/**
 * The source code files, properties files, other text files, and other files
 * in this package (the Software) are
 * 
 * Copyright (c) by the Regents of the University of Michigan
 *  
 * and were written or modified from other sources by the development team
 * of the National Center for Integrative Biomedical Informatics, University
 * of Michigan.
 * 
 * Development of the software is supported by National Institutes of Health,
 * Grant U54 DA021519
 * 
 * see www.ncibi.org for details.
 *
 * By using, modifying, or using derivative products of the software, you are
 * agreeing to these Terms of Use:
 * (see http://portal.ncibi.org/gateway/pdf/Terms%20of%20use-web.pdf)
 * 
 * General Use Policy:
 * 
 * For academic and non-profit institutions:
 *   - Permission is granted to access, use and/or download the Tools for
 *     internal use only
 *   - Users must inform NCIBI of any derivative works of the Tools created
 *     (e-mail: ncibihelp@umich.edu)
 *   - Use of the Tools must be acknowledged in resulting publications
 *     (see citation policy below)
 * 
 * For commercial and for-profit institutions:
 *   - Permission is granted to access, use, and/or download the Tools for
 *     internal use only
 *   - To create derivative works of the Tools for commercial purposes, source
 *     code or access to databases may be permitted through negotiation for a
 *     commercial license. Please send request through: ncibi-help@umich.edu
 *
 * Citation of use of this software must include reference to:
 *
 * National Center for Integrative Biomedical Informatics,
 * University of Michigan.
 *
 * Disclaimer:
 * THE USER AGREES THAT THE TOOLS ARE PROVIDED AS IS, WITHOUT REPRESENTATION
 * OR WARRANTY BY THE UNIVERSITY OF MICHIGAN OF ANY KIND, EITHER EXPRESS OR
 * IMPLIED, INCLUDING WITHOUT LIMITATION THE IMPLIED WARRANTIES OF
 * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. The Regents of the
 * University of Michigan shall not be liable for any damages, including
 * special, indirect, incidental or consequential damages, with respect to any
 * claim arising out of, or in connection with, the use of these Tools,
 * Software, or derivative products, even if it has been or is hereafter
 * advised of the possibility of such damages. Nothing in this license shall
 * be deemed to grant any rights of the University of Michigan except as
 * expressly stated herein. The names and trademarks of the University of
 * Michigan may NOT be used in advertising or publicity pertaining to your
 * use of the Tools, except as expressly stated herein.
 **/

import java.io.*;
import java.sql.*;
import java.util.*;
import java.net.*;

import javax.xml.parsers.*;
import org.w3c.dom.*;
import org.xml.sax.*;
import javax.xml.xpath.*;

public class NCIBI_NLP_Sample2 {
	public static void main(String[] args) {
		try {
			// string URL for the NCIBI NLP Web Service with the PMID, tagger,
			// and type parameters
			String urlString = "http://nlp.ncibi.org/fetch?pmid=17523140&tagger=nametagger&type=gene";

			// URL from the above string
			URL ncbiWS = new URL(urlString);

			// connection from the above URL
			URLConnection urlConnection = ncbiWS.openConnection();

			// input stream from the above connection
			InputStream inputStream = urlConnection.getInputStream();

			// factory to build the XML document
			DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
			factory.setCoalescing(true);
			factory.setNamespaceAware(true);

			// build the XML document from the parsed input stream
			Document xmlDocument = factory.newDocumentBuilder().parse(inputStream);

			// close the input stream since we now have the XML document
			inputStream.close();

			if (xmlDocument != null) {
				XPath xpath = XPathFactory.newInstance().newXPath();

				// will grab all the "Gene" Elements in the XML Document
				//String expression = "//Gene";

				// will grab all the "Sentence" Elements in the XML Document
				// that are parent to "Gene" elements
				//String expression = "//Gene/parent::node()";

				// will grab all the "Sentence" Elements in the XML Document
				// that are parent to "Gene" elements with id attribute '11137'
				String expression = "//Gene[@id='11137']/parent::node()";

				// apply xpath expression to the XML document
				NodeList nodes = (NodeList)xpath.evaluate(expression, xmlDocument, XPathConstants.NODESET);

				// loop through the nodes returned by the xpath query and print
				// them to standard out
				for (int i = 0; i < nodes.getLength(); i++) {
					Node sentenceNode = nodes.item(i);
					System.out.println(sentenceNode.getTextContent());
				}
			}
		} catch(Exception e) {
			e.printStackTrace();
		}
	}
}