Metacat

/**  '$RCSfile$'

 *  Copyright: 2010 Regents of the University of California and the

 *              National Center for Ecological Analysis and Synthesis

 *

 * This program is free software; you can redistribute it and/or modify

 * it under the terms of the GNU General Public License as published by

 * the Free Software Foundation; either version 2 of the License, or

 * (at your option) any later version.

 *

 * This program is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 * GNU General Public License for more details.

 *

 * You should have received a copy of the GNU General Public License

 * along with this program; if not, write to the Free Software

 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 */

package edu.ucsb.nceas.metacat.annotation;

import junit.framework.Test;

import junit.framework.TestSuite;

import edu.ucsb.nceas.MCTestCase;

public class OrcidServiceTest extends MCTestCase {

	/**

	 * constructor for the test

	 */

	public OrcidServiceTest(String name) {

		super(name);

	}

	/**

	 * Establish a testing framework by initializing appropriate objects

	 */

	public void setUp() throws Exception {

		super.setUp();

	}

	/**

	 * Release any objects after tests are complete

	 */

	public void tearDown() {

	}

	/**

	 * Create a suite of tests to be run together

	 */

	public static Test suite() {

		TestSuite suite = new TestSuite();

		suite.addTest(new OrcidServiceTest("testLookup"));

		return suite;

	}

	public void testLookup() {

		String[] otherNames = new String[] {"Matthew Jones"};

		String orcid = OrcidService.lookupOrcid(null, null, otherNames);

		assertEquals("http://sandbox-1.orcid.org/0000-0003-2141-4459", orcid);

	}

}

package edu.ucsb.nceas.metacat.annotation;

import java.io.InputStream;

import java.io.StringReader;

import java.net.URL;

import java.net.URLEncoder;

import org.apache.commons.io.IOUtils;

import org.apache.log4j.Logger;

import org.w3c.dom.Node;

import edu.ucsb.nceas.metacat.replication.ReplicationService;

import edu.ucsb.nceas.utilities.XMLUtilities;

public class OrcidService {

	private static Logger logMetacat = Logger.getLogger(OrcidService.class);

    private static final String REST_URL = "http://pub.sandbox.orcid.org/v1.1/search/orcid-bio";

    /**

	 * Look up possible ORCID from orcid service.

	 * @see "http://support.orcid.org/knowledgebase/articles/132354-searching-with-the-public-api"

	 * @param surName

	 * @param givenNames

	 * @param otherNames

	 * @return

	 */

	public static String lookupOrcid(String surName, String[] givenNames, String[] otherNames) {

		try {

			String urlParameters = "";

			if (surName != null) {

				urlParameters += "+family-name:\"" + surName + "\"";

			}

			if (otherNames != null) {

				for (String otherName: otherNames) {

					urlParameters += "+other-names:\"" + otherName + "\""; 

				}

			}

			if (givenNames != null) {

				for (String givenName: givenNames) {

					urlParameters += "+given-names:\"" + givenName + "\""; 

				}

			}

			urlParameters = URLEncoder.encode(urlParameters, "UTF-8");

			String url = REST_URL + "?q=" + urlParameters + "&rows=1";

			URL restURL = new URL(url);

			//InputStream is = restURL.openStream();

			InputStream is = ReplicationService.getURLStream(restURL);

			String results = IOUtils.toString(is);

			logMetacat.debug("RESULTS: " + results);

			Node doc = XMLUtilities.getXMLReaderAsDOMTreeRootNode(new StringReader(results));

			Node orcidUriNodeList = XMLUtilities.getNodeWithXPath(doc, "//*[local-name()=\"uri\"]");

			if (orcidUriNodeList != null) {

				String orcidUri = orcidUriNodeList.getFirstChild().getNodeValue();

				logMetacat.info("Found ORCID URI: " + orcidUri);

				return orcidUri;

			}

		} catch (Exception e) {

			logMetacat.error("Could not lookup ORCID for surName=" + surName, e);

		}

		return null;

	}

}

		// who should we attribute the annotation to?

		Individual p1 = m.createIndividual(ont.getURI() + "#person", personClass);

		// add an orcid annotation if we can find one from their system

		List<String> creators = dataPackage.getCreators();

		//creators = Arrays.asList("Matthew Jones");

		if (creators != null && creators.size() > 0) {

			p1.addProperty(nameProperty, creators.get(0));

			String orcidId = OrcidService.lookupOrcid(null, null, creators.toArray(new String[0]));

			if (orcidId != null) {

				p1.addProperty(identifierProperty, orcidId);

			}

		}

		return BioPortalService.lookupAnnotationClass(standardClass, unit);

		return BioPortalService.lookupAnnotationClass(characteristicClass, attribute.getDefinition());

package edu.ucsb.nceas.metacat.annotation;

import java.io.InputStream;

import java.io.InputStreamReader;

import java.net.URL;

import java.net.URLEncoder;

import org.apache.log4j.Logger;

import org.w3c.dom.Document;

import org.w3c.dom.NodeList;

import com.hp.hpl.jena.ontology.OntClass;

import com.hp.hpl.jena.rdf.model.Resource;

import edu.ucsb.nceas.metacat.replication.ReplicationService;

import edu.ucsb.nceas.utilities.XMLUtilities;

public class BioPortalService {

	private static Logger logMetacat = Logger.getLogger(BioPortalService.class);

    // for looking up concepts in BioPortal

    private static final String REST_URL = "http://data.bioontology.org";

    private static final String API_KEY = "24e4775e-54e0-11e0-9d7b-005056aa3316";

    /**

	 * Look up possible concept from BioPortal annotation service.

	 * @see "http://data.bioontology.org/documentation"

	 * @param superClass

	 * @param text

	 * @return

	 */

	public static Resource lookupAnnotationClass(OntClass superClass, String text) {

		try {

			String urlParameters = "apikey=" + API_KEY;

			urlParameters += "&format=xml";

			urlParameters += "&ontologies=OBOE-SBC";

//			urlParameters += "&ontologies=SWEET";

			urlParameters += "&text=" + URLEncoder.encode(text, "UTF-8");

			String url = REST_URL + "/annotator?" + urlParameters ;

			URL restURL = new URL(url);

			InputStream is = ReplicationService.getURLStream(restURL);

			Document doc = XMLUtilities.getXMLReaderAsDOMDocument(new InputStreamReader(is, "UTF-8"));

			NodeList classNodeList = XMLUtilities.getNodeListWithXPath(doc, "//annotation/annotatedClass/id");

			if (classNodeList != null && classNodeList.getLength() > 0) {

				String classURI = classNodeList.item(0).getFirstChild().getNodeValue();

				logMetacat.info("annotator suggested: " + classURI);

				Resource subclass = superClass.getModel().getResource(classURI);

				// check that it is a subclass of superClass

				if (superClass.hasSubClass(subclass)) {

					return subclass;

				}

			}

		} catch (Exception e) {

			logMetacat.error("Could not lookup BioPortal annotation for text= " + text, e);

		}

		return null;

	}

}