1342 lines
51 KiB
Java
1342 lines
51 KiB
Java
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package eu.dnetlib.dhp.oa.graph.raw;
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import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.cleanup;
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import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.fixVocabularyNames;
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import static org.junit.jupiter.api.Assertions.*;
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import static org.mockito.Mockito.lenient;
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import java.io.IOException;
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import java.util.List;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.stream.Collectors;
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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.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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import org.dom4j.DocumentException;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.mockito.Mock;
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import org.mockito.junit.jupiter.MockitoExtension;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.common.Constants;
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
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import eu.dnetlib.dhp.oa.graph.clean.CleaningRuleMap;
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import eu.dnetlib.dhp.oa.graph.clean.OafCleaner;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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import eu.dnetlib.dhp.schema.oaf.utils.PidType;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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@ExtendWith(MockitoExtension.class)
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class MappersTest {
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@Mock
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private ISLookUpService isLookUpService;
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@Mock
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private VocabularyGroup vocs;
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@BeforeEach
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public void setUp() throws Exception {
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lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs());
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lenient()
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.when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY))
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.thenReturn(synonyms());
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vocs = VocabularyGroup.loadVocsFromIS(isLookUpService);
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}
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@Test
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void testPublication() throws IOException {
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final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_record.xml")));
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final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
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assertEquals(1, list.stream().filter(o -> o instanceof Publication).count());
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assertEquals(4, list.stream().filter(o -> o instanceof Relation).count());
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Publication p = (Publication) list.stream().filter(o -> o instanceof Publication).findFirst().get();
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assertValidId(p.getId());
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assertEquals(2, p.getOriginalId().size());
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assertTrue(p.getOriginalId().contains("10.3897/oneeco.2.e13718"));
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assertValidId(p.getCollectedfrom().get(0).getKey());
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assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
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assertFalse(p.getDataInfo().getInvisible());
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assertEquals(1, p.getSource().size());
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assertTrue(StringUtils.isNotBlank(p.getDateofcollection()));
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assertTrue(StringUtils.isNotBlank(p.getDateoftransformation()));
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assertFalse(p.getAuthor().isEmpty());
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final Optional<Author> author = p
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.getAuthor()
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.stream()
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.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
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.findFirst();
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assertTrue(author.isPresent());
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final StructuredProperty pid = author
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.get()
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.getPid()
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.stream()
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.findFirst()
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.orElseThrow(() -> new IllegalStateException("missing author pid"));
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assertEquals("0000-0001-6651-1178", pid.getValue());
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assertEquals(ModelConstants.ORCID_PENDING, pid.getQualifier().getClassid());
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assertEquals(ModelConstants.ORCID_CLASSNAME, pid.getQualifier().getClassname());
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assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid());
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assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename());
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assertEquals("Votsi,Nefta", author.get().getFullname());
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assertEquals("Votsi", author.get().getSurname());
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assertEquals("Nefta", author.get().getName());
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assertFalse(p.getSubject().isEmpty());
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assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline()));
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assertTrue(StringUtils.isNotBlank(p.getJournal().getName()));
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assertTrue(p.getPid().isEmpty());
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assertNotNull(p.getInstance());
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assertFalse(p.getInstance().isEmpty());
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p
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.getInstance()
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.forEach(i -> {
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assertNotNull(i.getAccessright());
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assertEquals("OPEN", i.getAccessright().getClassid());
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});
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final Instance instance = p.getInstance().get(0);
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assertEquals("0001", instance.getRefereed().getClassid());
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assertNotNull(instance.getPid());
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assertTrue(instance.getPid().isEmpty());
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assertNotNull(instance.getInstanceTypeMapping());
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assertEquals(1, instance.getInstanceTypeMapping().size());
