D-Net

package eu.dnetlib.pace.clustering;

import org.junit.Before;

import org.junit.Test;

import eu.dnetlib.pace.AbstractProtoPaceTest;

import eu.dnetlib.pace.config.Config;

import eu.dnetlib.pace.config.Type;

import eu.dnetlib.pace.model.FieldListImpl;

import eu.dnetlib.pace.model.FieldValueImpl;

import eu.dnetlib.pace.model.MapDocument;

public class BlacklistAwareClusteringCombinerTest extends AbstractProtoPaceTest {

	private Config config;

	@Before

	public void setUp() {

		config = getResultFullConf();

	}

	@Test

	public void testCombine() {

		final MapDocument result =

				result(config, "A", "Dipping in Cygnus X-2 in a multi-wavelength campaign due to absorption of extended ADC emission", "2013");

		final FieldListImpl fl = new FieldListImpl();

		fl.add(new FieldValueImpl(Type.String, "desc", "hello world description pipeline"));

		result.getFieldMap().put("desc", fl);

		fl.clear();

		fl.add(new FieldValueImpl(Type.String, "title", "lorem ipsum cabalie qwerty"));

		final FieldListImpl field = (FieldListImpl) result.getFieldMap().get("title");

		field.add(fl);

		System.out.println(BlacklistAwareClusteringCombiner.filterAndCombine(result, config, config.blacklists()));

	}

}

package eu.dnetlib.pace.clustering;

import org.junit.Before;

import org.junit.Test;

import eu.dnetlib.pace.AbstractProtoPaceTest;

import eu.dnetlib.pace.config.Config;

import eu.dnetlib.pace.config.Type;

import eu.dnetlib.pace.model.FieldListImpl;

import eu.dnetlib.pace.model.FieldValueImpl;

import eu.dnetlib.pace.model.MapDocument;

public class ClusteringCombinerTest extends AbstractProtoPaceTest {

	private Config config;

	@Before

	public void setUp() {

		config = getResultFullConf();

	}

	@Test

	public void testCombine() {

		String title = "Dipping in Cygnus X-2 in a multi-wavelength campaign due to absorption of extended ADC emission";

		MapDocument result = result(config, "A", title, "2013");

		FieldListImpl fl = new FieldListImpl();

		fl.add(new FieldValueImpl(Type.String, "desc", "lorem ipsum cabalie qwerty"));

		result.getFieldMap().put("desc", fl);

		System.out.println(title);

		System.out.println(ClusteringCombiner.combine(result, config));

	}

}

package eu.dnetlib.pace;

import java.io.IOException;

import java.io.StringWriter;

import java.util.ArrayList;

import java.util.List;

import com.google.common.collect.Lists;

import com.google.gson.Gson;

import eu.dnetlib.data.mapreduce.util.DNGFTest;

import eu.dnetlib.data.proto.DNGFProtos.DNGF;

import eu.dnetlib.data.proto.DNGFProtos.DNGFEntity;

import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;

import eu.dnetlib.data.proto.FieldTypeProtos.StructuredProperty;

import eu.dnetlib.data.proto.FieldTypeProtos.StructuredProperty.Builder;

import eu.dnetlib.data.proto.OrganizationProtos.Organization;

import eu.dnetlib.data.proto.PersonProtos.Person;

import eu.dnetlib.data.proto.PublicationProtos.Publication;

import eu.dnetlib.data.proto.TypeProtos;

import eu.dnetlib.pace.config.Config;

import eu.dnetlib.pace.config.DedupConfig;

import eu.dnetlib.pace.config.Type;

import eu.dnetlib.pace.model.Field;

import eu.dnetlib.pace.model.FieldValueImpl;

import eu.dnetlib.pace.model.MapDocument;

import eu.dnetlib.pace.model.ProtoDocumentBuilder;

import eu.dnetlib.pace.model.gt.GTAuthor;

import eu.dnetlib.pace.model.gt.GTAuthorMapper;

import org.apache.commons.io.IOUtils;

import org.apache.commons.lang3.RandomStringUtils;

import org.apache.commons.lang3.StringUtils;

public abstract class AbstractProtoPaceTest extends DNGFTest {

	protected DedupConfig getResultFullConf() {

		return DedupConfig.load(readFromClasspath("/eu/dnetlib/pace/result.full.pace.conf"));

	}

	protected DedupConfig getResultSimpleConf() {

		return DedupConfig.load(readFromClasspath("/eu/dnetlib/pace/result.simple.pace.conf"));

	}

	protected DedupConfig getResultConf() {

		return DedupConfig.load(readFromClasspath("/eu/dnetlib/pace/result.pace.conf"));

	}

	protected DedupConfig getOrganizationSimpleConf() {

		return DedupConfig.load(readFromClasspath("/eu/dnetlib/pace/organization.pace.conf"));

	}

	protected DedupConfig getResultAuthorsConf() {

		return DedupConfig.load(readFromClasspath("/eu/dnetlib/pace/result.authors.pace.conf"));

	}

	protected DedupConfig getPersonConf() {

		return DedupConfig.load(readFromClasspath("/eu/dnetlib/pace/person.pace.conf"));

	}

	protected DedupConfig getResultProdConf() {

		return DedupConfig.load(readFromClasspath("/eu/dnetlib/pace/result.prod.pace.conf"));

	}

	protected MapDocument person(final Config conf, final String id, final DNGF oaf) {

		return ProtoDocumentBuilder.newInstance(id, oaf.getEntity(), conf.model());

	}

	protected DNGF getPersonGT(final String path) {

		return new GTAuthorMapper().map(getGTAuthor(path));

	}

	protected GTAuthor getGTAuthor(final String path) {

		final Gson gson = new Gson();

		final String json = readFromClasspath(path);

		final GTAuthor gta = gson.fromJson(json, GTAuthor.class);

		return gta;

