D-Net

{"type_source": "SVN", "goal": "package -U -T 4C source:jar", "url": "http://svn-public.driver.research-infrastructures.eu/driver/dnet40/modules/dnet-openaireplus-mapping-utils/trunk/", "deploy_repository": "dnet4-snapshots", "version": "4", "mail": "sandro.labruzzo@isti.cnr.it,michele.artini@isti.cnr.it, claudio.atzori@isti.cnr.it, alessia.bardi@isti.cnr.it", "deploy_repository_url": "http://maven.research-infrastructures.eu/nexus/content/repositories/dnet4-snapshots", "name": "dnet-openaireplus-mapping-utils"}

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.List;

import org.apache.commons.io.IOUtils;

import org.apache.commons.lang.RandomStringUtils;

import org.apache.commons.lang.StringUtils;

import com.google.gson.Gson;

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

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.OafProtos.Oaf;

import eu.dnetlib.data.proto.OafProtos.OafEntity;

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

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

import eu.dnetlib.data.proto.ResultProtos.Result;

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;

public abstract class AbstractProtoPaceTest extends OafTest {

	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 Oaf oaf) {

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

	}

	protected Oaf 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("/eu/dnetlib/pace/model/gt.author.manghi1.json");

		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, null, null);

	}

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

		return result(config, id, title, date, null, 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) {

		final Result.Metadata.Builder metadata = Result.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 OafEntity.Builder entity = oafEntity(id, eu.dnetlib.data.proto.TypeProtos.Type.result);

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

		if (authors != null) {

			for (final String author : authors) {

				result.addAuthor(person(author));

			}

		}

		entity.setResult(result);

		if (!StringUtils.isBlank(pid)) {

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

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

		}

		final OafEntity 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 OafEntity.Builder oafEntity(final String id, final eu.dnetlib.data.proto.TypeProtos.Type type) {

		final OafEntity.Builder entity = OafEntity.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 OafEntity.Builder entity = oafEntity(id, eu.dnetlib.data.proto.TypeProtos.Type.result);

		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.List;

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 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 double d = new PaceDocumentDistance().between(resA, resB, config);

		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 double d = new PaceDocumentDistance().between(resA, resB, config);

		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 double d = new PaceDocumentDistance().between(resA, resB, config);

		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 double d = new PaceDocumentDistance().between(resA, resB, config);

		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 double d = new PaceDocumentDistance().between(resA, resB, config);

		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 double d = new PaceDocumentDistance().between(resA, resB, config);

		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 double d = new PaceDocumentDistance().between(orgA, orgB, config);

		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 double d = new PaceDocumentDistance().between(resA, resB, config);

		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", "http://dx.doi.org/10.1594/PANGAEA.726855");

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

		final double d = new PaceDocumentDistance().between(resA, resB, config);

		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", "http://dx.doi.org/10.1594/PANGAEA.726855");

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

		final double d = new PaceDocumentDistance().between(resA, resB, config);

		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 double d = new PaceDocumentDistance().between(resA, resB, config);

		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 double d = new PaceDocumentDistance().between(resA, resB, config);

		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 double d = new PaceDocumentDistance().between(resA, resB, config);

		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 double d = new PaceDocumentDistance().between(resA, resB, config);

		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);

	}

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

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

		final double d = new PaceDocumentDistance().between(resA, resB, config);

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

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

		final double d = new PaceDocumentDistance().between(resA, resB, config);

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

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

		final double d = new PaceDocumentDistance().between(resA, resB, config);

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

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

		final double d = new PaceDocumentDistance().between(resA, resB, config);

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

		// assertTrue(d == 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", null,

						authorsB);

		final double d = new PaceDocumentDistance().between(resA, resB, config);

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

		// assertTrue(d == 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 double d = new PaceDocumentDistance().between(resA, resB, config);

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

		// assertTrue(d == 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 double d = new PaceDocumentDistance().between(resA, resB, config);

