forked from D-Net/dnet-hadoop
You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
456 lines
17 KiB
Java
456 lines
17 KiB
Java
|
|
package eu.dnetlib.dhp.oa.graph.raw;
|
|
|
|
import static org.junit.jupiter.api.Assertions.assertEquals;
|
|
import static org.junit.jupiter.api.Assertions.assertFalse;
|
|
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
|
import static org.junit.jupiter.api.Assertions.assertTrue;
|
|
import static org.mockito.Mockito.lenient;
|
|
|
|
import java.io.IOException;
|
|
import java.util.List;
|
|
import java.util.Optional;
|
|
|
|
import org.apache.commons.io.IOUtils;
|
|
import org.apache.commons.lang3.StringUtils;
|
|
import org.junit.jupiter.api.BeforeEach;
|
|
import org.junit.jupiter.api.Test;
|
|
import org.junit.jupiter.api.extension.ExtendWith;
|
|
import org.mockito.Mock;
|
|
import org.mockito.junit.jupiter.MockitoExtension;
|
|
|
|
import com.fasterxml.jackson.core.JsonProcessingException;
|
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
|
|
import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest;
|
|
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
|
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
|
import eu.dnetlib.dhp.schema.oaf.Author;
|
|
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
|
import eu.dnetlib.dhp.schema.oaf.Field;
|
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
|
import eu.dnetlib.dhp.schema.oaf.Publication;
|
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
import eu.dnetlib.dhp.schema.oaf.Software;
|
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
|
|
|
@ExtendWith(MockitoExtension.class)
|
|
public class MappersTest {
|
|
|
|
@Mock
|
|
private ISLookUpService isLookUpService;
|
|
|
|
@Mock
|
|
private VocabularyGroup vocs;
|
|
|
|
@BeforeEach
|
|
public void setUp() throws Exception {
|
|
lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs());
|
|
lenient()
|
|
.when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY))
|
|
.thenReturn(synonyms());
|
|
|
|
vocs = VocabularyGroup.loadVocsFromIS(isLookUpService);
|
|
}
|
|
|
|
@Test
|
|
void testPublication() throws IOException {
|
|
|
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml"));
|
|
|
|
final List<Oaf> list = new OafToOafMapper(vocs, false).processMdRecord(xml);
|
|
|
|
assertEquals(3, list.size());
|
|
assertTrue(list.get(0) instanceof Publication);
|
|
assertTrue(list.get(1) instanceof Relation);
|
|
assertTrue(list.get(2) instanceof Relation);
|
|
|
|
final Publication p = (Publication) list.get(0);
|
|
final Relation r1 = (Relation) list.get(1);
|
|
final Relation r2 = (Relation) list.get(2);
|
|
|
|
assertValidId(p.getId());
|
|
|
|
assertTrue(p.getOriginalId().size() == 1);
|
|
assertEquals("10.3897/oneeco.2.e13718", p.getOriginalId().get(0));
|
|
|
|
assertValidId(p.getCollectedfrom().get(0).getKey());
|
|
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
|
assertFalse(p.getDataInfo().getInvisible());
|
|
assertTrue(p.getSource().size() == 1);
|
|
assertTrue(StringUtils.isNotBlank(p.getDateofcollection()));
|
|
assertTrue(StringUtils.isNotBlank(p.getDateoftransformation()));
|
|
|
|
assertTrue(p.getAuthor().size() > 0);
|
|
final Optional<Author> author = p
|
|
.getAuthor()
|
|
.stream()
|
|
.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
|
|
.findFirst();
|
|
assertTrue(author.isPresent());
|
|
|
|
final StructuredProperty pid = author
|
|
.get()
|
|
.getPid()
|
|
.stream()
|
|
.findFirst()
|
|
.get();
|
|
assertEquals("0000-0001-6651-1178", pid.getValue());
|
|
assertEquals("ORCID", pid.getQualifier().getClassid());
|
|
assertEquals("Open Researcher and Contributor ID", pid.getQualifier().getClassname());
|
|
assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid());
|
|
assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename());
|
|
assertEquals("Votsi,Nefta", author.get().getFullname());
|
|
assertEquals("Votsi", author.get().getSurname());
|
|
assertEquals("Nefta", author.get().getName());
|
|
|
|
assertTrue(p.getSubject().size() > 0);
|
|
assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline()));
