349 lines
12 KiB
Java
349 lines
12 KiB
Java
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package eu.dnetlib.doiboost.orcidnodoi.xml;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import java.io.IOException;
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import java.util.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.google.common.collect.Lists;
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import com.ximpleware.NavException;
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import com.ximpleware.ParseException;
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import com.ximpleware.XPathEvalException;
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import com.ximpleware.XPathParseException;
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import eu.dnetlib.dhp.parser.utility.VtdException;
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import eu.dnetlib.dhp.schema.orcid.AuthorData;
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import eu.dnetlib.doiboost.orcidnodoi.model.Contributor;
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import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
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import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher;
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public class OrcidNoDoiTest {
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private static final Logger logger = LoggerFactory.getLogger(OrcidNoDoiTest.class);
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static String nameA = "Khairy";
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static String surnameA = "Abdel Dayem";
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static String orcidIdA = "0000-0003-2760-1191";
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@Test
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public void readPublicationFieldsTest()
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throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException {
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logger.info("running loadPublicationFieldsTest ....");
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String xml = IOUtils
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.toString(
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OrcidNoDoiTest.class.getResourceAsStream("activity_work_0000-0002-2536-4498.xml"));
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if (xml == null) {
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logger.info("Resource not found");
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}
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XMLRecordParserNoDoi p = new XMLRecordParserNoDoi();
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if (p == null) {
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logger.info("XMLRecordParserNoDoi null");
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}
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WorkDataNoDoi workData = null;
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try {
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workData = p.VTDParseWorkData(xml.getBytes());
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} catch (Exception e) {
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logger.error("parsing xml", e);
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}
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assertNotNull(workData);
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assertNotNull(workData.getOid());
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logger.info("oid: " + workData.getOid());
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assertNotNull(workData.getTitles());
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logger.info("titles: ");
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workData.getTitles().forEach(t -> {
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logger.info(t);
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});
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logger.info("source: " + workData.getSourceName());
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logger.info("type: " + workData.getType());
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logger.info("urls: ");
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workData.getUrls().forEach(u -> {
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logger.info(u);
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});
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logger.info("publication date: ");
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workData.getPublicationDates().forEach(d -> {
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logger.info(d.getYear() + " - " + d.getMonth() + " - " + d.getDay());
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});
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logger.info("external id: ");
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workData.getExtIds().removeIf(e -> e.getRelationShip() != null && !e.getRelationShip().equals("self"));
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workData.getExtIds().forEach(e -> {
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logger.info(e.getType() + " - " + e.getValue() + " - " + e.getRelationShip());
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});
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logger.info("contributors: ");
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workData.getContributors().forEach(c -> {
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logger
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.info(
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c.getName() + " - " + c.getRole() + " - " + c.getSequence());
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});
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}
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@Test
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public void authorDoubleMatchTest() throws Exception {
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logger.info("running authorSimpleMatchTest ....");
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String orcidWork = "activity_work_0000-0003-2760-1191-similarity.xml";
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AuthorData author = new AuthorData();
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author.setName(nameA);
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author.setSurname(surnameA);
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author.setOid(orcidIdA);
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String xml = IOUtils
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.toString(
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OrcidNoDoiTest.class.getResourceAsStream(orcidWork));
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if (xml == null) {
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logger.info("Resource not found");
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}
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XMLRecordParserNoDoi p = new XMLRecordParserNoDoi();
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if (p == null) {
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logger.info("XMLRecordParserNoDoi null");
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}
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WorkDataNoDoi workData = null;
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try {
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workData = p.VTDParseWorkData(xml.getBytes());
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} catch (Exception e) {
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logger.error("parsing xml", e);
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}
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assertNotNull(workData);
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Contributor a = workData.getContributors().get(0);
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assertTrue(a.getCreditName().equals("Abdel-Dayem K"));
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AuthorMatcher.match(author, workData.getContributors());
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assertTrue(workData.getContributors().size() == 6);
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}
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@Test
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public void readContributorsTest()
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throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException {
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logger.info("running loadPublicationFieldsTest ....");
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String xml = IOUtils
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.toString(
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OrcidNoDoiTest.class.getResourceAsStream("activity_work_0000-0003-2760-1191_contributors.xml"));
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if (xml == null) {