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Optional<InstanceTypeMapping> coarType = instance
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.getInstanceTypeMapping()
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.stream()
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.filter(itm -> ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName()))
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.findFirst();
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assertTrue(coarType.isPresent());
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assertNull(coarType.get().getTypeCode());
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assertNull(coarType.get().getTypeLabel());
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Optional<InstanceTypeMapping> userType = instance
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.getInstanceTypeMapping()
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.stream()
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.filter(itm -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName()))
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.findFirst();
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assertFalse(userType.isPresent());
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assertFalse(instance.getAlternateIdentifier().isEmpty());
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assertEquals("doi", instance.getAlternateIdentifier().get(0).getQualifier().getClassid());
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assertEquals("10.3897/oneeco.2.e13718", instance.getAlternateIdentifier().get(0).getValue());
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assertNotNull(instance.getFulltext());
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assertEquals("https://oneecosystem.pensoft.net/article/13718/", instance.getFulltext());
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assertNotNull(p.getBestaccessright());
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assertEquals("OPEN", p.getBestaccessright().getClassid());
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assertNotNull(p.getFulltext());
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assertEquals(1, p.getFulltext().size());
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assertEquals("https://oneecosystem.pensoft.net/article/13718/", p.getFulltext().get(0).getValue());
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// RESULT PROJECT
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List<Relation> resultProject = list
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.stream()
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.filter(o -> o instanceof Relation)
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.map(o -> (Relation) o)
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.filter(r -> ModelConstants.RESULT_PROJECT.equals(r.getRelType()))
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.collect(Collectors.toList());
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assertEquals(2, resultProject.size());
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final Relation rp1 = resultProject.get(0);
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final Relation rp2 = resultProject.get(1);
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verifyRelation(rp1);
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verifyRelation(rp2);
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assertTrue(rp1.getValidated());
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assertTrue(rp2.getValidated());
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assertEquals("2020-01-01", rp1.getValidationDate());
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assertEquals("2020-01-01", rp2.getValidationDate());
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assertEquals(rp1.getSource(), rp2.getTarget());
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assertEquals(rp2.getSource(), rp1.getTarget());
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// AFFILIATIONS
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List<Relation> affiliation = list
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.stream()
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.filter(o -> o instanceof Relation)
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.map(o -> (Relation) o)
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.filter(r -> ModelConstants.RESULT_ORGANIZATION.equals(r.getRelType()))
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.collect(Collectors.toList());
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assertEquals(2, affiliation.size());
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final Relation aff1 = affiliation.get(0);
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final Relation aff2 = affiliation.get(1);
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verifyRelation(aff1);
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verifyRelation(aff2);
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assertEquals(aff1.getSource(), aff2.getTarget());
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assertEquals(aff2.getSource(), aff1.getTarget());
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// COUNTRIES
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assertEquals(3, p.getCountry().size());
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assertEquals("IT", p.getCountry().get(0).getClassid());
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assertEquals("FR", p.getCountry().get(1).getClassid());
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assertEquals("DE", p.getCountry().get(2).getClassid());
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}
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private void verifyRelation(Relation r) {
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assertValidId(r.getSource());
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assertValidId(r.getTarget());
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assertValidId(r.getCollectedfrom().get(0).getKey());
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assertNotNull(r.getDataInfo());
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assertNotNull(r.getDataInfo().getTrust());
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assertTrue(StringUtils.isNotBlank(r.getRelClass()));
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assertTrue(StringUtils.isNotBlank(r.getRelType()));
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}
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@Test
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void testPublication_PubMed() throws IOException, DocumentException {
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final String xml = IOUtils
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.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_record_pubmed.xml")));
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final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
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assertEquals(1, list.size());
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assertTrue(list.get(0) instanceof Publication);
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final Publication p = (Publication) list.get(0);
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assertValidId(p.getId());
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assertEquals(2, p.getOriginalId().size());
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assertTrue(p.getOriginalId().contains("oai:pubmedcentral.nih.gov:1517292"));
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assertValidId(p.getCollectedfrom().get(0).getKey());
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assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
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assertFalse(p.getDataInfo().getInvisible());
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assertTrue(StringUtils.isNotBlank(p.getDateofcollection()));