	}

	private String readFromClasspath(final String filename) {

		final StringWriter sw = new StringWriter();

		try {

			IOUtils.copy(getClass().getResourceAsStream(filename), sw);

			return sw.toString();

		} catch (final IOException e) {

			throw new RuntimeException("cannot load resource from classpath: " + filename);

		}

	}

	protected MapDocument result(final Config config, final String id, final String title) {

		return result(config, id, title, null, new ArrayList<String>(), null);

	}

	protected MapDocument result(final Config config, final String id, final String title, final String date) {

		return result(config, id, title, date, new ArrayList<String>(), null);

	}

	protected MapDocument result(final Config config, final String id, final String title, final String date, final List<String> pid) {

		return result(config, id, title, date, pid, null);

	}

	protected MapDocument result(final Config config, final String id, final String title, final String date, final String pid) {

		return result(config, id, title, date, pid, null);

	}

	protected MapDocument result(final Config config, final String id, final String title, final String date, final String pid, final List<String> authors) {

		return result(config, id, title, date, Lists.newArrayList(pid), authors);

	}

	protected MapDocument result(final Config config, final String id, final String title, final String date, final List<String> pid, final List<String> authors) {

		final Publication.Metadata.Builder metadata = Publication.Metadata.newBuilder();

		if (!StringUtils.isBlank(title)) {

			metadata.addTitle(getStruct(title, getQualifier("main title", "dnet:titles")));

			metadata.addTitle(getStruct(RandomStringUtils.randomAlphabetic(10), getQualifier("alternative title", "dnet:titles")));

		}

		if (!StringUtils.isBlank(date)) {

			metadata.setDateofacceptance(sf(date));

		}

		final DNGFEntity.Builder entity = dngfEntity(id, TypeProtos.Type.publication);

		final Publication.Builder result = Publication.newBuilder().setMetadata(metadata);

		if (authors != null) {

			for (final String author : authors) {

				result.addAuthor(person(author));

			}

		}

		entity.setPublication(result);

		if (pid != null) {

			for(String p : pid) {

				if (!StringUtils.isBlank(p)) {

					entity.addPid(sp(p, "doi"));

					//entity.addPid(sp(RandomStringUtils.randomAlphabetic(10), "oai"));

				}

			}

		}

		final DNGFEntity build = entity.build();

		return ProtoDocumentBuilder.newInstance(id, build, config.model());

	}

	private Person.Builder person(final String author) {

		final Person.Builder person = Person.newBuilder();

		final eu.dnetlib.pace.model.Person p = new eu.dnetlib.pace.model.Person(author, false);

		final Person.Metadata.Builder metadata = Person.Metadata.newBuilder();

		if (p.isAccurate()) {

			metadata.setFirstname(sf(p.getNormalisedFirstName()));

			metadata.addSecondnames(sf(p.getNormalisedSurname()));

			metadata.setFullname(sf(p.getNormalisedFullname()));

		} else {

			metadata.setFullname(sf(p.getOriginal()));

		}

		return person.setMetadata(metadata);

	}

	private DNGFEntity.Builder dngfEntity(final String id, final eu.dnetlib.data.proto.TypeProtos.Type type) {

		final DNGFEntity.Builder entity = DNGFEntity.newBuilder().setId(id).setType(type);

		return entity;

	}

	protected MapDocument organization(final Config config, final String id, final String legalName) {

		return organization(config, id, legalName, null);

	}

	protected MapDocument organization(final Config config, final String id, final String legalName, final String legalShortName) {

		final Organization.Metadata.Builder metadata = Organization.Metadata.newBuilder();

		if (legalName != null) {

			metadata.setLegalname(sf(legalName));

		}

		if (legalShortName != null) {

			metadata.setLegalshortname(sf(legalShortName));

		}

		final DNGFEntity.Builder entity = dngfEntity(id, TypeProtos.Type.publication);

		entity.setOrganization(Organization.newBuilder().setMetadata(metadata));

		return ProtoDocumentBuilder.newInstance(id, entity.build(), config.model());

	}

	private StructuredProperty sp(final String pid, final String type) {

		final Builder pidSp =

				StructuredProperty.newBuilder().setValue(pid)

						.setQualifier(Qualifier.newBuilder().setClassid(type).setClassname(type).setSchemeid("dnet:pid_types").setSchemename("dnet:pid_types"));

		return pidSp.build();

	}

	protected Field title(final String s) {

		return new FieldValueImpl(Type.String, "title", s);

	}

	protected static StructuredProperty.Builder getStruct(final String value, final Qualifier.Builder qualifier) {

		return StructuredProperty.newBuilder().setValue(value).setQualifier(qualifier);

	}

	/*

	 * protected static StringField.Builder sf(final String s) { return StringField.newBuilder().setValue(s); }

	 * 

	 * protected static Qualifier.Builder getQualifier(final String classname, final String schemename) { return

	 * Qualifier.newBuilder().setClassid(classname).setClassname(classname).setSchemeid(schemename).setSchemename(schemename); }

	 */

}

package eu.dnetlib.pace.model;

import static org.junit.Assert.assertFalse;

import static org.junit.Assert.assertTrue;

import org.junit.Test;

import com.google.common.collect.Iterables;

import com.google.common.collect.Sets;

import com.google.common.collect.Sets.SetView;

import eu.dnetlib.pace.AbstractProtoPaceTest;

import eu.dnetlib.pace.config.Config;

public class ProtoDocumentBuilderTest extends AbstractProtoPaceTest {

	@Test

	public void test_serialise1() {

		final String id = "12345";

		final Config config = getResultFullConf();

		final MapDocument document = ProtoDocumentBuilder.newInstance(id, getResult(id), config.model());

		assertFalse(document.fieldNames().isEmpty());

		assertFalse(Iterables.isEmpty(document.fields()));

