
private QueryParser getQueryParser(String searchField, Analyzer analyzer){
|
||||||
|
// searchField indicates which field to search against when there is no term
|
||||||
|
// indicated in the query string.
|
||||||
|
// The analyzer is needed so that we use the same analyzer on the search queries as
|
||||||
|
// was used on the text that was indexed.
|
||||||
|
QueryParser qp = new QueryParser(searchField,analyzer);
|
||||||
|
//this sets the query parser to AND all of the query terms it finds.
|
||||||
|
qp.setDefaultOperator(QueryParser.AND_OPERATOR);
|
||||||
|
return qp;
|
||||||
|
}
|
||||||
|
|
||||||
|
private Query getReconcileQuery(VitroRequest request, PortalFlag portalState,
|
||||||
|
Analyzer analyzer, String querystr, String typeParam, ArrayList<String[]> propertiesList) throws SearchException{
|
||||||
|
|
||||||
|
// System.out.println("querystr: " + querystr);
|
||||||
|
Query query = null;
|
||||||
|
try {
|
||||||
|
if( querystr == null){
|
||||||
|
log.error("There was no Parameter '"+ QUERY_PARAMETER_NAME
|
||||||
|
+"' in the request.");
|
||||||
|
return null;
|
||||||
|
}else if( querystr.length() > MAX_QUERY_LENGTH ){
|
||||||
|
log.debug("The search was too long. The maximum " +
|
||||||
|
"query length is " + MAX_QUERY_LENGTH );
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
query = makeReconcileNameQuery(querystr, analyzer, request);
|
||||||
|
|
||||||
|
|
||||||
|
// filter by type
|
||||||
|
if (typeParam != null) {
|
||||||
|
System.out.println("typeParam: " + typeParam);
|
||||||
|
BooleanQuery boolQuery = new BooleanQuery();
|
||||||
|
boolQuery.add( new TermQuery(
|
||||||
|
new Term(VitroLuceneTermNames.RDFTYPE,
|
||||||
|
typeParam)),
|
||||||
|
BooleanClause.Occur.MUST);
|
||||||
|
boolQuery.add(query, BooleanClause.Occur.MUST);
|
||||||
|
query = boolQuery;
|
||||||
|
}
|
||||||
|
|
||||||
|
// if propertiesList has elements, add extra queries to query
|
||||||
|
Iterator<String[]> it = propertiesList.iterator();
|
||||||
|
while (it.hasNext()) {
|
||||||
|
String[] pvPair = it.next();
|
||||||
|
System.out.println("property val: " + pvPair[0] + " " + pvPair[1]);
|
||||||
|
Query extraQuery = makeReconcileNameQuery(pvPair[1], analyzer, request);
|
||||||
|
if (!"".equals(pvPair[0]) && pvPair[0] != null) {
|
||||||
|
BooleanQuery boolQuery = new BooleanQuery();
|
||||||
|
boolQuery.add(new TermQuery(new Term(
|
||||||
|
VitroLuceneTermNames.RDFTYPE, pvPair[0])),
|
||||||
|
BooleanClause.Occur.MUST);
|
||||||
|
boolQuery.add(extraQuery, BooleanClause.Occur.MUST);
|
||||||
|
extraQuery = boolQuery;
|
||||||
|
}
|
||||||
|
((BooleanQuery)query).add(extraQuery, BooleanClause.Occur.MUST);
|
||||||
|
}
|
||||||
|
} catch (Exception ex) {
|
||||||
|
throw new SearchException(ex.getMessage());
|
||||||
|
}
|
||||||
|
|
||||||
|
return query;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
Loading…
Add table
Add a link
Reference in a new issue