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assertTrue(StringUtils.isNotBlank(p.getDateoftransformation()));
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assertFalse(p.getAuthor().isEmpty());
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final Optional<Author> author = p
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.getAuthor()
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.stream()
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.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
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.findFirst();
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assertTrue(author.isPresent());
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final StructuredProperty pid = author
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.get()
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.getPid()
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.stream()
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.findFirst()
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.get();
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assertEquals("0000-0001-6651-1178", pid.getValue());
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assertEquals(ModelConstants.ORCID_PENDING, pid.getQualifier().getClassid());
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assertEquals(ModelConstants.ORCID_CLASSNAME, pid.getQualifier().getClassname());
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assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid());
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assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename());
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assertEquals("Votsi,Nefta", author.get().getFullname());
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assertEquals("Votsi", author.get().getSurname());
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assertEquals("Nefta", author.get().getName());
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assertFalse(p.getSubject().isEmpty());
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assertFalse(p.getPid().isEmpty());
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assertEquals("PMC1517292", p.getPid().get(0).getValue());
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assertEquals("pmc", p.getPid().get(0).getQualifier().getClassid());
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assertNotNull(p.getInstance());
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assertFalse(p.getInstance().isEmpty());
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p
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.getInstance()
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.forEach(i -> {
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assertNotNull(i.getAccessright());
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assertEquals("OPEN", i.getAccessright().getClassid());
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});
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Publication p_cleaned = cleanup(p, vocs);
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assertEquals("0002", p_cleaned.getInstance().get(0).getRefereed().getClassid());
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assertEquals("nonPeerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname());
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assertNotNull(p.getInstance().get(0).getPid());
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assertEquals(2, p.getInstance().get(0).getPid().size());
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assertEquals(1, p.getInstance().get(0).getAlternateIdentifier().size());
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assertEquals("doi", p.getInstance().get(0).getAlternateIdentifier().get(0).getQualifier().getClassid());
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assertEquals("10.3897/oneeco.2.e13718", p.getInstance().get(0).getAlternateIdentifier().get(0).getValue());
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assertNotNull(p.getBestaccessright());
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assertEquals("OPEN", p.getBestaccessright().getClassid());
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}
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@Test
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void testPublicationInvisible() throws IOException, DocumentException {
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final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_record.xml")));
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final List<Oaf> list = new OafToOafMapper(vocs, true, true).processMdRecord(xml);
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assertFalse(list.isEmpty());
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assertTrue(list.get(0) instanceof Publication);
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final Publication p = (Publication) list.get(0);
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assertTrue(p.getDataInfo().getInvisible());
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}
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@Test
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void testOdfFwfEBookLibrary() throws IOException {
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final String xml = IOUtils
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.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_fwfebooklibrary.xml")));
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assertThrows(
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IllegalArgumentException.class,
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() -> new OdfToOafMapper(vocs, false, true).processMdRecord(xml));
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}
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@Test
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void testDataset() throws IOException, DocumentException {
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final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_dataset.xml")));
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final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
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assertEquals(3, list.size());
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assertTrue(list.get(0) instanceof Dataset);
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assertTrue(list.get(1) instanceof Relation);
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assertTrue(list.get(2) instanceof Relation);
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final Dataset d = (Dataset) list.get(0);
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final Relation r1 = (Relation) list.get(1);
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final Relation r2 = (Relation) list.get(2);
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assertEquals(d.getId(), r1.getSource());
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assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r1.getTarget());
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assertEquals(ModelConstants.RESULT_PROJECT, r1.getRelType());
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assertEquals(ModelConstants.OUTCOME, r1.getSubRelType());
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assertEquals(ModelConstants.IS_PRODUCED_BY, r1.getRelClass());
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assertTrue(r1.getValidated());
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assertEquals("2020-01-01", r1.getValidationDate());
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assertEquals(d.getId(), r2.getTarget());
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assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r2.getSource());
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assertEquals(ModelConstants.RESULT_PROJECT, r2.getRelType());
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assertEquals(ModelConstants.OUTCOME, r2.getSubRelType());
