updates for concept addition and integration of umls/agrovoc search services
This commit is contained in:
hjkhjk54
parent
943315a9c6
commit
ce84967d01
28 changed files with 3472 additions and 71 deletions
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package edu.cornell.mannlib.semservices.service;
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import java.util.List;
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import edu.cornell.mannlib.semservices.bo.Concept;
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public interface ExternalConceptService {
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// this is the only method that needs to be exposed
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List<Concept> processResults(String term);
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}
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package edu.cornell.mannlib.semservices.service.impl;
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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.io.StringWriter;
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import java.net.MalformedURLException;
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import java.net.URL;
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import java.rmi.RemoteException;
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import java.util.ArrayList;
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import java.util.List;
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import javax.xml.parsers.ParserConfigurationException;
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import javax.xml.rpc.ServiceException;
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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.fao.gilw.aims.webservices.AgrovocWS;
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import org.fao.gilw.aims.webservices.AgrovocWSServiceLocator;
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import org.w3c.dom.Attr;
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import org.w3c.dom.Document;
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import org.w3c.dom.NamedNodeMap;
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import org.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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import org.xml.sax.SAXException;
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import edu.cornell.mannlib.semservices.bo.Concept;
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import edu.cornell.mannlib.semservices.service.ExternalConceptService;
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import edu.cornell.mannlib.semservices.util.XMLUtils;
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public class AgrovocService implements ExternalConceptService {
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protected final Log logger = LogFactory.getLog(getClass());
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private java.lang.String AgrovocWS_address = "http://www.fao.org/webservices/AgrovocWS";
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public List<Concept> processResults(String term) {
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List<Concept> conceptList = new ArrayList<Concept>();
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String termcode;
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try {
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termcode = getTermcodeByTerm(term);
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} catch (Exception e1) {
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logger.error("Could not get termcode from service", e1);
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return null;
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}
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String format = "SKOS";
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// if the termcode is null it means that either the service is not responding
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// or there was not a match for the string
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//System.out.println("Got termcode: "+termcode);
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String results = getConceptInfoByTermcodeXML(termcode, format);
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//XMLUtils.prettyPrint(results);
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try {
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Document doc = XMLUtils.parse(results);
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String prefLabelQuery = "child::*[@xml:lang='EN']";
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NodeList nodes = doc.getElementsByTagName("skos:Concept");
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//System.out.println("Found this many nodes: "+ nodes.getLength());
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for (int i=0; i < nodes.getLength(); i++) {
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Node node = nodes.item(i);
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//XMLUtils.serializeNode(node); System.out.println();
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Concept concept = new Concept();
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concept.setDefinedBy("Agrovoc");
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concept.setConceptId(termcode);
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NamedNodeMap attrs = node.getAttributes();
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Attr idAttr = (Attr) attrs.getNamedItem("rdf:about");
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String conceptUri = idAttr.getTextContent();
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concept.setUri(conceptUri);
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Node prefLabelNode = XMLUtils.getNodeWithXpath(node, prefLabelQuery);
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if (prefLabelNode != null) {
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String prefLabel = prefLabelNode.getTextContent();
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concept.setLabel(prefLabel);
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}
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conceptList.add(concept);
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}
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} catch (IOException e) {
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e.printStackTrace();