		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.json"));

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

		final double d = new PaceDocumentDistance().between(p1, p2, config);

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

		// assertTrue(d == 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;

import eu.dnetlib.miscutils.functional.xml.IndentXmlString;

public class OafDecoderTest {

	@Test

	public void testAsXml() {

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

		assertNotNull(decoder);

		assertNotNull(decoder.asXml());

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

	}

	@Test

	public void testGetFieldValues() {

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

		final String path = "result/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 OafRowKeyDecoderTest {

	@Test

	public void test() {

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

		OafRowKeyDecoder d = OafRowKeyDecoder.decode(id1);

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

	}

}

package eu.dnetlib.data.mapreduce.util;

import static org.junit.Assert.assertEquals;

import static org.junit.Assert.assertNotNull;

import org.junit.Before;

import org.junit.Test;

import com.google.protobuf.Descriptors.FieldDescriptor;

import eu.dnetlib.data.proto.OafProtos.OafRel;

import eu.dnetlib.data.proto.PersonResultProtos.PersonResult.Authorship;

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

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

public class OafRelDecoderTest {

	private OafRel oafRel;

	@Before

	public void setUp() {

		oafRel = OafTest.getPersonResult("ID_1", "ID_2", "1", "isAuthor");

	}

	@Test

	public void testSetClass() {

		OafRelDecoder d1 = OafRelDecoder.decode(oafRel);

		assertNotNull(d1);

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

		OafRelDecoder d2 = OafRelDecoder.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("personResult_authorship_isAuthorOf", OafRelDecoder.getCFQ(RelType.personResult, SubRelType.authorship, Authorship.RelName.isAuthorOf));

		assertEquals("personResult_authorship_isAuthorOf", OafRelDecoder.getCFQ(RelType.personResult, SubRelType.authorship, "isAuthorOf"));

	}

}

package eu.dnetlib.data.transform;

import static org.junit.Assert.assertFalse;

import static org.junit.Assert.assertNotNull;

import java.io.IOException;

import java.io.StringWriter;

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 com.google.protobuf.InvalidProtocolBufferException;

import com.googlecode.protobuf.format.JsonFormat;

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

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

import eu.dnetlib.data.proto.OafProtos.Oaf;

import eu.dnetlib.data.proto.OafProtos.OafEntity;

import eu.dnetlib.functionality.index.solr.feed.InputDocumentFactory;

public class SolrProtoMapperTest {

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

	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 OafEntity.Builder entity = OafTest.getResultBuilder("01");

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

		final Oaf oaf = OafTest.embed(entity.build(), Kind.entity).getOaf();

		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(Oaf.parseFrom(decodeBase64)));

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

		assertNotNull(doc);

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

			log.info(f);

		}

	}

}

{ 

	"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" : { } 		

	}

}

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			"title" : [

				"(?i)^Cases? of Puerperal Convulsions$",

				"(?i)^Operative Gyna?ecology$",

				"(?i)^Mind the gap\!?\:?$",

				"^Chronic fatigue syndrome\.?$",

				"^Cartas? ao editor Letters? to the Editor$",

				"^Note from the Editor$",

				"^Anesthesia Abstract$",

				"^Annual report$",

				"(?i)^“?THE RADICAL PREVENTION OF VENEREAL DISEASE\.?”?$",

				"(?i)^Graph and Table of Infectious Diseases?$",

				"^Presentation$",

				"(?i)^Reviews and Information on Publications$",

				"(?i)^PUBLIC HEALTH SERVICES?$",

				"(?i)^COMBINED TEXT-?BOOK OF OBSTETRICS AND GYN(Æ|ae)COLOGY$",

				"(?i)^Adrese autora$",

				"(?i)^Systematic Part .*\. Catalogus Fossilium Austriae, Band 2: Echinoidea neogenica$",