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assertEquals(ModelConstants.PRODUCES, r2.getRelClass());
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assertTrue(r2.getValidated());
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assertEquals("2020-01-01", r2.getValidationDate());
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assertValidId(d.getId());
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assertEquals("50|doi_________::000374d100a9db469bd42b69dbb40b36", d.getId());
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assertEquals(2, d.getOriginalId().size());
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assertTrue(d.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:zenodo.org:3234526")));
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assertValidId(d.getCollectedfrom().get(0).getKey());
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assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
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assertFalse(d.getAuthor().isEmpty());
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final Optional<Author> author = d
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.getAuthor()
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.stream()
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.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
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.findFirst();
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assertTrue(author.isPresent());
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final Optional<StructuredProperty> oPid = author
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.get()
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.getPid()
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.stream()
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.findFirst();
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assertTrue(oPid.isPresent());
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final StructuredProperty pid = oPid.get();
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assertEquals("0000-0001-9074-1619", pid.getValue());
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assertEquals(ModelConstants.ORCID_PENDING, pid.getQualifier().getClassid());
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assertEquals(ModelConstants.ORCID_CLASSNAME, pid.getQualifier().getClassname());
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assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid());
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assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename());
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assertEquals("Baracchini, Theo", author.get().getFullname());
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assertEquals("Baracchini", author.get().getSurname());
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assertEquals("Theo", author.get().getName());
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assertEquals(1, author.get().getAffiliation().size());
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final Optional<Field<String>> opAff = author
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.get()
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.getAffiliation()
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.stream()
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.findFirst();
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assertTrue(opAff.isPresent());
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final Field<String> affiliation = opAff.get();
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assertEquals("ISTI-CNR", affiliation.getValue());
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assertFalse(d.getSubject().isEmpty());
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assertFalse(d.getInstance().isEmpty());
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assertFalse(d.getContext().isEmpty());
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assertFalse(d.getContext().get(0).getId().isEmpty());
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assertNotNull(d.getInstance());
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assertFalse(d.getInstance().isEmpty());
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d
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.getInstance()
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.forEach(i -> {
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assertNotNull(i.getAccessright());
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assertEquals("OPEN", i.getAccessright().getClassid());
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});
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assertEquals("0001", d.getInstance().get(0).getRefereed().getClassid());
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assertNotNull(d.getInstance().get(0).getPid());
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assertFalse(d.getInstance().get(0).getPid().isEmpty());
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assertEquals("doi", d.getInstance().get(0).getPid().get(0).getQualifier().getClassid());
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assertEquals("10.5281/zenodo.3234526", d.getInstance().get(0).getPid().get(0).getValue());
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assertTrue(d.getInstance().get(0).getAlternateIdentifier().isEmpty());
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assertValidId(r1.getSource());
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assertValidId(r1.getTarget());
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assertValidId(r2.getSource());
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assertValidId(r2.getTarget());
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assertNotNull(r1.getDataInfo());
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assertNotNull(r2.getDataInfo());
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assertNotNull(r1.getDataInfo().getTrust());
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assertNotNull(r2.getDataInfo().getTrust());
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assertEquals(r1.getSource(), r2.getTarget());
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assertEquals(r2.getSource(), r1.getTarget());
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assertTrue(StringUtils.isNotBlank(r1.getRelClass()));
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assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
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assertTrue(StringUtils.isNotBlank(r1.getRelType()));
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assertTrue(StringUtils.isNotBlank(r2.getRelType()));
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assertTrue(r1.getValidated());
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assertTrue(r2.getValidated());
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assertEquals("2020-01-01", r1.getValidationDate());
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assertEquals("2020-01-01", r2.getValidationDate());
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assertNotNull(d.getTitle());
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assertEquals(2, d.getTitle().size());
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verifyTitle(d, "main title", "Temperature and ADCP data collected on Lake Geneva between 2015 and 2017");
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verifyTitle(d, "Subtitle", "survey");
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}
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private void verifyTitle(Dataset d, String titleType, String title) {
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Optional
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.of(
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d
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.getTitle()
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.stream()
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.filter(t -> titleType.equals(t.getQualifier().getClassid()))