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} catch (SAXException e) {
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e.printStackTrace();
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} catch (ParserConfigurationException e) {
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e.printStackTrace();
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}
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return conceptList;
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//JSONObject jsonObject = null;
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//jsonObject = BeanToJsonSerializer.serializeToJsonObject(conceptList);
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//return jsonObject.toString();
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}
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protected String getAgrovocLanguages() {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getAgrovocLanguages();
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} catch (ServiceException e) {
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String getTermcodeByTerm(String term) throws Exception {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getTermcodeByTerm(term);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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throw e;
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} catch (RemoteException e) {
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logger.error("remote exception", e);
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throw e;
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} catch (MalformedURLException e) {
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logger.error("malformed URL exception", e);
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throw e;
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}
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return result;
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}
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protected String getTermcodeByTermXML(String term, String format) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getTermcodeByTermXML(term, format);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String getTermByLanguage(int termcode, String language) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getTermByLanguage(termcode, language);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String getTermByLanguageXML(int termcode, String language, String format) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getTermByLanguageXML(termcode, language, format);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String getTermsListByLanguage2(String termcodes, String language, String sep) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getTermsListByLanguage2(termcodes, language, sep);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String getTermsListByLanguageXML(String termcodes, String language, String format) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getTermsListByLanguageXML(termcodes, language, format);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String getAllLabelsByTermcode2(int termcode, String sep) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getAllLabelsByTermcode2(termcode, sep);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String getAllLabelsByTermcodeXML(int termcode, String format) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getAllLabelsByTermcodeXML(termcode, format);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String simpleSearchByMode2(String term, String mode, String sep ) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.simpleSearchByMode2(term, mode, sep);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String simpleSearchByModeXML(String term, String mode, String format) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.simpleSearchByModeXML(term, mode, format);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String searchByTerm2(String term, String sep) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.searchByTerm2(term, sep);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String searchByTermXML(String term, String format) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.searchByTermXML(term, format);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String searchCategoryByMode(String term, String lang, String schemeid, String mode, String sep) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.searchCategoryByMode(term, lang, schemeid, mode, sep);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String searchCategoryByModeXML(String term, String mode, String schemeid, String lang, String format) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.searchCategoryByModeXML(term, mode, schemeid, lang, format);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String[] getConceptInfoByTermcode(String termcode) {
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String result[] = null;
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getConceptInfoByTermcode(termcode);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String getConceptInfoByTermcodeXML(String termcode, String format) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getConceptInfoByTermcodeXML(termcode, format);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String[] getDefinitions(int termcode, String lang) {
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String[] result = null;
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getDefinitions(termcode, lang);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String getDefinitionsXML(int termcode, String lang, String format) {
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String result = null;
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getDefinitionsXML(termcode, lang, format);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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e.printStackTrace();
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} catch (RemoteException e) {
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e.printStackTrace();
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} catch (MalformedURLException e) {
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e.printStackTrace();
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}
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return result;
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}
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protected String getTermExpansion(String aQuery, String langugage) {