				"(?i)^Acknowledgement to Referees$",

				"(?i)^Behçet's disease\.?$",

				"(?i)^Isolation and identification of restriction endonuclease.*$",

				"(?i)^CEREBROVASCULAR DISEASES?.?$",

				"(?i)^Screening for abdominal aortic aneurysms?\.?$",

				"^Event management$",

				"(?i)^Breakfast and Crohn's disease.*\.?$",

				"^Cálculo de concentraciones en disoluciones acuosas. Ejercicio interactivo\..*\.$",

				"(?i)^Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of Autism spectrum disorders?\.?$",

				"^Gushi hakubutsugaku$",

				"^Starobosanski nadpisi u Bosni i Hercegovini \(.*\)$",							

				"^Intestinal spirocha?etosis$",

				"^Treatment of Rodent Ulcer$",

				"(?i)^\W*Cloud Computing\W*$",

				"^Compendio mathematico : en que se contienen todas las materias mas principales de las Ciencias que tratan de la cantidad$",				

				"^Free Communications, Poster Presentations: Session [A-F]$",

				"^“The Historical Aspects? of Quackery\.?”$",

				"^A designated centre for people with disabilities operated by St John of God Community Services (Limited|Ltd), Louth$",

				"^P(er|re)-Mile Premiums for Auto Insurance\\.?$",

				"(?i)^Case Report$",							

				"^Boletín Informativo$",

				"(?i)^Glioblastoma Multiforme$",

				"(?i)^Nuevos táxones animales descritos en la península Ibérica y Macaronesia desde 1994 \\(.*\\)$",

				"^Zaměstnanecké výhody$",

				"(?i)^The Economics of Terrorism and Counter-Terrorism: A Survey \\(Part .*\\)$",

				"(?i)^Carotid body tumours?\\.?$", 

				"(?i)^\\[Españoles en Francia : La condición Emigrante.*\\]$",

				"^Avant-propos$",

				"(?i)^St\. Patrick's Cathedral, Dublin, County Dublin - Head(s)? and Capital(s)?$",

				"(?i)^St\. Patrick's Cathedral, Dublin, County Dublin - Bases?$",

				"(?i)^PUBLIC HEALTH VERSUS THE STATE$",							

				"^Viñetas de Cortázar$",

				"(?i)^Search for heavy neutrinos and W(\\[|_|\\(|_\\{|-)?R(\\]|\\)|\\})? bosons with right-handed couplings in a left-right symmetric model in pp collisions at.*TeV(\.)?$",

				"(?i)^Measurement of the pseudorapidity and centrality dependence of the transverse energy density in Pb(-?)Pb collisions at.*tev(\.?)$",				

				"(?i)^Search for resonances decaying into top-quark pairs using fully hadronic decays in pp collisions with ATLAS at.*TeV$",

				"(?i)^Search for neutral minimal supersymmetric standard model Higgs bosons decaying to tau pairs in pp collisions at.*tev$",

				"(?i)^Relatório de Estágio (de|em) Angiologia e Cirurgia Vascular$",

				"^Aus der AGMB$",				

				"^Znanstveno-stručni prilozi$",

				"^Zhodnocení finanční situace podniku a návrhy na zlepšení$",

				"^Evaluation of the Financial Situation in the Firm and Proposals to its Improvement$",

				"^Finanční analýza podniku$",

				"^Financial analysis( of business)?$",

				"(?i)^Textbook of Gyn(a)?(Æ)?(e)?cology$",

				"^Jikken nihon shūshinsho$",

				"(?i)^CORONER('|s)(s|') INQUESTS$",

				"(?i)^(Μελέτη παραγόντων )?risk management( για ανάπτυξη και εφαρμογή ενός πληροφοριακού συστήματος| και ανάπτυξη συστήματος)?$",				

				"(?i)^Consultants' contract(s)?$",

				"(?i)^Upute autorima$",

				"(?i)^Bijdrage tot de Kennis van den Godsdienst der Dajaks van Lan(d|f)ak en Tajan$",