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.collect(Collectors.toList()))
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.ifPresent(t -> {
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assertEquals(1, t.size());
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assertEquals(title, t.get(0).getValue());
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});
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}
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@Test
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void testOdfBielefeld() throws IOException, DocumentException {
|
|
final String xml = IOUtils
|
|
.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_bielefeld.xml")));
|
|
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
assertEquals(1, list.size());
|
|
assertTrue(list.get(0) instanceof Publication);
|
|
|
|
final Publication p = (Publication) list.get(0);
|
|
|
|
assertValidId(p.getId());
|
|
assertEquals(2, p.getOriginalId().size());
|
|
|
|
assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:pub.uni-bielefeld.de:2949739")));
|
|
// assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0));
|
|
|
|
assertValidId(p.getCollectedfrom().get(0).getKey());
|
|
assertFalse(p.getAuthor().isEmpty());
|
|
|
|
final Optional<Author> author = p
|
|
.getAuthor()
|
|
.stream()
|
|
.findFirst();
|
|
assertTrue(author.isPresent());
|
|
|
|
assertEquals("Potwarka, Luke R.", author.get().getFullname());
|
|
assertEquals("Potwarka", author.get().getSurname());
|
|
assertEquals("Luke R.", author.get().getName());
|
|
|
|
assertFalse(p.getSubject().isEmpty());
|
|
assertFalse(p.getInstance().isEmpty());
|
|
|
|
assertNotNull(p.getTitle());
|
|
assertFalse(p.getTitle().isEmpty());
|
|
|
|
assertNotNull(p.getInstance());
|
|
assertFalse(p.getInstance().isEmpty());
|
|
p
|
|
.getInstance()
|
|
.forEach(i -> {
|
|
assertNotNull(i.getAccessright());
|
|
assertEquals("OPEN", i.getAccessright().getClassid());
|
|
});
|
|
|
|
Publication p_cleaned = cleanup(p, vocs);
|
|
assertEquals("0002", p_cleaned.getInstance().get(0).getRefereed().getClassid());
|
|
assertEquals("nonPeerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname());
|
|
}
|
|
|
|
@Test
|
|
void testOpentrial() throws IOException, DocumentException {
|
|
final String xml = IOUtils
|
|
.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_opentrial.xml")));
|
|
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
assertEquals(1, list.size());
|
|
assertTrue(list.get(0) instanceof Dataset);
|
|
final Dataset d = (Dataset) list.get(0);
|
|
|
|
assertNotNull(d.getDateofcollection());
|
|
assertEquals("2019-03-27T15:15:22.22Z", d.getDateofcollection());
|
|
|
|
assertNotNull(d.getDateoftransformation());
|
|
assertEquals("2019-04-17T16:04:20.586Z", d.getDateoftransformation());
|
|
|
|
assertNotNull(d.getDataInfo());
|
|
assertFalse(d.getDataInfo().getInvisible());
|
|
assertFalse(d.getDataInfo().getDeletedbyinference());
|
|
assertEquals("0.9", d.getDataInfo().getTrust());
|
|
|
|
assertEquals("", d.getDataInfo().getInferenceprovenance());
|
|
|
|
assertEquals("sysimport:crosswalk:datasetarchive", d.getDataInfo().getProvenanceaction().getClassid());
|
|
assertEquals("sysimport:crosswalk:datasetarchive", d.getDataInfo().getProvenanceaction().getClassname());
|
|
assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, d.getDataInfo().getProvenanceaction().getSchemeid());
|
|
assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, d.getDataInfo().getProvenanceaction().getSchemename());
|
|
|
|
assertValidId(d.getId());
|
|
assertEquals(2, d.getOriginalId().size());
|
|
|
|
assertEquals("feabb67c-1fd1-423b-aec6-606d04ce53c6", d.getOriginalId().get(0));
|
|
assertValidId(d.getCollectedfrom().get(0).getKey());
|
|
|
|
assertNotNull(d.getTitle());
|
|
assertEquals(1, d.getTitle().size());
|
|
assertEquals(
|
|
"Validation of the Goodstrength System for Assessment of Abdominal Wall Strength in Patients With Incisional Hernia",
|
|
d
|
|
.getTitle()
|
|
.get(0)
|
|
.getValue());
|
|
|
|
assertNotNull(d.getDescription());
|
|
assertEquals(1, d.getDescription().size());
|
|
assertTrue(StringUtils.isNotBlank(d.getDescription().get(0).getValue()));
|
|
|
|
assertEquals(1, d.getAuthor().size());
|
|
assertEquals("Jensen, Kristian K", d.getAuthor().get(0).getFullname());
|
|
assertEquals("Kristian K.", d.getAuthor().get(0).getName());
|
|
assertEquals("Jensen", d.getAuthor().get(0).getSurname());
|
|
|
|
assertNotNull(d.getAuthor().get(0).getPid());
|
|
assertTrue(d.getAuthor().get(0).getPid().isEmpty());
|
|
|
|
assertNotNull(d.getPid());
|
|
assertEquals(0, d.getPid().size());
|
|
|
|
assertNotNull(d.getPublisher());
|
|
assertEquals("nct", d.getPublisher().getValue());
|
|
|
|
assertTrue(d.getSubject().isEmpty());
|
|
assertTrue(d.getContext().isEmpty());
|
|
|
|
assertNotNull(d.getInstance());
|
|
assertEquals(1, d.getInstance().size());
|
|
|
|
final Instance i = d.getInstance().get(0);
|
|
|
|
assertNotNull(i.getAccessright());
|
|
assertEquals(ModelConstants.DNET_ACCESS_MODES, i.getAccessright().getSchemeid());
|
|
assertEquals(ModelConstants.DNET_ACCESS_MODES, i.getAccessright().getSchemename());
|
|
assertEquals("OPEN", i.getAccessright().getClassid());
|
|
assertEquals("Open Access", i.getAccessright().getClassname());
|
|
|
|
assertNotNull(i.getCollectedfrom());
|
|
assertEquals("10|openaire____::b292fc2d7de505f78e3cae1b06ea8548", i.getCollectedfrom().getKey());
|
|
assertEquals("OpenTrials", i.getCollectedfrom().getValue());
|
|
|
|
assertNotNull(i.getHostedby());
|
|
assertEquals("10|openaire____::b292fc2d7de505f78e3cae1b06ea8548", i.getHostedby().getKey());
|
|
assertEquals("OpenTrials", i.getHostedby().getValue());
|
|
|
|
assertNotNull(i.getInstancetype());
|
|
assertEquals("0037", i.getInstancetype().getClassid());
|
|
assertEquals("Clinical Trial", i.getInstancetype().getClassname());
|
|
assertEquals(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getSchemeid());
|
|
assertEquals(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getSchemename());
|
|
|
|
assertNull(i.getLicense());
|
|
assertNotNull(i.getDateofacceptance());
|
|
assertEquals("2014-11-11", i.getDateofacceptance().getValue());
|
|
|
|
assertNull(i.getDistributionlocation());
|
|
assertNull(i.getProcessingchargeamount());
|
|
assertNull(i.getProcessingchargecurrency());
|
|
|
|
assertNotNull(i.getPid());
|
|
assertEquals(0, i.getPid().size());
|
|
|
|
assertNotNull(i.getAlternateIdentifier());
|
|
assertEquals(1, i.getAlternateIdentifier().size());
|
|
assertEquals("NCT02321059", i.getAlternateIdentifier().get(0).getValue());
|
|
assertEquals("nct", i.getAlternateIdentifier().get(0).getQualifier().getClassid());
|
|
assertEquals("ClinicalTrials.gov Identifier", i.getAlternateIdentifier().get(0).getQualifier().getClassname());
|
|
assertEquals(ModelConstants.DNET_PID_TYPES, i.getAlternateIdentifier().get(0).getQualifier().getSchemeid());
|
|
assertEquals(ModelConstants.DNET_PID_TYPES, i.getAlternateIdentifier().get(0).getQualifier().getSchemename());
|
|
|
|
assertNotNull(i.getUrl());
|
|
assertEquals(2, i.getUrl().size());
|
|
assertTrue(i.getUrl().contains("http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT02321059"));
|
|
assertTrue(i.getUrl().contains("https://clinicaltrials.gov/ct2/show/NCT02321059"));
|
|
|
|
Dataset d_cleaned = cleanup(d, vocs);
|
|
assertEquals("0002", d_cleaned.getInstance().get(0).getRefereed().getClassid());
|
|
assertEquals("nonPeerReviewed", d_cleaned.getInstance().get(0).getRefereed().getClassname());
|
|
}
|
|
|
|
@Test
|
|
void test_record_from_Crossref() throws IOException {
|
|
|
|
final CleaningRuleMap mapping = CleaningRuleMap.create(vocs);
|
|
|
|
final String xml = IOUtils
|
|
.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_crossref.xml")));
|
|
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
assertEquals(1, list.size());
|
|
assertTrue(list.get(0) instanceof Publication);
|
|
|
|
final Publication p = OafCleaner.apply(fixVocabularyNames((Publication) list.get(0)), mapping);
|
|
|
|
assertNotNull(p.getDateofcollection());
|
|
assertEquals("2020-08-06T07:04:09.62Z", p.getDateofcollection());
|
|
|
|
assertNotNull(p.getDateoftransformation());
|
|