		System.out.println("original:\n" + document);

		final String stringDoc = MapDocumentSerializer.toString(document);

		System.out.println("srialization:\n" + stringDoc);

		final MapDocument decoded = MapDocumentSerializer.decode(stringDoc.getBytes());

		final SetView<String> diff = Sets.difference(document.fieldNames(), decoded.fieldNames());

		assertTrue(diff.isEmpty());

		System.out.println("decoded:\n" + decoded);

	}

	@Test

	public void test_serialise2() {

		final String id = "12345";

		final String path = "/eu/dnetlib/pace/model/gt.author.manghi1.json";

		final Config config = getPersonConf();

		final MapDocument document = ProtoDocumentBuilder.newInstance(id, getPersonGT(path).getEntity(), config.model());

		assertFalse(document.fieldNames().isEmpty());

		assertFalse(Iterables.isEmpty(document.fields()));

		System.out.println("original:\n" + document);

		final String stringDoc = MapDocumentSerializer.toString(document);

		System.out.println("srialization:\n" + stringDoc);

		final MapDocument decoded = MapDocumentSerializer.decode(stringDoc.getBytes());

		final SetView<String> diff = Sets.difference(document.fieldNames(), decoded.fieldNames());

		assertTrue(diff.isEmpty());

		System.out.println("decoded:\n" + decoded);

	}

}

package eu.dnetlib.pace.model.gt;

import static org.junit.Assert.assertTrue;

import java.util.Set;

import org.junit.Test;

import com.google.common.collect.Sets;

import eu.dnetlib.pace.model.gt.Author;

import eu.dnetlib.pace.model.gt.Authors;

public class AuthorTest {

	@Test

	public void test() {

		final Set<Author> s1 = getAuthors(3);

		final Set<Author> s2 = getAuthors(3);

		final Set<Author> i = Sets.intersection(s1, s2);

		System.out.println(i);

		assertTrue(i.size() == 3);

	}

	@Test

	public void test1() {

		final Authors a1 = new Authors(a("1", "Wang, M."));

		final Authors a2 = new Authors(a("1", "Wang, M."));

		final Set<Author> i = Sets.intersection(a1, a2);

		assertTrue(i.size() == 1);

	}

	private Set<Author> getAuthors(final int n) {

		final Set<Author> s = Sets.newHashSet();

		for (int i = 0; i < n; i++) {

			s.add(a(i + "", "name" + i));

		}

		return s;

	}

	private Author a(final String id, final String fullname) {

		final Author a = new Author();

		a.setId(id);

		a.setFullname(fullname);

		return a;

	}

}

package eu.dnetlib.pace.distance;

import static org.junit.Assert.assertTrue;

import java.util.ArrayList;

import java.util.List;

import eu.dnetlib.pace.distance.eval.ScoreResult;

import org.junit.Test;

import com.google.common.collect.Lists;

import eu.dnetlib.pace.AbstractProtoPaceTest;

import eu.dnetlib.pace.config.Config;

import eu.dnetlib.pace.model.MapDocument;

public class DetectorTest extends AbstractProtoPaceTest {

	@Test

	public void testScoreResult() {

		final Config config = getResultProdConf();

		final MapDocument resA = result(config, "A", "Recent results from CDFsd");

		final MapDocument resB = result(config, "B", "Recent results from CDF");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		System.out.println(sr.toString());

	}

	@Test

	public void testDistanceResultSimple() {

		final Config config = getResultSimpleConf();

		final MapDocument resA = result(config, "A", "Recent results from CDF");

		final MapDocument resB = result(config, "B", "Recent results from CDF");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		final double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue(d == 1.0);

	}

	@Test

	public void testDistanceResultSimpleMissingDates() {

		final Config config = getResultSimpleConf();

		final MapDocument resA = result(config, "A", "Recent results from BES");

		final MapDocument resB = result(config, "A", "Recent results from CES");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		final double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue(d > 0.97);

	}

	@Test

	public void testDistanceResultInvalidDate() {

		final Config config = getResultConf();

		final MapDocument resA = result(config, "A", "title title title 6BESR", "2013-01-05");

		final MapDocument resB = result(config, "B", "title title title 6BESR", "qwerty");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		final double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue(d == 1.0);

	}

	@Test

	public void testDistanceResultMissingOneDate() {

		final Config config = getResultConf();

		final MapDocument resA = result(config, "A", "title title title 6BESR", null);

		final MapDocument resB = result(config, "B", "title title title 6CLER", "2012-02");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue((d > 0.9) && (d < 1.0));

	}

	@Test

	public void testDistanceResult() {

		final Config config = getResultConf();

		final MapDocument resA = result(config, "A", "title title title BES", "");

		final MapDocument resB = result(config, "B", "title title title CLEO");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue((d > 0.9) && (d < 1.0));

	}

	@Test

	public void testDistanceResultMissingTwoDate() {

		final Config config = getResultConf();

		final MapDocument resA = result(config, "A", "title title title 6BESR");

		final MapDocument resB = result(config, "B", "title title title 6CLER");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue((d > 0.9) && (d < 1.0));

	}

	@Test

	public void testDistanceOrganizationIgnoreMissing() {

		final Config config = getOrganizationSimpleConf();

		final MapDocument orgA = organization(config, "A", "CONSIGLIO NAZIONALE DELLE RICERCHE");

		final MapDocument orgB = organization(config, "B", "CONSIGLIO NAZIONALE DELLE RICERCHE", "CNR");

		final ScoreResult sr = new PaceDocumentDistance().between(orgA, orgB, config);

		final double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue(d == 1.0);