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logger.info("Resource not found");
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}
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XMLRecordParserNoDoi p = new XMLRecordParserNoDoi();
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if (p == null) {
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logger.info("XMLRecordParserNoDoi null");
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}
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WorkDataNoDoi workData = null;
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try {
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workData = p.VTDParseWorkData(xml.getBytes());
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} catch (Exception e) {
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logger.error("parsing xml", e);
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}
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assertNotNull(workData.getContributors());
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assertTrue(workData.getContributors().size() == 5);
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assertTrue(StringUtils.isBlank(workData.getContributors().get(0).getCreditName()));
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assertTrue(workData.getContributors().get(0).getSequence().equals("seq0"));
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assertTrue(workData.getContributors().get(0).getRole().equals("role0"));
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assertTrue(workData.getContributors().get(1).getCreditName().equals("creditname1"));
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assertTrue(StringUtils.isBlank(workData.getContributors().get(1).getSequence()));
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assertTrue(StringUtils.isBlank(workData.getContributors().get(1).getRole()));
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assertTrue(workData.getContributors().get(2).getCreditName().equals("creditname2"));
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assertTrue(workData.getContributors().get(2).getSequence().equals("seq2"));
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assertTrue(StringUtils.isBlank(workData.getContributors().get(2).getRole()));
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assertTrue(workData.getContributors().get(3).getCreditName().equals("creditname3"));
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assertTrue(StringUtils.isBlank(workData.getContributors().get(3).getSequence()));
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assertTrue(workData.getContributors().get(3).getRole().equals("role3"));
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assertTrue(StringUtils.isBlank(workData.getContributors().get(4).getCreditName()));
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assertTrue(workData.getContributors().get(4).getSequence().equals("seq4"));
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assertTrue(workData.getContributors().get(4).getRole().equals("role4"));
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}
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@Test
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public void authorSimpleMatchTest() throws Exception {
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String orcidWork = "activity_work_0000-0002-5982-8983.xml";
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AuthorData author = new AuthorData();
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author.setName("Parkhouse");
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author.setSurname("H.");
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author.setOid("0000-0002-5982-8983");
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String xml = IOUtils
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.toString(
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OrcidNoDoiTest.class.getResourceAsStream(orcidWork));
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if (xml == null) {
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logger.info("Resource not found");
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}
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XMLRecordParserNoDoi p = new XMLRecordParserNoDoi();
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if (p == null) {
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logger.info("XMLRecordParserNoDoi null");
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}
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WorkDataNoDoi workData = null;
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try {
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workData = p.VTDParseWorkData(xml.getBytes());
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} catch (Exception e) {
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logger.error("parsing xml", e);
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}
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assertNotNull(workData);
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Contributor a = workData.getContributors().get(0);
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assertTrue(a.getCreditName().equals("Parkhouse, H."));
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AuthorMatcher.match(author, workData.getContributors());
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assertTrue(workData.getContributors().size() == 2);
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Contributor c = workData.getContributors().get(0);
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assertTrue(c.getOid().equals("0000-0002-5982-8983"));
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assertTrue(c.getName().equals("Parkhouse"));
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assertTrue(c.getSurname().equals("H."));
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assertTrue(c.getCreditName().equals("Parkhouse, H."));
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}
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@Test
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public void match() {
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AuthorData author = new AuthorData();
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author.setName("Joe");
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author.setSurname("Dodge");
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author.setOid("0000-1111-2222-3333");
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Contributor contributor = new Contributor();
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contributor.setCreditName("Joe Dodge");
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List<Contributor> contributors = Arrays.asList(contributor);
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AuthorMatcher am = new AuthorMatcher();
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int matchCounter = 0;
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List<Integer> matchCounters = Arrays.asList(matchCounter);
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contributors
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.stream()
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.filter(c -> !StringUtils.isBlank(c.getCreditName()))
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.forEach(c -> {
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if (am.simpleMatch(c.getCreditName(), author.getName()) ||
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am.simpleMatch(c.getCreditName(), author.getSurname()) ||
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am.simpleMatchOnOtherNames(c.getCreditName(), author.getOtherNames())) {
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matchCounters.set(0, matchCounters.get(0) + 1);
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c.setSimpleMatch(true);
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}
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});
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assertTrue(matchCounters.get(0) == 1);
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am.updateAuthorsSimpleMatch(contributors, author);
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assertTrue(contributors.get(0).getName().equals("Joe"));
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assertTrue(contributors.get(0).getSurname().equals("Dodge"));
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assertTrue(contributors.get(0).getCreditName().equals("Joe Dodge"));
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assertTrue(contributors.get(0).getOid().equals("0000-1111-2222-3333"));
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AuthorData authorX = new AuthorData();
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authorX.setName(nameA);
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authorX.setSurname(surnameA);
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authorX.setOid(orcidIdA);
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Contributor contributorA = new Contributor();
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contributorA.setCreditName("Abdel-Dayem Khai");