assertEquals("2020-08-06T07:20:57.911Z", p.getDateoftransformation());
|
|
|
|
assertNotNull(p.getDataInfo());
|
|
assertFalse(p.getDataInfo().getInvisible());
|
|
assertFalse(p.getDataInfo().getDeletedbyinference());
|
|
assertEquals("0.9", p.getDataInfo().getTrust());
|
|
|
|
assertValidId(p.getId());
|
|
assertEquals(2, p.getOriginalId().size());
|
|
|
|
assertEquals("50|doi_________::7f0f7807f17db50e5c2b5c452ccaf06d", p.getOriginalId().get(0));
|
|
assertValidId(p.getCollectedfrom().get(0).getKey());
|
|
|
|
assertNotNull(p.getTitle());
|
|
assertEquals(1, p.getTitle().size());
|
|
assertEquals(
|
|
"A case report of serious haemolysis in a glucose-6-phosphate dehydrogenase-deficient COVID-19 patient receiving hydroxychloroquine",
|
|
p
|
|
.getTitle()
|
|
.get(0)
|
|
.getValue());
|
|
|
|
assertNotNull(p.getDescription());
|
|
assertEquals(0, p.getDescription().size());
|
|
|
|
assertEquals(8, p.getAuthor().size());
|
|
|
|
assertNotNull(p.getInstance());
|
|
assertEquals(1, p.getInstance().size());
|
|
|
|
final Instance i = p.getInstance().get(0);
|
|
|
|
assertNotNull(i.getAccessright());
|
|
assertEquals(ModelConstants.DNET_ACCESS_MODES, i.getAccessright().getSchemeid());
|
|
assertEquals(ModelConstants.DNET_ACCESS_MODES, i.getAccessright().getSchemename());
|
|
assertEquals("OPEN", i.getAccessright().getClassid());
|
|
assertEquals("Open Access", i.getAccessright().getClassname());
|
|
|
|
assertNotNull(i.getCollectedfrom());
|
|
assertEquals("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", i.getCollectedfrom().getKey());
|
|
assertEquals("Crossref", i.getCollectedfrom().getValue());
|
|
|
|
assertNotNull(i.getHostedby());
|
|
assertEquals("10|openaire____::55045bd2a65019fd8e6741a755395c8c", i.getHostedby().getKey());
|
|
assertEquals("Unknown Repository", i.getHostedby().getValue());
|
|
|
|
assertNotNull(i.getInstancetype());
|
|
assertEquals("0001", i.getInstancetype().getClassid());
|
|
assertEquals("Article", i.getInstancetype().getClassname());
|
|
assertEquals(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getSchemeid());
|
|
assertEquals(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getSchemename());
|
|
|
|
assertNull(i.getLicense());
|
|
assertNotNull(i.getDateofacceptance());
|
|
assertEquals("2020-06-04", i.getDateofacceptance().getValue());
|
|
|
|
assertNull(i.getProcessingchargeamount());
|
|
assertNull(i.getProcessingchargecurrency());
|
|
|
|
assertNotNull(i.getPid());
|
|
assertEquals(1, i.getPid().size());
|
|
|
|
assertNotNull(i.getAlternateIdentifier());
|
|
assertEquals(0, i.getAlternateIdentifier().size());
|
|
|
|
assertNotNull(i.getUrl());
|
|
assertEquals(1, i.getUrl().size());
|
|
assertTrue(i.getUrl().contains("http://dx.doi.org/10.1080/23744235.2020.1774644"));
|
|
|
|
assertEquals("", p.getInstance().get(0).getRefereed().getClassid());
|
|
assertEquals("", p.getInstance().get(0).getRefereed().getClassname());
|
|
|
|
Publication p_cleaned = cleanup(p, vocs);
|
|
|
|
assertEquals("0001", p_cleaned.getInstance().get(0).getRefereed().getClassid());
|
|
assertEquals("peerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname());
|
|
|
|
assertNull(p_cleaned.getMetaResourceType());
|
|
|
|
assertNotNull(p_cleaned.getInstance().get(0).getInstanceTypeMapping());
|
|
assertEquals(1, p_cleaned.getInstance().get(0).getInstanceTypeMapping().size());
|
|
|
|
assertTrue(
|
|
p_cleaned
|
|
.getInstance()
|
|
.get(0)
|
|
.getInstanceTypeMapping()
|
|
.stream()
|
|
.anyMatch(
|
|
t -> "journal-article".equals(t.getOriginalType()) &&
|
|
ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName()) &&
|
|
Objects.isNull(t.getTypeCode()) && Objects.isNull(t.getTypeLabel())));
|
|
|
|
assertTrue(
|
|
p_cleaned
|
|
.getInstance()
|
|
.get(0)
|
|
.getInstanceTypeMapping()
|
|
.stream()
|
|
.noneMatch(
|
|
t -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(t.getVocabularyName())));
|
|
}
|
|
|
|
@Test
|
|
void testSoftware() throws IOException, DocumentException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_software.xml")));
|
|
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
assertEquals(3, list.size());
|
|
assertTrue(list.get(0) instanceof Software);
|
|
assertTrue(list.get(1) instanceof Relation);
|
|
assertTrue(list.get(2) instanceof Relation);
|
|
|
|
final Software s = (Software) list.get(0);
|
|
|
|
assertValidId(s.getId());
|
|
assertValidId(s.getCollectedfrom().get(0).getKey());
|
|
assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue()));
|
|
assertFalse(s.getAuthor().isEmpty());
|
|
assertFalse(s.getSubject().isEmpty());
|
|
assertFalse(s.getInstance().isEmpty());
|
|
|
|
final Relation r1 = (Relation) list.get(1);
|
|
final Relation r2 = (Relation) list.get(2);
|
|
|
|
assertEquals(s.getId(), r1.getSource());
|
|
assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r1.getTarget());
|
|
assertEquals(ModelConstants.RESULT_RESULT, r1.getRelType());
|
|
assertEquals(ModelConstants.RELATIONSHIP, r1.getSubRelType());
|
|
assertEquals(ModelConstants.IS_REFERENCED_BY, r1.getRelClass());
|
|
|
|
assertEquals(s.getId(), r2.getTarget());
|
|
assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r2.getSource());
|
|
assertEquals(ModelConstants.RESULT_RESULT, r2.getRelType());
|
|
assertEquals(ModelConstants.RELATIONSHIP, r2.getSubRelType());
|
|
assertEquals(ModelConstants.REFERENCES, r2.getRelClass());
|
|
|
|
}
|
|
|
|
@Test
|
|
void testClaimDedup() throws IOException, DocumentException {
|
|
final String xml = IOUtils
|
|
.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_claim_dedup.xml")));
|
|
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
assertNotNull(list);
|
|
assertFalse(list.isEmpty());
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
}
|
|
|
|
@Test
|
|
void testNakala() throws IOException, DocumentException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_nakala.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
|
|
assertEquals(1, list.size());
|
|
assertTrue(list.get(0) instanceof Dataset);
|
|
|
|
final Dataset d = (Dataset) list.get(0);
|
|
|
|
assertValidId(d.getId());
|
|
assertValidId(d.getCollectedfrom().get(0).getKey());
|
|
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
|
|
assertEquals(1, d.getAuthor().size());
|
|
assertEquals(1, d.getSubject().size());
|
|
assertEquals(1, d.getInstance().size());
|
|
assertNotNull(d.getPid());
|
|
assertEquals(1, d.getPid().size());
|
|
assertTrue(PidType.isValid(d.getPid().get(0).getQualifier().getClassid()));
|
|
assertEquals(PidType.handle, PidType.valueOf(d.getPid().get(0).getQualifier().getClassid()));
|
|
|
|
assertNotNull(d.getInstance().get(0).getUrl());
|
|
}
|
|
|
|
@Test
|
|
void testEnermaps() throws IOException, DocumentException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("enermaps.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
|
|
assertEquals(1, list.size());
|
|
assertTrue(list.get(0) instanceof Dataset);
|
|
|
|
final Dataset d = (Dataset) list.get(0);
|
|
|
|
assertValidId(d.getId());
|
|
assertValidId(d.getCollectedfrom().get(0).getKey());
|
|
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
|
|
assertEquals(1, d.getAuthor().size());
|
|
assertEquals(1, d.getInstance().size());
|
|
assertNotNull(d.getInstance().get(0).getUrl());
|
|
assertNotNull(d.getContext());
|
|
assertTrue(StringUtils.isNotBlank(d.getContext().get(0).getId()));
|
|
assertEquals("enermaps::selection::tgs00004", d.getContext().get(0).getId());
|
|
}
|
|
|
|
@Test
|
|
void testClaimFromCrossref() throws IOException, DocumentException {
|
|
final String xml = IOUtils
|
|
.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_claim_crossref.xml")));
|
|
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
|
|
final Publication p = (Publication) list.get(0);
|
|
assertValidId(p.getId());
|
|
assertValidId(p.getCollectedfrom().get(0).getKey());
|
|
System.out.println(p.getTitle().get(0).getValue());
|
|
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
|
}
|
|
|
|
@Test
|
|
void testODFRecord() throws IOException, DocumentException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_record.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
final Dataset p = (Dataset) list.get(0);