	}

	@Test

	public void testDistanceResultCase1() {

		final Config config = getResultConf();

		final MapDocument resA = result(config, "A", "Search the Standard Model Higgs boson", "2003");

		final MapDocument resB = result(config, "B", "Search for the Standard Model Higgs Boson", "2003");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue((d > 0.9) && (d < 1.0));

	}

	@Test

	public void testDistanceResultCaseDoiMatch1() {

		final Config config = getResultConf();

		final MapDocument resA = result(config, "A", "Search the Standard Model Higgs boson", "2003", "10.1594/PANGAEA.726855");

		final MapDocument resB = result(config, "B", "Search the Standard Model Higgs Boson", "2003", "10.1594/PANGAEA.726855");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue("exact DOIs will produce an exact match", d == 1.0);

	}

	@Test

	public void testDistanceResultCaseDoiMatch2() {

		final Config config = getResultConf();

		final MapDocument resA = result(config, "A", "Conference proceedings on X. Appendix", "2003", "10.1594/PANGAEA.726855");

		final MapDocument resB = result(config, "B", "Search the Standard Model Higgs Boson", "2005", "10.1594/PANGAEA.726855");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue("exact DOIs will produce an exact match, regardless of different titles or publication years", d == 1.0);

	}

	@Test

	public void testDistanceResultCaseDoiMatch3() {

		final Config config = getResultConf();

		final MapDocument resA = result(config, "A", "Conference proceedings on X. Appendix", "2003", "10.1016/j.jmb.2010.12.024");

		final MapDocument resB = result(config, "B", "Conference proceedings on X. Appendix", "2003");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue("a missing DOI will casue the comparsion to continue with the following conditions", d == 1.0);

	}

	@Test

	public void testDistanceResultCaseDoiMatch4() {

		final Config config = getResultConf();

		final MapDocument resA = result(config, "A", "Conference proceedings on X. Appendix", "2003", "10.1016/j.jmb.2010.12.024");

		final MapDocument resB = result(config, "B", "Conference proceedings on X. Appendix", "2005");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue("a missing DOI, comparsion continues with the following conditions, different publication years will drop the score to 0", d == 0.0);

	}

	@Test

	public void testDistanceResultCaseDoiMatch5() {

		final Config config = getResultConf();

		final MapDocument resA = result(config, "A", "Search for the Standard Model Higgs Boson", "2003", "10.1016/j.jmb.2010.12.020");

		final MapDocument resB = result(config, "B", "Search the Standard Model Higgs Boson", "2003");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue("a missing DOI, comparsion continues with the following conditions", (d > 0.9) && (d < 1.0));

	}

	@Test

	public void testDistanceResultCaseDoiMatch6() {

		final Config config = getResultConf();

		final MapDocument resA = result(config, "A", "Conference proceedings on X. Appendix", "2003", "10.1016/j.jmb.2010.12.024");

		final MapDocument resB = result(config, "B", "Conference proceedings on X. Appendix", "2003", "anotherDifferentDOI");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue("different DOIs will drop the score to 0, regardless of the other fields", d == 0.0);

	}

	@Test

	public void testDistanceResultCaseDoiMatch7() {

		final Config config = getResultConf();

		final MapDocument resA = result(config, "A", "Adrenal Insufficiency asd asd", "1951", Lists.newArrayList("PMC2037944", "axdsds"));

		final MapDocument resB = result(config, "B", "Adrenal Insufficiency", "1951", "PMC2037944");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue("different DOIs will drop the score to 0, regardless of the other fields", d > 0.9 & d < 1);

	}

	// http://dx.doi.org/10.1594/PANGAEA.726855 doi:10.1594/PANGAEA.726855

	@Test

	public void testDistanceResultCaseAuthor1() {

		final Config config = getResultAuthorsConf();

		final List<String> authorsA = Lists.newArrayList("a", "b", "c", "d");

		final List<String> authorsB = Lists.newArrayList("a", "b", "c");

		final List<String> pid = Lists.newArrayList();

		final MapDocument resA = result(config, "A", "Search the Standard Model Higgs Boson", "2003", pid, authorsA);

		final MapDocument resB = result(config, "B", "Search the Standard Model Higgs Boson", "2003", pid, authorsB);

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		final double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue(d == 0.0);

	}

	@Test

	public void testDistanceResultCaseAuthor2() {

		final Config config = getResultAuthorsConf();

		final List<String> authorsA = Lists.newArrayList("a", "b", "c");

		final List<String> authorsB = Lists.newArrayList("a", "b", "c");

		final List<String> pid = Lists.newArrayList();

		final MapDocument resA = result(config, "A", "Search the Standard Model Higgs Boson", "2003", pid, authorsA);

		final MapDocument resB = result(config, "B", "Search the Standard Model Higgs Boson", "2003", pid, authorsB);

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		final double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue(d == 1.0);

	}

	@Test

	public void testDistanceResultCaseAuthor3() {

		final Config config = getResultAuthorsConf();

		final List<String> authorsA = Lists.newArrayList("Bardi, A.", "Manghi, P.", "Artini, M.");

		final List<String> authorsB = Lists.newArrayList("Bardi Alessia", "Manghi Paolo", "Artini Michele");

		final List<String> pid = Lists.newArrayList();

		final MapDocument resA = result(config, "A", "Search the Standard Model Higgs Boson", "2003", pid, authorsA);

		final MapDocument resB = result(config, "B", "Search the Standard Model Higgs Boson", "2003", pid, authorsB);

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue((d > 0.9) && (d < 1.0));

	}

	@Test

	public void testDistanceResultCaseAuthor4() {

		final Config config = getResultAuthorsConf();

		final List<String> authorsA = Lists.newArrayList("Bardi, Alessia", "Manghi, Paolo", "Artini, Michele", "a");

		final List<String> authorsB = Lists.newArrayList("Bardi Alessia", "Manghi Paolo", "Artini Michele");

		final List<String> pid = Lists.newArrayList();

		final MapDocument resA = result(config, "A", "Search the Standard Model Higgs Boson", "2003", pid, authorsA);

		final MapDocument resB = result(config, "B", "Search the Standard Model Higgs Boson", "2003", pid, authorsB);