				"^Joshi shin kokubun$",

				"^Kōtō shōgaku dokuhon nōson'yō$",

				"^Jinjō shōgaku shōka$",

				"^Shōgaku shūjichō$",

				"^Nihon joshi dokuhon$",

				"^Joshi shin dokuhon$",

				"^Chūtō kanbun dokuhon$",

				"^Wabun dokuhon$",

				"(?i)^(Analysis of economy selected village or town|Rozbor hospodaření vybrané obce či města)$",

				"(?i)^cardiac rehabilitation$",

				"(?i)^Analytical summary$",

				"^Thesaurus resolutionum Sacrae Congregationis Concilii$",

				"(?i)^Sumario analítico(\\s{1})?(Analitic summary)?$", 

				"^Prikazi i osvrti$",

				"^Rodinný dům s provozovnou$",

				"^Family house with an establishment$",

				"^Shinsei chūtō shin kokugun$",

				"^Pulmonary alveolar proteinosis(\\.?)$",

				"^Shinshū kanbun$",

				"^Viñeta(s?) de Rodríguez$",

				"(?i)^RUBRIKA UREDNIKA$",

				"^A Matching Model of the Academic Publication Market$",

				"^Yōgaku kōyō$",

				"^Internetový marketing$",

				"^Internet marketing$",

				"^Chūtō kokugo dokuhon$",

				"^Kokugo dokuhon$",

				"^Antibiotic Cover for Dental Extraction(s?)$",

				"^Strategie podniku$",				

				"^Strategy of an Enterprise$",

				"(?i)^respiratory disease(s?)(\.?)$",

				"^Award(s?) for Gallantry in Civil Defence$",

				"^Podniková kultura$",

				"^Corporate Culture$",

				"^Severe hyponatraemia in hospital inpatient(s?)(\.?)$",

				"^Pracovní motivace$",

				"^Work Motivation$",

				"^Kaitei kōtō jogaku dokuhon$",

				"^Konsolidovaná účetní závěrka$",

				"^Consolidated Financial Statements$",

				"(?i)^intracranial tumour(s?)$",

				"^Climate Change Mitigation Options and Directed Technical Change: A Decentralized Equilibrium Analysis$",

				"^\\[CERVECERIAS MAHOU(\\.|\\:) INTERIOR\\] \\[Material gráfico\\]$",

				"^Housing Market Dynamics(\\:|\\.) On the Contribution of Income Shocks and Credit Constraint(s?)$",

				"^\\[Funciones auxiliares de la música en Radio París,.*\\]$",

				"^Úroveň motivačního procesu jako způsobu vedení lidí$",

				"^The level of motivation process as a leadership$",

				"^Pay-beds in N(\\.?)H(\\.?)S(\\.?) Hospitals$",

				"(?i)^news and events$",

				"(?i)^NOVOSTI I DOGAĐAJI$",

				"^Sansū no gakushū$",

				"^Posouzení informačního systému firmy a návrh změn$",

				"^Information System Assessment and Proposal for ICT Modification$",

				"^Stresové zatížení pracovníků ve vybrané profesi$",

				"^Stress load in a specific job$",

				"^Sunday: Poster Sessions, Pt.*$",

				"^Monday: Poster Sessions, Pt.*$",

				"^Wednesday: Poster Sessions, Pt.*",

				"^Tuesday: Poster Sessions, Pt.*$",

				"^Analýza reklamy$",

				"^Analysis of advertising$",

				"^Shōgaku shūshinsho$",

				"^Shōgaku sansū$",

				"^Shintei joshi kokubun$",

				"^Taishō joshi kokubun dokuhon$",

				"^Joshi kokubun$",				

				"^Účetní uzávěrka a účetní závěrka v ČR$",

				"(?i)^The \"?Causes\"? of Cancer$",

				"^Normas para la publicación de artículos$",

				"^Editor('|s)(s|') [Rr]eply$",

				"^Editor(’|s)(s|’) letter$",

				"^Redaktoriaus žodis$",		

				"^DISCUSSION ON THE PRECEDING PAPER$",

				"^Kōtō shōgaku shūshinsho jidōyō$",

				"^Shōgaku nihon rekishi$",

				"^(Theory of the flow of action currents in isolated myelinated nerve fibers).*$",