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String result = new String();
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AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
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try {
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URL url = new URL(AgrovocWS_address);
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AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
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result = agrovoc_service.getTermExpansion(aQuery, langugage);
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} catch (ServiceException e) {
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logger.error("service exception", e);
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||||
e.printStackTrace();
|
||||
} catch (RemoteException e) {
|
||||
e.printStackTrace();
|
||||
} catch (MalformedURLException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
protected String getWsdl() {
|
||||
String result = new String();
|
||||
try {
|
||||
|
||||
StringWriter sw = new StringWriter();
|
||||
URL rss = new URL(AgrovocWS_address + "?wsdl");
|
||||
|
||||
BufferedReader in = new BufferedReader(new InputStreamReader(rss.openStream()));
|
||||
String inputLine;
|
||||
while ((inputLine = in.readLine()) != null) {
|
||||
sw.write(inputLine);
|
||||
}
|
||||
in.close();
|
||||
|
||||
result = sw.toString();
|
||||
|
||||
} catch (Exception ex) {
|
||||
logger.error("error occurred in servlet", ex);
|
||||
}
|
||||
return result;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,152 @@
|
|||
package edu.cornell.mannlib.semservices.service.impl;
|
||||
|
||||
import java.io.BufferedReader;
|
||||
import java.io.InputStreamReader;
|
||||
import java.io.StringWriter;
|
||||
import java.net.URL;
|
||||
import java.net.URLEncoder;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import net.sf.json.JSONArray;
|
||||
import net.sf.json.JSONObject;
|
||||
import net.sf.json.JSONSerializer;
|
||||
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
|
||||
import edu.cornell.mannlib.semservices.bo.Concept;
|
||||
import edu.cornell.mannlib.semservices.service.ExternalConceptService;
|
||||
|
||||
/**
|
||||
* @author jaf30
|
||||
*
|
||||
*/
|
||||
public class UMLSService implements ExternalConceptService {
|
||||
protected final Log logger = LogFactory.getLog(getClass());
|
||||
private static final String submissionUrl = "http://link.informatics.stonybrook.edu/MeaningLookup/MlServiceServlet?";
|
||||
private static final String baseUri = "http://link.informatics.stonybrook.edu/umls/CUI/";
|
||||
|
||||
public List<Concept> processResults(String term) {
|
||||
String results = null;
|
||||
String dataUrl = submissionUrl + "textToProcess="
|
||||
+ URLEncoder.encode(term) + "&format=json";
|
||||
|
||||
try {
|
||||
|
||||
StringWriter sw = new StringWriter();
|
||||
URL rss = new URL(dataUrl);
|
||||
|
||||
BufferedReader in = new BufferedReader(new InputStreamReader(rss.openStream()));
|
||||
String inputLine;
|
||||
while ((inputLine = in.readLine()) != null) {
|
||||
sw.write(inputLine);
|
||||
}
|
||||
in.close();
|
||||
|
||||
results = sw.toString();
|
||||
|
||||
} catch (Exception ex) {
|
||||
logger.error("error occurred in servlet", ex);
|
||||
return null;
|
||||
}
|
||||
//System.out.println("results before processing: "+results);
|
||||
List<Concept> conceptList = processOutput(results);
|
||||
return conceptList;
|
||||
}
|
||||
|
||||
/**
|
||||
* @param results
|
||||
* @return
|
||||
*/
|
||||
private List<Concept> processOutput(String results) {
|
||||
|
||||
List<Concept> conceptList = new ArrayList<Concept>();
|
||||
List<String> bestMatchIdList = new ArrayList<String>();
|
||||
String bestMatchId = new String();
|
||||
try {
|
||||
JSONObject json = (JSONObject) JSONSerializer.toJSON( results );
|
||||
|
||||
if (json.has("Best Match")) {
|
||||
//System.out.println("Best Match");
|
||||
|
||||
JSONArray bestMatchArray = json.getJSONArray("Best Match");
|
||||
int len = bestMatchArray.size();
|
||||
if (len > 1) {
|
||||
System.out.println("Found this many best matches: "+ len);
|
||||
}
|
||||
int i;
|
||||
for (i = 0; i < len; i++) {
|
||||
JSONObject o = bestMatchArray.getJSONObject(i);
|
||||
//System.out.println(o.toString());
|
||||
Concept concept = new Concept();
|
||||
concept.setDefinedBy("UMLS");
|
||||
concept.setBestMatch("true");
|
||||
String cui = getJsonValue(o, "CUI");
|
||||
bestMatchIdList.add(cui);
|
||||
|
||||
concept.setConceptId(cui);
|
||||
concept.setLabel(getJsonValue(o, "label"));
|
||||
concept.setType(getJsonValue(o, "type"));
|
||||
concept.setDefinition(getJsonValue(o, "definition"));
|
||||
concept.setUri(baseUri + cui);
|
||||
conceptList.add(concept);
|
||||
}
|
||||
}
|
||||
if (json.has("All")) {
|
||||
|
||||
JSONArray allArray = json.getJSONArray("All");
|
||||
int len = allArray.size();
|
||||
//System.out.println("size of best match array: "+ len);
|
||||
int i;
|
||||
for (i = 0; i < len; i++) {
|
||||
JSONObject o = allArray.getJSONObject(i);
|
||||
//System.out.println(o.toString());
|
||||
Concept concept = new Concept();
|
||||
concept.setDefinedBy("UMLS");
|
||||
String cui = getJsonValue(o, "CUI");
|
||||
concept.setConceptId(cui);
|
||||
|
||||
concept.setLabel(getJsonValue(o, "label"));
|
||||
concept.setType(getJsonValue(o, "type"));
|
||||
concept.setDefinition(getJsonValue(o, "definition"));
|
||||
concept.setUri(baseUri + cui);
|
||||
// prevent duplicate concepts in list
|
||||
if (! bestMatchIdList.contains(cui)) {
|
||||
concept.setBestMatch("false");
|
||||
conceptList.add(concept);
|
||||
}
|
||||
}
|
||||
}
|
||||
} catch (Exception ex ) {
|
||||
ex.printStackTrace();
|
||||
logger.error("Could not get concepts", ex);
|
||||
}
|
||||
return conceptList;
|
||||
|
||||
//
|
||||
// now serialize the list of Concepts to a JSON String
|
||||
//
|
||||
//JSONObject jsonObject = null;
|
||||
//jsonObject = BeanToJsonSerializer.serializeToJsonObject(conceptList);
|
||||
//System.out.println(jsonObject.toString());
|
||||
//return jsonObject.toString();
|
||||
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Get a string from a json object or an empty string if there is no value for the given key
|
||||
* @param obj
|
||||
* @param key
|
||||
* @return
|
||||
*/
|
||||
protected String getJsonValue(JSONObject obj, String key) {
|
||||
if (obj.has(key)) {
|
||||
return obj.getString(key);
|
||||
} else {
|
||||
return new String("");
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Add table
Add a link
Reference in a new issue