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		final double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		// assertTrue(d.getScore() == 0.0);

	}

	@Test

	public void testDistanceResultFullConf() {

		final Config config = getResultFullConf();

		final List<String> authorsA = Lists.newArrayList("Nagarajan Pranesh", "Guy Vautier", "Punyanganie de Silva");

		final List<String> authorsB = Lists.newArrayList("Pranesh Nagarajan", "Vautier Guy", "de Silva Punyanganie");

		final MapDocument resA =

				result(config, "A", "Presentations of perforated colonic pathology in patients with polymyalgia rheumatica: two case reports", "2010",

						"10.1186/1752-1947-4-299", authorsA);

		final MapDocument resB =

				result(config, "B", "Presentations of perforated colonic pathology in patients with polymyalgia rheumatica: two case reports", "2010",

						"10.1186/1752-1947-4-299", authorsB);

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		final double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		// assertTrue(d.getScore() == 0.0);

	}

	@Test

	public void testDistanceProdConf1() {

		final Config config = getResultProdConf();

		final MapDocument resA =

				result(config,

						"A",

						" Analysis of Transfer Embryo-Derived de-duplication");

		final MapDocument resB =

				result(config,

						"B",

						" Analysis of Transfer Embryo Derived deduplication");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		final double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		// assertTrue(d.getScore() == 0.0);

	}

	@Test

	public void testDistanceProdConf2() {

		final Config config = getResultProdConf();

		final MapDocument resA =

				result(config,

						"A",

						"qwerty aaabbbbbbbb bbb ccc ddddd");

		final MapDocument resB =

				result(config,

						"B",

						"qwert aaabbbbbbbb bbb ccc ddddd");

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		final double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		// assertTrue(d.getScore() == 0.0);

	}

	@Test

	public void testDistanceProdConf3() {

		final Config config = getResultProdConf();

		final List<String> authorsA = Lists.newArrayList("Bardi, Alessia", "Manghi, Paolo", "Artini, Michele", "a");

		final List<String> authorsB = Lists.newArrayList("Bardi Alessia", "Manghi Paolo", "Artini Michele");

		final List<String> pid = Lists.newArrayList();

		final MapDocument resA =

				result(config,

						"A",

						"qwerty aaabbbbbbbb bbb ccc ddddd", "2003", pid, authorsA);

		final MapDocument resB =

				result(config,

						"B",

						"qwert aaabbbbbbbb bbb ccc ddddd", "2003", pid, authorsB);

		final ScoreResult sr = new PaceDocumentDistance().between(resA, resB, config);

		final double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		assertTrue(d == 0.0);

	}

	@Test

	public void testDistancePersonConf1() {

		final Config config = getPersonConf();

		final MapDocument p1 = person(config, "p1_id", getPersonGT("/eu/dnetlib/pace/model/gt.author.manghi1.fo.json"));

		final MapDocument p2 = person(config, "p2_id", getPersonGT("/eu/dnetlib/pace/model/gt.author.manghi2.fo.json"));

		final ScoreResult sr = new PaceDocumentDistance().between(p1, p2, config);

		final double d = sr.getScore();

		System.out.println(String.format(" d ---> %s", d));

		// assertTrue(d.getScore() == 0.0);

	}

}

package eu.dnetlib.data.mapreduce.util;

import static org.junit.Assert.assertFalse;

import static org.junit.Assert.assertNotNull;

import java.util.List;

import org.junit.Test;

import eu.dnetlib.data.proto.KindProtos.Kind;

public class DNGFDecoderTest {

	@Test

	public void testAsXml() {

		final DNGFDecoder decoder = DNGFTest.embed(DNGFTest.getResult("50|id_1"), Kind.entity);

		assertNotNull(decoder);

		assertNotNull(decoder.asXml());

		System.out.println(decoder.asXml());

	}

	@Test

	public void testGetFieldValues() {

		final DNGFDecoder decoder = DNGFTest.embed(DNGFTest.getResult("50|id_1"), Kind.entity);

		final String path = "publication/metadata/title/value";

		final List<String> titles = decoder.decodeEntity().getFieldValues(path);

		assertNotNull(titles);

		assertFalse(titles.isEmpty());

	}

}

package eu.dnetlib.data.mapreduce.util;

import org.junit.Test;

public class DNGFRowKeyDecoderTest {

	@Test

	public void test() {

		String id1 = "50|acnbad______::0a454baf9c61e63d42fb83ab549f8062";

		DNGFRowKeyDecoder d = DNGFRowKeyDecoder.decode(id1);

		System.out.println(d.getId());

	}

}

package eu.dnetlib.data.mapreduce.util;

import com.google.protobuf.Descriptors.FieldDescriptor;

import eu.dnetlib.data.proto.DNGFProtos.DNGFRel;

import eu.dnetlib.data.proto.RelTypeProtos.RelType;

import eu.dnetlib.data.proto.RelTypeProtos.SubRelType;

import eu.dnetlib.data.proto.SubRelProtos.Authorship;

import org.junit.Before;

import org.junit.Test;

import static org.junit.Assert.assertEquals;

import static org.junit.Assert.assertNotNull;

public class DNGFRelDecoderTest {

	private DNGFRel dngfRel;

	@Before

	public void setUp() {

		dngfRel = DNGFTest.getPersonPublication("ID_1", "ID_2", "1", "isAuthor");

	}

	@Test

	public void testSetClass() {

		DNGFRelDecoder d1 = DNGFRelDecoder.decode(dngfRel);

		assertNotNull(d1);

		assertEquals("isAuthor", d1.getRelClass());