|
|
assertValidId(p.getId());
|
|
assertValidId(p.getCollectedfrom().get(0).getKey());
|
|
System.out.println(p.getTitle().get(0).getValue());
|
|
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
|
|
|
// COUNTRIES
|
|
assertEquals(3, p.getCountry().size());
|
|
assertEquals("IT", p.getCountry().get(0).getClassid());
|
|
assertEquals("FR", p.getCountry().get(1).getClassid());
|
|
assertEquals("DE", p.getCountry().get(2).getClassid());
|
|
}
|
|
|
|
@Test
|
|
void testTextGrid() throws IOException, DocumentException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("textgrid.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
|
|
final Dataset p = (Dataset) list.get(0);
|
|
assertValidId(p.getId());
|
|
assertValidId(p.getCollectedfrom().get(0).getKey());
|
|
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
|
assertEquals(1, p.getAuthor().size());
|
|
assertEquals("OPEN", p.getBestaccessright().getClassid());
|
|
|
|
assertEquals(1, p.getPid().size());
|
|
assertTrue(PidType.isValid(p.getPid().get(0).getQualifier().getClassid()));
|
|
assertEquals(PidType.handle, PidType.valueOf(p.getPid().get(0).getQualifier().getClassid()));
|
|
assertEquals("hdl:11858/00-1734-0000-0003-EE73-2", p.getPid().get(0).getValue());
|
|
assertEquals("dataset", p.getResulttype().getClassname());
|
|
assertEquals(1, p.getInstance().size());
|
|
assertEquals("OPEN", p.getInstance().get(0).getAccessright().getClassid());
|
|
assertValidId(p.getInstance().get(0).getCollectedfrom().getKey());
|
|
assertValidId(p.getInstance().get(0).getHostedby().getKey());
|
|
assertEquals(
|
|
"http://creativecommons.org/licenses/by/3.0/de/legalcode", p.getInstance().get(0).getLicense().getValue());
|
|
|
|
assertEquals(1, p.getInstance().size());
|
|
assertNotNull(p.getInstance().get(0).getAlternateIdentifier());
|
|
assertEquals(0, p.getInstance().get(0).getAlternateIdentifier().size());
|
|
assertEquals(1, p.getInstance().get(0).getUrl().size());
|
|
}
|
|
|
|
@Test
|
|
void testBologna() throws IOException, DocumentException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf-bologna.xml")));
|
|
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
|
|
final Publication p = (Publication) list.get(0);
|
|
assertValidId(p.getId());
|
|
assertValidId(p.getCollectedfrom().get(0).getKey());
|
|
System.out.println(p.getTitle().get(0).getValue());
|
|
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
|
System.out.println(p.getTitle().get(0).getValue());
|
|
}
|
|
|
|
@Test
|
|
void testJairo() throws IOException, DocumentException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_jairo.xml")));
|
|
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
|
|
final Publication p = (Publication) list.get(0);
|
|
assertValidId(p.getId());
|
|
assertValidId(p.getCollectedfrom().get(0).getKey());
|
|
|
|
assertNotNull(p.getTitle());
|
|
assertFalse(p.getTitle().isEmpty());
|
|
assertEquals(1, p.getTitle().size());
|
|
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
|
|
|
final Publication p_cleaned = cleanup(fixVocabularyNames(p), vocs);
|
|
|
|
assertNotNull(p_cleaned.getTitle());
|
|
assertFalse(p_cleaned.getTitle().isEmpty());
|
|
}
|
|
|
|
@Test
|
|
void test_instance_url_validation() throws IOException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("idus_sevilla.xml")));
|
|
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
final Publication p = (Publication) list.get(0);
|
|
|
|
assertNotNull(p.getInstance());
|
|
assertFalse(p.getInstance().isEmpty());
|
|
assertNotNull(p.getInstance().get(0).getUrl());
|
|
assertFalse(p.getInstance().get(0).getUrl().isEmpty());
|
|
assertEquals("https://idus.us.es/handle//11441/118940", p.getInstance().get(0).getUrl().get(0));
|
|
}
|
|
|
|
@Test
|
|
void testZenodo() throws IOException, DocumentException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_zenodo.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
|
|
final Publication p = (Publication) list.get(0);
|
|
assertValidId(p.getId());
|
|
assertValidId(p.getCollectedfrom().get(0).getKey());
|
|
|
|
assertNotNull(p.getTitle());
|
|
assertFalse(p.getTitle().isEmpty());
|
|
assertEquals(1, p.getTitle().size());
|
|
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
|
|
|
assertNotNull(p.getAuthor());
|
|
assertEquals(2, p.getAuthor().size());
|
|
|
|
Author author = p
|
|
.getAuthor()
|
|
.stream()
|
|
.filter(a -> a.getPid().stream().anyMatch(pi -> pi.getValue().equals("0000-0003-3272-8007")))
|
|
.findFirst()
|
|
.get();
|
|
assertNotNull(author);
|
|
assertTrue(StringUtils.isBlank(author.getSurname()));
|
|
assertTrue(StringUtils.isBlank(author.getName()));
|
|
assertEquals("Anne van Weerden", author.getFullname());
|
|
|
|
author = p
|
|
.getAuthor()
|
|
.stream()
|
|
.filter(a -> a.getPid().stream().anyMatch(pi -> pi.getValue().equals("0000-0003-3272-8008")))
|
|
.findFirst()
|
|
.get();
|
|
assertNotNull(author);
|
|
assertFalse(StringUtils.isBlank(author.getSurname()));
|
|
assertFalse(StringUtils.isBlank(author.getName()));
|
|
assertFalse(StringUtils.isBlank(author.getFullname()));
|
|
|
|
}
|
|
|
|
@Test
|
|
void testOdfFromHdfs() throws IOException, DocumentException {
|
|
final String xml = IOUtils
|
|
.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_from_hdfs.xml")));
|
|
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
assertEquals(1, list.size());
|
|
|
|
System.out.println(list.get(0).getClass());
|
|
|
|
assertTrue(list.get(0) instanceof Dataset);
|
|
|
|
final Dataset p = (Dataset) list.get(0);
|
|
|
|
assertValidId(p.getId());
|
|
assertEquals(2, p.getOriginalId().size());
|
|
assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("df76e73f-0483-49a4-a9bb-63f2f985574a")));
|
|
assertValidId(p.getCollectedfrom().get(0).getKey());
|
|
assertFalse(p.getAuthor().isEmpty());
|
|
|
|
final Optional<Author> author = p
|
|
.getAuthor()
|
|
.stream()
|
|
.findFirst();
|
|
assertTrue(author.isPresent());
|
|
|
|
assertEquals("Museum Sønderjylland", author.get().getFullname());
|
|
|
|
assertFalse(p.getSubject().isEmpty());
|
|
assertFalse(p.getInstance().isEmpty());
|
|
|
|
assertNotNull(p.getTitle());
|
|
assertFalse(p.getTitle().isEmpty());
|
|
|
|
assertNotNull(p.getInstance());
|
|
assertFalse(p.getInstance().isEmpty());
|
|
p
|
|
.getInstance()
|
|
.forEach(i -> {
|
|
assertNotNull(i.getAccessright());
|
|
assertEquals("UNKNOWN", i.getAccessright().getClassid());
|
|
});
|
|
|
|
Dataset p_cleaned = cleanup(p, vocs);
|
|
assertEquals("0002", p_cleaned.getInstance().get(0).getRefereed().getClassid());
|
|
assertEquals("nonPeerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname());
|
|
}
|
|
|
|
@Test
|
|
void testXMLEncodedURL() throws IOException, DocumentException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("encoded-url.xml")));
|
|
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
|
|
final Publication p = (Publication) list.get(0);
|
|
assertTrue(p.getInstance().size() > 0);
|
|
|
|
String decoded = "https://www.ec.europa.eu/research/participants/documents/downloadPublic?documentIds=080166e5af388993&appId=PPGMS";
|
|
assertEquals(decoded, p.getInstance().get(0).getUrl().get(0));
|
|
}
|
|
|
|
@Test
|
|
void testXMLEncodedURL_ODF() throws IOException, DocumentException {
|
|
final String xml = IOUtils
|
|
.toString(Objects.requireNonNull(getClass().getResourceAsStream("encoded-url_odf.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
|
|
final Dataset p = (Dataset) list.get(0);
|
|
assertFalse(p.getInstance().isEmpty());
|
|
for (String url : p.getInstance().get(0).getUrl()) {
|
|
System.out.println(url);
|
|
assertFalse(url.contains("&"));
|
|
}
|
|
}
|
|
|
|
@Test
|
|
void testOpenAPC() throws IOException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_openapc.xml")));
|
|
final List<Oaf> list = new OafToOafMapper(vocs, true, true).processMdRecord(xml);
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
|
|
final Optional<Oaf> o = list.stream().filter(r -> r instanceof Publication).findFirst();
|
|
assertTrue(o.isPresent());
|
|
|
|
Publication p = (Publication) o.get();
|
|
assertFalse(p.getInstance().isEmpty());
|
|
|
|
assertEquals("https://doi.org/10.1155/2015/439379", p.getInstance().get(0).getUrl().get(0));