				"^Préface$",

				"^Occupational [Hh]ealth [Ss]ervices.$",

				"^In Memoriam Professor Toshiyuki TAKESHIMA$",

				"^Účetní závěrka ve vybraném podniku.*$",

				"^Financial statements in selected company$",

				"^Abdominal [Aa]ortic [Aa]neurysms.*$",

				"^Pseudomyxoma peritonei$",

				"^Kazalo autora$",			

				"(?i)^uvodna riječ$",

				"^Motivace jako způsob vedení lidí$",

				"^Motivation as a leadership$",

				"^Polyfunkční dům$",

				"^Multi\\-funkcional building$",

				"^Podnikatelský plán$",

				"^Business Plan$",

				"^Oceňování nemovitostí$",

				"^Marketingová komunikace$",

				"^Marketing communication$",

				"^Sumario Analítico$",

				"^Riječ uredništva$",

				"^Savjetovanja i priredbe$",

				"^Índice$",

				"^(Starobosanski nadpisi).*$",

				"^Vzdělávání pracovníků v organizaci$",

				"^Staff training in organization$",

				"^(Life Histories of North American Geometridae).*$",

				"^Strategická analýza podniku$",

				"^Strategic Analysis of an Enterprise$",

				"^Sadržaj$",

				"^Upute suradnicima$",

				"^Rodinný dům$",

				"(?i)^Fami(l)?ly house$",

				"^Upute autorima$",

				"^Strategic Analysis$",

				"^Finanční analýza vybraného podniku$",

				"^Finanční analýza$",

				"^Riječ urednika$",

				"(?i)^Content(s?)$",

				"(?i)^Inhalt$",

				"^Jinjō shōgaku shūshinsho jidōyō$",

				"(?i)^Index$",

				"^Chūgaku kokubun kyōkasho$",

				"^Retrato de una mujer$",

				"^Retrato de un hombre$",

				"^Kōtō shōgaku dokuhon$",

				"^Shotōka kokugo$",

				"^Shōgaku dokuhon$",

				"^Jinjō shōgaku kokugo dokuhon$",

				"^Shinsei kokugo dokuhon$",

				"^Teikoku dokuhon$",

				"^Instructions to Authors$",

				"^KİTAP TAHLİLİ$",

				"^PRZEGLĄD PIŚMIENNICTWA$",

				"(?i)^Presentación$",

				"^İçindekiler$",

				"(?i)^Tabl?e of contents$",

				"^(CODICE DEL BEATO DE LOS REYES FERNANDO I Y SANCHA).*$",

				"^(\\[MADRID\\. BIBL\\. NAC\\. N.*KING FERDINAND I.*FROM SAN ISIDORO DE LEON\\. FACUNDUS SCRIPSIT DATED.*\\]).*",

				"^Editorial( Board)?$",

				"(?i)^Editorial \\(English\\)$",

				"^Editörden$",			

				"^(Corpus Oral Dialectal \\(COD\\)\\.).*$",

				"^(Kiri Karl Morgensternile).*$",

				"^(\\[Eksliibris Aleksandr).*\\]$",

				"^(\\[Eksliibris Aleksandr).*$",

				"^(Eksliibris Aleksandr).*$",

				"^(Kiri A\\. de Vignolles).*$",

				"^(2 kirja Karl Morgensternile).*$",

				"^(Pirita kloostri idaosa arheoloogilised).*$",

				"^(Kiri tundmatule).*$",

				"^(Kiri Jenaer Allgemeine Literaturzeitung toimetusele).*$",

				"^(Eksliibris Nikolai Birukovile).*$",

				"^(Eksliibris Nikolai Issakovile).*$",

				"^(WHP Cruise Summary Information of section).*$",

				"^(Measurement of the top quark\\-pair production cross section with ATLAS in pp collisions at).*$",