		DNGFRelDecoder d2 = DNGFRelDecoder.decode(d1.setClassId("hasAuthor").build());

		assertEquals("hasAuthor", d2.getRelClass());

		assertEquals("hasAuthor", d2.getRelMetadata().getSemantics().getClassid());

		assertEquals("hasAuthor", d2.getRelMetadata().getSemantics().getClassname());

		FieldDescriptor fd = Authorship.getDescriptor().findFieldByName("ranking");

		assertEquals(d1.getSubRel().getField(fd), d2.getSubRel().getField(fd));

	}

	@Test

	public void testGetCF() {

		assertEquals("personPublication_authorship_isAuthorOf", DNGFRelDecoder.getCFQ(RelType.personPublication, SubRelType.authorship, Authorship.RelName.isAuthorOf));

		assertEquals("personPublication_authorship_isAuthorOf", DNGFRelDecoder.getCFQ(RelType.personPublication, SubRelType.authorship, "isAuthorOf"));

	}

}

package eu.dnetlib.data.actionmanager.actions;

import java.io.IOException;

import java.io.InputStream;

import java.io.StringReader;

import java.io.StringWriter;

import java.util.Arrays;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import javax.xml.transform.TransformerException;

import eu.dnetlib.data.proto.DNGFProtos.DNGF;

import eu.dnetlib.rmi.data.hadoop.actionmanager.ActionManagerException;

import eu.dnetlib.rmi.data.hadoop.actionmanager.Agent;

import eu.dnetlib.rmi.data.hadoop.actionmanager.Operation;

import eu.dnetlib.rmi.data.hadoop.actionmanager.Provenance;

import eu.dnetlib.rmi.data.hadoop.actionmanager.actions.ActionFactory;

import eu.dnetlib.rmi.data.hadoop.actionmanager.actions.AtomicAction;

import eu.dnetlib.rmi.data.hadoop.actionmanager.actions.XsltInfoPackageAction;

import org.apache.commons.io.IOUtils;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

import org.dom4j.Document;

import org.dom4j.DocumentException;

import org.dom4j.io.SAXReader;

import org.junit.Before;

import org.junit.Test;

import org.junit.runner.RunWith;

import org.mockito.Mock;

import org.mockito.Mockito;

import org.mockito.runners.MockitoJUnitRunner;

import org.springframework.core.io.Resource;

import static org.junit.Assert.*;

@RunWith(MockitoJUnitRunner.class)

public class ActionFactoryTest {

	private static final Log log = LogFactory.getLog(ActionFactoryTest.class);

	private static String basePathProfiles = "/eu/dnetlib/bootstrap/profiles/TransformationRuleDSResources/TransformationRuleDSResourceType/";

	private final static Agent agent = new Agent("agentId", "agentName", Agent.AGENT_TYPE.algo);

	private final static String trust = "0.9";

	private final InputStream recordOdfInputStream = getClass().getResourceAsStream("recordOdf.xml");

	private final InputStream recordOafInputStream = getClass().getResourceAsStream("recordOaf.xml");

	private ActionFactory actionFactory;

	private Map<String, Resource> xslts = new HashMap<>();

	@Mock

	private Resource oaf2insertActions;

	@Mock

	private Resource oaf2updateActions;

	@Mock

	private Resource odf2insertActions;

	@Mock

	private Resource odf2updateActions;

	@Mock

	private Resource rels2actions;

	@Before

	public void setUp() throws Exception {

		actionFactory = new ActionFactory();

		xslts.put("oaf2insertActions", oaf2insertActions);

		xslts.put("oaf2updateActions", oaf2updateActions);

		xslts.put("odf2insertActions", odf2insertActions);

		xslts.put("odf2updateActions", odf2updateActions);

		xslts.put("rels2actions", rels2actions);

		Mockito.when(oaf2insertActions.getInputStream()).thenReturn(loadFromTransformationProfile("oaf2insertActions.xml"));

		Mockito.when(oaf2updateActions.getInputStream()).thenReturn(loadFromTransformationProfile("oaf2updateActions.xml"));

		Mockito.when(odf2insertActions.getInputStream()).thenReturn(loadFromTransformationProfile("odf2insertActions.xml"));

		Mockito.when(odf2updateActions.getInputStream()).thenReturn(loadFromTransformationProfile("odf2updateActions.xml"));

//		Mockito.when(rels2actions.getInputStream()).thenReturn(loadFromTransformationProfile("rels2actions.xml"));

		actionFactory.setXslts(xslts);

	}

	@Test

	public void testBeans() {

		assertNotNull(actionFactory);

		assertNotNull(actionFactory.getXslts());

		assertFalse(actionFactory.getXslts().isEmpty());

	}

	@Test

	public void testDataciteInsert() throws ActionManagerException, IOException, TransformerException, DocumentException {

		XsltInfoPackageAction action =

				actionFactory.generateInfoPackageAction("odf2insertActions", "rawSet", agent, Operation.INSERT, asString(recordOdfInputStream),

						Provenance.sysimport_crosswalk_datasetarchive, "datacite____", trust);

		checkActions(action, action.asAtomicActions());

	}

	@Test

	public void testDataciteUpdate() throws ActionManagerException, IOException, TransformerException, DocumentException {

		XsltInfoPackageAction action =

				actionFactory.generateInfoPackageAction("odf2updateActions", "rawSet", agent, Operation.UPDATE, asString(recordOdfInputStream),

						Provenance.sysimport_crosswalk_datasetarchive, "datacite____", trust);

		checkActions(action, action.asAtomicActions());

	}

	@Test

	public void testRecordOafInsert() throws ActionManagerException, IOException, TransformerException, DocumentException {