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Contributor contributorB = new Contributor();
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contributorB.setCreditName("Abdel-Dayem Fake");
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List<Contributor> contributorList = new ArrayList<>();
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contributorList.add(contributorA);
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contributorList.add(contributorB);
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int matchCounter2 = 0;
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List<Integer> matchCounters2 = Arrays.asList(matchCounter2);
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contributorList
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.stream()
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.filter(c -> !StringUtils.isBlank(c.getCreditName()))
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.forEach(c -> {
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if (am.simpleMatch(c.getCreditName(), authorX.getName()) ||
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am.simpleMatch(c.getCreditName(), authorX.getSurname()) ||
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am.simpleMatchOnOtherNames(c.getCreditName(), author.getOtherNames())) {
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int currentCounter = matchCounters2.get(0);
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currentCounter += 1;
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matchCounters2.set(0, currentCounter);
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c.setSimpleMatch(true);
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}
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});
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assertTrue(matchCounters2.get(0) == 2);
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assertTrue(contributorList.get(0).isSimpleMatch());
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assertTrue(contributorList.get(1).isSimpleMatch());
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Optional<Contributor> optCon = contributorList
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.stream()
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.filter(c -> c.isSimpleMatch())
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.filter(c -> !StringUtils.isBlank(c.getCreditName()))
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.map(c -> {
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c.setScore(am.bestMatch(authorX.getName(), authorX.getSurname(), c.getCreditName()));
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return c;
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})
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.filter(c -> c.getScore() >= AuthorMatcher.threshold)
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.max(Comparator.comparing(c -> c.getScore()));
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assertTrue(optCon.isPresent());
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final Contributor bestMatchContributor = optCon.get();
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bestMatchContributor.setBestMatch(true);
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assertTrue(bestMatchContributor.getCreditName().equals("Abdel-Dayem Khai"));
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assertTrue(contributorList.get(0).isBestMatch());
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assertTrue(!contributorList.get(1).isBestMatch());
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am.updateAuthorsSimilarityMatch(contributorList, authorX);
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assertTrue(contributorList.get(0).getName().equals(nameA));
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assertTrue(contributorList.get(0).getSurname().equals(surnameA));
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assertTrue(contributorList.get(0).getCreditName().equals("Abdel-Dayem Khai"));
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assertTrue(contributorList.get(0).getOid().equals(orcidIdA));
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assertTrue(StringUtils.isBlank(contributorList.get(1).getOid()));
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}
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@Test
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public void authorBestMatchTest() throws Exception {
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String name = "Khairy";
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String surname = "Abdel Dayem";
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String orcidWork = "activity_work_0000-0003-2760-1191.xml";
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AuthorData author = new AuthorData();
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author.setName(name);
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author.setSurname(surname);
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author.setOid(orcidIdA);
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String xml = IOUtils
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.toString(
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OrcidNoDoiTest.class.getResourceAsStream(orcidWork));
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if (xml == null) {
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logger.info("Resource not found");
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}
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XMLRecordParserNoDoi p = new XMLRecordParserNoDoi();
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if (p == null) {
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logger.info("XMLRecordParserNoDoi null");
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}
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WorkDataNoDoi workData = null;
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try {
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workData = p.VTDParseWorkData(xml.getBytes());
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} catch (Exception e) {
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logger.error("parsing xml", e);
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}
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AuthorMatcher.match(author, workData.getContributors());
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assertTrue(workData.getContributors().size() == 5);
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List<Contributor> c = workData.getContributors();
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assertTrue(c.get(0).getName().equals(name));
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assertTrue(c.get(0).getSurname().equals(surname));
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assertTrue(c.get(0).getCreditName().equals("Khair Abde Daye"));
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assertTrue(c.get(0).getOid().equals(orcidIdA));
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}
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@Test
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public void otherNamesMatchTest()
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throws VtdException, ParseException, IOException, XPathEvalException, NavException, XPathParseException {
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AuthorData author = new AuthorData();
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author.setName("Joe");
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author.setSurname("Dodge");
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author.setOid("0000-1111-2222-3333");
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String otherName1 = new String("Joe Dr. Dodge");
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String otherName2 = new String("XY");
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List<String> others = Lists.newArrayList();
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others.add(otherName1);
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others.add(otherName2);
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author.setOtherNames(others);
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Contributor contributor = new Contributor();
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contributor.setCreditName("XY");
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List<Contributor> contributors = Arrays.asList(contributor);
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AuthorMatcher.match(author, contributors);
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assertTrue(contributors.get(0).getName().equals("Joe"));
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assertTrue(contributors.get(0).getSurname().equals("Dodge"));
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assertTrue(contributors.get(0).getOid().equals("0000-1111-2222-3333"));
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}
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}
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