|
|
|
|
assertNotNull(p.getProcessingchargeamount());
|
|
assertNotNull(p.getProcessingchargecurrency());
|
|
|
|
assertEquals("1721.47", p.getProcessingchargeamount().getValue());
|
|
assertEquals("EUR", p.getProcessingchargecurrency().getValue());
|
|
|
|
List<Oaf> affiliations = list.stream().filter(r -> r instanceof Relation).collect(Collectors.toList());
|
|
assertEquals(2, affiliations.size());
|
|
|
|
for (Oaf aff : affiliations) {
|
|
Relation r = (Relation) aff;
|
|
assertEquals(ModelConstants.AFFILIATION, r.getSubRelType());
|
|
assertEquals(ModelConstants.RESULT_ORGANIZATION, r.getRelType());
|
|
String source = r.getSource();
|
|
if (StringUtils.startsWith(source, "50")) {
|
|
assertEquals(ModelConstants.HAS_AUTHOR_INSTITUTION, r.getRelClass());
|
|
} else if (StringUtils.startsWith(source, "20")) {
|
|
assertTrue(StringUtils.contains(source, "::"));
|
|
assertEquals("20|" + Constants.ROR_NS_PREFIX, StringUtils.substringBefore(source, "::"));
|
|
assertEquals(ModelConstants.IS_AUTHOR_INSTITUTION_OF, r.getRelClass());
|
|
} else {
|
|
throw new IllegalArgumentException("invalid source / target prefixes for affiliation relations");
|
|
}
|
|
|
|
List<KeyValue> apcInfo = r.getProperties();
|
|
assertEquals(
|
|
"EUR", apcInfo
|
|
.stream()
|
|
.filter(kv -> "apc_currency".equals(kv.getKey()))
|
|
.map(KeyValue::getValue)
|
|
.findFirst()
|
|
.orElse(""));
|
|
assertEquals(
|
|
"1721.47", apcInfo
|
|
.stream()
|
|
.filter(kv -> "apc_amount".equals(kv.getKey()))
|
|
.map(KeyValue::getValue)
|
|
.findFirst()
|
|
.orElse(""));
|
|
}
|
|
}
|
|
|
|
@Test
|
|
void testROHub() throws IOException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
assertEquals(5, list.size());
|
|
final OtherResearchProduct p = (OtherResearchProduct) list.get(0);
|
|
assertValidId(p.getId());
|
|
assertTrue(p.getId().startsWith("50|w3id"));
|
|
assertValidId(p.getCollectedfrom().get(0).getKey());
|
|
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
|
assertEquals(1, p.getInstance().size());
|
|
assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", p.getPid().get(0).getValue());
|
|
Instance inst = p.getInstance().get(0);
|
|
assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", inst.getPid().get(0).getValue());
|
|
assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", inst.getUrl().get(0));
|
|
assertEquals(1, p.getEoscifguidelines().size());
|
|
assertEquals("EOSC::RO-crate", p.getEoscifguidelines().get(0).getCode());
|
|
assertEquals("EOSC::RO-crate", p.getEoscifguidelines().get(0).getLabel());
|
|
assertEquals("", p.getEoscifguidelines().get(0).getUrl());
|
|
assertEquals("compliesWith", p.getEoscifguidelines().get(0).getSemanticRelation());
|
|
|
|
}
|
|
|
|
@Test
|
|
void test_Zenodo2() throws IOException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_zenodo2.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
|
|
assertEquals(3, list.size());
|
|
Publication p = cleanup((Publication) list.get(0), vocs);
|
|
|
|
assertNotNull(p.getInstance());
|
|
assertEquals(1, p.getInstance().size());
|
|
|
|
final Instance instance = p.getInstance().get(0);
|
|
|
|
assertNotNull(instance.getInstanceTypeMapping());
|
|
assertEquals(1, instance.getInstanceTypeMapping().size());
|
|
|
|
Optional<InstanceTypeMapping> coarType = instance
|
|
.getInstanceTypeMapping()
|
|
.stream()
|
|
.filter(itm -> ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName()))
|
|
.findFirst();
|
|
|
|
assertTrue(coarType.isPresent());
|
|
assertNotNull(coarType.get().getOriginalType());
|
|
assertNull(coarType.get().getTypeCode());
|
|
assertNull(coarType.get().getTypeLabel());
|
|
}
|
|
|
|
@Test
|
|
void testROHub2() throws IOException {
|
|
final String xml = IOUtils
|
|
.toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub-modified.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
assertEquals(7, list.size());
|
|
final OtherResearchProduct p = (OtherResearchProduct) list.get(0);
|
|
assertValidId(p.getId());
|
|
assertValidId(p.getCollectedfrom().get(0).getKey());
|
|
assertEquals("50|w3id________::afc7592914ae190a50570db90f55f9c2", p.getId());
|
|
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
|
assertEquals("w3id", (p.getPid().get(0).getQualifier().getClassid()));
|
|
assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", (p.getPid().get(0).getValue()));
|
|
|
|
assertEquals(1, list.stream().filter(o -> o instanceof OtherResearchProduct).count());
|
|
assertEquals(6, list.stream().filter(o -> o instanceof Relation).count());
|
|
|
|
for (Oaf oaf : list) {
|
|
if (oaf instanceof Relation) {
|
|
String source = ((Relation) oaf).getSource();
|
|
String target = ((Relation) oaf).getTarget();
|
|
assertNotEquals(source, target);
|
|
assertTrue(source.equals(p.getId()) || target.equals(p.getId()));
|
|
assertNotNull(((Relation) oaf).getSubRelType());
|
|
assertNotNull(((Relation) oaf).getRelClass());
|
|
assertNotNull(((Relation) oaf).getRelType());
|
|
}
|
|
}
|
|
}
|
|
|
|
@Test
|
|
void testRiunet() throws IOException, DocumentException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("riunet.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
final Publication p = (Publication) list.get(0);
|
|
assertNotNull(p.getInstance().get(0).getUrl().get(0));
|
|
|
|
}
|
|
|
|
@Test
|
|
void testEOSCFuture_ROHub() throws IOException {
|
|
final String xml = IOUtils
|
|
.toString(Objects.requireNonNull(getClass().getResourceAsStream("photic-zone-transformed.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
final OtherResearchProduct rocrate = (OtherResearchProduct) list.get(0);
|
|
assertNotNull(rocrate.getEoscifguidelines());
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(rocrate));
|
|
System.out.println("***************");
|
|
}
|
|
|
|
@Test
|
|
void testD4ScienceTraining() throws IOException {
|
|
final String xml = IOUtils
|
|
.toString(Objects.requireNonNull(getClass().getResourceAsStream("d4science-1-training.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
final OtherResearchProduct trainingMaterial = (OtherResearchProduct) list.get(0);
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(trainingMaterial));
|
|
System.out.println("***************");
|
|
}
|
|
|
|
@Test
|
|
void testD4ScienceDataset() throws IOException {
|
|
final String xml = IOUtils
|
|
.toString(Objects.requireNonNull(getClass().getResourceAsStream("d4science-2-dataset.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
final Dataset trainingMaterial = (Dataset) list.get(0);
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(trainingMaterial));
|
|
System.out.println("***************");
|
|
}
|
|
|
|
@Test
|
|
void testIRISPub() throws IOException, DocumentException {
|
|
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("iris-odf.xml")));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
final Publication p = (Publication) list.get(0);
|
|
assertNotNull(p.getInstance().get(0).getUrl().get(0));
|
|
assertValidId(p.getId());
|
|
System.out.println(p.getInstance().get(0).getUrl());
|
|
p.getPid().forEach(x -> System.out.println(x.getValue()));
|
|
p.getInstance().get(0).getAlternateIdentifier().forEach(x -> System.out.println(x.getValue()));
|
|
|
|
}
|
|
|
|
@Test
|
|
void testNotWellFormed() throws IOException {
|
|
final String xml = IOUtils
|
|
.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml")));
|
|
final List<Oaf> actual = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
|
|
assertNotNull(actual);
|
|
assertTrue(actual.isEmpty());
|
|
}
|
|
|
|
private void assertValidId(final String id) {
|
|
// System.out.println(id);
|
|
|
|
assertEquals(49, id.length());
|
|
assertEquals(IdentifierFactory.ID_PREFIX_SEPARATOR, id.substring(2, 3));
|
|
assertEquals(IdentifierFactory.ID_SEPARATOR, id.substring(15, 17));
|
|
}
|
|
|
|
private List<String> vocs() throws IOException {
|
|
return IOUtils
|
|
.readLines(
|
|
Objects
|
|
.requireNonNull(MappersTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")));
|
|
}
|
|
|
|
private List<String> synonyms() throws IOException {
|
|
return IOUtils
|
|
.readLines(
|
|
Objects
|
|
.requireNonNull(
|
|
MappersTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")));
|
|
}
|
|
|
|
}
|