		XsltInfoPackageAction action =

				actionFactory.generateInfoPackageAction("oaf2insertActions", "rawSet", agent, Operation.INSERT, asString(recordOafInputStream),

						Provenance.sysimport_crosswalk_datasetarchive, "od_______296", trust);

		checkActions(action, action.asAtomicActions());

	}

	@Test

	public void testRecordOafUpdate() throws ActionManagerException, IOException, TransformerException, DocumentException {

		XsltInfoPackageAction action =

				actionFactory.generateInfoPackageAction("oaf2updateActions", "rawSet", agent, Operation.INSERT, asString(recordOafInputStream),

						Provenance.sysimport_crosswalk_datasetarchive, "od_______296", trust);

		checkActions(action, action.asAtomicActions());

	}

	private void checkActions(final XsltInfoPackageAction action, final List<AtomicAction> atomicActionList)

			throws TransformerException, DocumentException, com.google.protobuf.InvalidProtocolBufferException {

		for (AtomicAction a : action.calculateAtomicActions()) {

			assertNotNull(a.getTargetValue());

			String actionJSON = AtomicActionSerialiser.toJSON(a);

			log.info(actionJSON);

			final AtomicAction aa = AtomicActionDeserialiser.fromJSON(actionJSON);

			assertEquals(a.getRawSet(), aa.getRawSet());

			assertEquals(a.getTargetColumn(), aa.getTargetColumn());

			assertEquals(a.getTargetColumnFamily(), aa.getTargetColumnFamily());

			assertEquals(a.getTargetRowKey(), aa.getTargetRowKey());

			assertEquals(a.getActionType(), aa.getActionType());

			assertEquals(a.getRowKey(), aa.getRowKey());

			assertEquals(a.getAgent().getId(), aa.getAgent().getId());

			assertEquals(a.getAgent().getName(), aa.getAgent().getName());

			assertEquals(a.getAgent().getType(), aa.getAgent().getType());

			assertTrue(Arrays.equals(a.getTargetValue(), aa.getTargetValue()));

			System.out.println(DNGF.parseFrom(aa.getTargetValue()));

		}

		for (AtomicAction aa : atomicActionList) {

			assertNotNull(aa);

		}

		log.info("N. puts: " + atomicActionList.size());

	}

	private String asString(final InputStream i) throws IOException {

		StringWriter writer = new StringWriter();

		IOUtils.copy(i, writer);

		return writer.toString();

	}

	private InputStream loadFromTransformationProfile(final String profilePath) {

		log.info("Loading xslt from: " + basePathProfiles + profilePath);

		InputStream profile = getClass().getResourceAsStream(basePathProfiles + profilePath);

		final String s;

		try {

			s = IOUtils.toString(profile);

			log.debug("profile: " + s);

		} catch (IOException e) {

			e.printStackTrace();

			throw new RuntimeException(e);

		}

		final SAXReader saxReader = new SAXReader();

		Document doc = null;

		try {

			doc = saxReader.read(new StringReader(s));

		} catch (DocumentException e) {

			e.printStackTrace();

			throw new RuntimeException(e);

		}

		String xslt = doc.selectSingleNode("//SCRIPT/CODE/*[local-name()='stylesheet']").asXML();

		return IOUtils.toInputStream(xslt);

	}

}

package eu.dnetlib.data.transform.xml;

import java.util.List;

import eu.dnetlib.data.transform.xml.OpenTrialsXsltFunctions.JsonProv;

import org.junit.After;

import org.junit.Before;

import org.junit.Test;

import static org.junit.Assert.assertEquals;

/**

 * OpenTrialsXsltFunctions Tester.

 *

 */

public class OpenTrialsXsltFunctionsTest {

	private String jsonProv = "[{\"url\" : \"http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT00378508\", \"sourceID\" : \"77eb42c5-0ec7-4e31-963a-5736b66f2d26\", \"sourceName\" : \"ictrp\"},{\"url\" : \"https://www.clinicaltrials.gov/ct2/show/NCT00378508?lup_e=02%2F04%2F2016&lup_s=01%2F01%2F2001&rank=175075&resultsxml=true\", \"sourceID\" : \"b389497c-0833-432b-a09b-930526b7b4d4\", \"sourceName\" : \"nct\"}]";

	private String jsonProvWithNull = "[{\"url\" : \"\", \"sourceID\" : \"77eb42c5-0ec7-4e31-963a-5736b66f2d26\", \"sourceName\" : \"ictrp\"},{\"url\" : \"https://www.clinicaltrials.gov/ct2/show/NCT00378508?lup_e=02%2F04%2F2016&lup_s=01%2F01%2F2001&rank=175075&resultsxml=true\", \"sourceID\" : \"b389497c-0833-432b-a09b-930526b7b4d4\", \"sourceName\" : \"nct\"}]";

	private String jidentifiers = "{112683,NCT00920439}";

	@Before

	public void before() throws Exception {

	}

	@After

	public void after() throws Exception {

	}

	/**

	 * Method: getProvs(String jsonProvList)

	 */

	@Test

	public void testGetProvs() throws Exception {

		List<JsonProv> list = OpenTrialsXsltFunctions.getProvs(jsonProv);

		assertEquals(2, list.size());

	}

	/**

	 * Method: getMainIdentifierURL(String jsonProvList)

	 */

	@Test

	public void testGetMainIdentifierURL() throws Exception {

		String url = OpenTrialsXsltFunctions.getMainIdentifierURL(jsonProv);

		assertEquals( "http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT00378508", url );

		url = OpenTrialsXsltFunctions.getMainIdentifierURL(jsonProvWithNull);

		assertEquals("https://www.clinicaltrials.gov/ct2/show/NCT00378508?lup_e=02%2F04%2F2016&lup_s=01%2F01%2F2001&rank=175075&resultsxml=true", url);