				"^(Measurement of the spin\\-dependent structure function).*"

			] }	

	}

}

{ 

	"wf" : { 

        "threshold" : "0.99", 

        "run" : "001", 

        "entityType" : "result", 

        "orderField" : "title", 

        "queueMaxSize" : "2000",

        "groupMaxSize" : "10",

        "slidingWindowSize" : "200",

        "rootBuilder" : [ "result" ],

        "includeChildren" : "true" 

    },

	"pace" : {

  		"conditions" : [

  			{ "name" : "sizeMatch", "fields" : [ "authors" ] },

  			{ "name" : "titleVersionMatch", "fields" : [ "title" ] }		

  		 ],		

		"model" : [	

			{ "name" : "title", "algo" : "JaroWinkler", "type" : "String", "weight" : "0.5", "ignoreMissing" : "false", "path" : "result/metadata/title[qualifier#classid = {main title}]/value" },

			{ "name" : "authors", "algo" : "SortedLevel2JaroWinkler", "type" : "List", "weight" : "0.5", "ignoreMissing" : "true", "path" : "result/author/metadata/fullname/value" }

		],

		"blacklists" : { } 		

	}

}

<FIELDS>

	<FIELD name="oaftype" path="entity/type" tokenizable="false" indexable="true" stat="false" result="false"/>

	<FIELD name="objIdentifier" path="entity/id" tokenizable="false" indexable="true" stat="false" result="false"/>

	<FIELD name="collectedfrom" path="entity/collectedfrom/value" tokenizable="false" indexable="true" result="false" stat="false" />

	<FIELD name="pid" path="entity/pid[qualifier#classid = {doi}]/value" tokenizable="false" stat="false" result="false" indexable="true"/>

	<FIELD name="deletedbyinference" path="dataInfo/deletedbyinference" tokenizable="false" stat="false" result="false" indexable="true"/>        

	<FIELD name="inferred" path="dataInfo/inferred" tokenizable="false" stat="false" result="false" indexable="true"/>

	<!-- ORGANIZATION FIELDS -->

	<FIELD name="organizationlegalname" path="entity/organization/metadata/legalname/value" type="ngramtext" stat="false" indexable="true" result="false"/>

	<FIELD name="organizationlegalshortname" path="entity/organization/metadata/legalshortname/value" type="ngramtext" stat="false" indexable="true" result="false"/>

	<FIELD name="organizationwebsiteurl" path="entity/organization/metadata/websiteurl/value" stat="false" indexable="true" result="false"/>

	<!-- PERSON FIELDS -->

	<FIELD name="personfirstname" path="entity/person/metadata/firstname/value" stat="false" indexable="true" result="false"/>

	<FIELD name="personsecondnames" path="entity/person/metadata/secondnames/value" stat="false" indexable="true" result="false"/>

	<FIELD name="personfullname" path="entity/person/metadata/fullname/value" stat="false" indexable="true" result="false"/>

	<!-- RESULT FIELDS -->

	<FIELD name="resulttitle" path="entity/result/metadata/title/value | entity/children/result/metadata/title/value" stat="false" result="false" indexable="true"/>

	<FIELD name="resultdescription" path="entity/result/metadata/description/value" result="false" indexable="true" stat="false"/>

    <FIELD name="resultauthor" path="entity/result/author/metadata/fullname/value | entity/children/result/author/metadata/fullname/value" result="false" indexable="true" stat="false"/>

</FIELDS>

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<record>

  <metadata>