	}

} 

package eu.dnetlib.data.transform;

import java.io.IOException;

import java.io.StringWriter;

import java.text.ParseException;

import java.text.SimpleDateFormat;

import java.util.Arrays;

import java.util.List;

import com.google.protobuf.InvalidProtocolBufferException;

import com.googlecode.protobuf.format.JsonFormat;

import eu.dnetlib.data.mapreduce.util.DNGFTest;

import eu.dnetlib.data.proto.DNGFProtos.DNGF;

import eu.dnetlib.data.proto.DNGFProtos.DNGFEntity;

import eu.dnetlib.data.proto.KindProtos.Kind;

import org.apache.commons.codec.binary.Base64;

import org.apache.commons.io.IOUtils;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

import org.apache.solr.common.SolrInputDocument;

import org.apache.solr.common.SolrInputField;

import org.dom4j.DocumentException;

import org.junit.Before;

import org.junit.Test;

import static org.junit.Assert.assertFalse;

import static org.junit.Assert.assertNotNull;

public class SolrProtoMapperTest {

	private static final Log log = LogFactory.getLog(SolrProtoMapper.class); // NOPMD by marko on 11/24/08 5:02 PM

	private static final String outFormat = new String("yyyy-MM-dd'T'hh:mm:ss'Z'");

	private final static List<String> dateFormats = Arrays.asList("yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "dd-MM-yyyy", "dd/MM/yyyy", "yyyy");

	private String fields;

	@Before

	public void setUp() throws IOException {

		final StringWriter sw = new StringWriter();

		IOUtils.copy(getClass().getResourceAsStream("fields.xml"), sw);

		fields = sw.toString();

		assertNotNull(fields);

		assertFalse(fields.isEmpty());

		log.info(fields);

	}

	@Test

	public void testProto2SolrDocument() throws DocumentException, InvalidProtocolBufferException {

		final SolrProtoMapper mapper = new SolrProtoMapper(fields);

		assertNotNull(mapper);

		final DNGFEntity.Builder entity = DNGFTest.getResultBuilder("01");

		entity.addChildren(DNGFTest.getResultBuilder("01_children"));

		final DNGF oaf = DNGFTest.embed(entity.build(), Kind.entity).getDNGF();

		assertNotNull(oaf.getEntity().getChildrenList());

		assertFalse(oaf.getEntity().getChildrenList().isEmpty());

		log.info("byte[] size: " + oaf.toByteArray().length);

		log.info("json size:   " + JsonFormat.printToString(oaf).length());

		log.info("base64 size: " + Base64.encodeBase64String(oaf.toByteArray()).length());

		final byte[] decodeBase64 = Base64.decodeBase64(Base64.encodeBase64String(oaf.toByteArray()));

		log.info("decoded: " + JsonFormat.printToString(DNGF.parseFrom(decodeBase64)));

		final SolrInputDocument doc = mapper.map(oaf, getParsedDateField("2015-02-15"), "asd", "action-set");

		assertNotNull(doc);

		for (final SolrInputField f : doc.values()) {

			log.info(f);

		}

	}

	/**

	 * method return a solr-compatible string representation of a date

	 *

	 * @param date

	 * @return

	 * @throws DocumentException

	 * @throws ParseException

	 */

	public String getParsedDateField(final String date) {

		for (String formatString : dateFormats) {

			try {

				return new SimpleDateFormat(outFormat).format(new SimpleDateFormat(formatString).parse(date));

			} catch (ParseException e) {}

		}

		throw new IllegalStateException("unable to parse date: " + date);

	}

}

net.sf.saxon.TransformerFactoryImpl

{ 

	"wf" : { 

        "threshold" : "0.99", 

        "run" : "001", 

        "entityType" : "organization", 

        "orderField" : "title", 

        "queueMaxSize" : "2000",

        "groupMaxSize" : "10",

        "slidingWindowSize" : "200",

        "rootBuilder" : [ "organization" ],

        "includeChildren" : "true" 

    },

	"pace" : {		

  		"conditions" : [ ],		

		"model" : [

			{ "name" : "legalname", "algo" : "JaroWinkler", "type" : "String", "weight" : "0.6", "ignoreMissing" : "false", "path" : "organization/metadata/legalname/value" },

			{ "name" : "legalshortname", "algo" : "JaroWinkler", "type" : "String", "weight" : "0.4", "ignoreMissing" : "true", "path" : "organization/metadata/legalshortname/value" }

		],

		"blacklists" : { } 		

	}

}

{"id":"30|dedup_wf_001::e78059705c3885a10440c8021afbdd4a","author":{"frequency":6,"id":"30|od______2294::9897283f935d7c2f4c11cebf65ae3098","fullname":"Manghi, Paolo","firstname":"Paolo","secondnames":"Manghi"},"merged":[{"id":"30|od______2294::9897283f935d7c2f4c11cebf65ae3098","fullname":"Manghi, Paolo","firstname":"Paolo","secondnames":"Manghi"},{"id":"30|doaj10829873::6cff63f7eafbb51fd6a1c268f4f0227f","fullname":"Manghi, Paolo","firstname":"Paolo","secondnames":"Manghi"},{"id":"30|od______2367::9897283f935d7c2f4c11cebf65ae3098","fullname":"Manghi, Paolo","firstname":"Paolo","secondnames":"Manghi"},{"id":"30|doaj10829873::f67c45f3bd4e4e4c4942a373799e0457","fullname":"Manghi, Paolo","firstname":"Paolo","secondnames":"Manghi"},{"id":"30|doaj10829873::39a29e7c15e04cdef8aecaa062b4f000","fullname":"Manghi, Paolo","firstname":"Paolo","secondnames":"Manghi"},{"id":"30|doaj10829873::f9b4de41343d956271d88f93ba68c31d","fullname":"Manghi, 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