|
|
assertTrue(StringUtils.isNotBlank(p.getJournal().getName()));
|
|
|
|
assertTrue(p.getPid().size() > 0);
|
|
assertEquals(p.getPid().get(0).getValue(), "10.3897/oneeco.2.e13718");
|
|
assertEquals(p.getPid().get(0).getQualifier().getClassid(), "doi");
|
|
|
|
assertNotNull(p.getInstance());
|
|
assertTrue(p.getInstance().size() > 0);
|
|
p
|
|
.getInstance()
|
|
.stream()
|
|
.forEach(i -> {
|
|
assertNotNull(i.getAccessright());
|
|
assertEquals("OPEN", i.getAccessright().getClassid());
|
|
});
|
|
assertEquals("0001", p.getInstance().get(0).getRefereed().getClassid());
|
|
|
|
assertNotNull(p.getBestaccessright());
|
|
assertEquals("OPEN", p.getBestaccessright().getClassid());
|
|
assertValidId(r1.getSource());
|
|
assertValidId(r1.getTarget());
|
|
assertValidId(r2.getSource());
|
|
assertValidId(r2.getTarget());
|
|
assertValidId(r1.getCollectedfrom().get(0).getKey());
|
|
assertValidId(r2.getCollectedfrom().get(0).getKey());
|
|
assertNotNull(r1.getDataInfo());
|
|
assertNotNull(r2.getDataInfo());
|
|
assertNotNull(r1.getDataInfo().getTrust());
|
|
assertNotNull(r2.getDataInfo().getTrust());
|
|
assertEquals(r1.getSource(), r2.getTarget());
|
|
assertEquals(r2.getSource(), r1.getTarget());
|
|
assertTrue(StringUtils.isNotBlank(r1.getRelClass()));
|
|
assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
|
|
assertTrue(StringUtils.isNotBlank(r1.getRelType()));
|
|
assertTrue(StringUtils.isNotBlank(r2.getRelType()));
|
|
assertTrue(r1.getValidated());
|
|
assertTrue(r2.getValidated());
|
|
assertEquals(r1.getValidationDate(), "2020-01-01");
|
|
assertEquals(r2.getValidationDate(), "2020-01-01");
|
|
// System.out.println(new ObjectMapper().writeValueAsString(p));
|
|
// System.out.println(new ObjectMapper().writeValueAsString(r1));
|
|
// System.out.println(new ObjectMapper().writeValueAsString(r2));
|
|
}
|
|
|
|
@Test
|
|
void testPublicationInvisible() throws IOException {
|
|
|
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml"));
|
|
|
|
final List<Oaf> list = new OafToOafMapper(vocs, true).processMdRecord(xml);
|
|
|
|
assertTrue(list.size() > 0);
|
|
assertTrue(list.get(0) instanceof Publication);
|
|
|
|
final Publication p = (Publication) list.get(0);
|
|
|
|
assertTrue(p.getDataInfo().getInvisible());
|
|
|
|
}
|
|
|
|
@Test
|
|
void testDataset() throws IOException {
|
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset.xml"));
|
|
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false).processMdRecord(xml);
|
|
|
|
assertEquals(3, list.size());
|
|
assertTrue(list.get(0) instanceof Dataset);
|
|
assertTrue(list.get(1) instanceof Relation);
|
|
assertTrue(list.get(2) instanceof Relation);
|
|
|
|
final Dataset d = (Dataset) list.get(0);
|
|
final Relation r1 = (Relation) list.get(1);
|
|
final Relation r2 = (Relation) list.get(2);
|
|
|
|
assertValidId(d.getId());
|
|
assertTrue(d.getOriginalId().size() == 1);
|
|
assertEquals("oai:zenodo.org:3234526", d.getOriginalId().get(0));
|
|
assertValidId(d.getCollectedfrom().get(0).getKey());
|
|
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
|
|
assertTrue(d.getAuthor().size() > 0);
|
|
|
|
final Optional<Author> author = d
|
|
.getAuthor()
|
|
.stream()
|
|
.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
|
|
.findFirst();
|
|
assertTrue(author.isPresent());
|
|
final StructuredProperty pid = author
|
|
.get()
|
|
.getPid()
|
|
.stream()
|
|
.findFirst()
|
|
.get();
|
|
assertEquals("0000-0001-9074-1619", pid.getValue());
|
|
assertEquals("ORCID", pid.getQualifier().getClassid());
|
|
assertEquals("Open Researcher and Contributor ID", pid.getQualifier().getClassname());
|
|
assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid());
|
|
assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename());
|
|
assertEquals("Baracchini, Theo", author.get().getFullname());
|
|
assertEquals("Baracchini", author.get().getSurname());
|
|
assertEquals("Theo", author.get().getName());
|
|
|
|
assertEquals(1, author.get().getAffiliation().size());
|
|
final Optional<Field<String>> opAff = author
|
|
.get()
|
|
.getAffiliation()
|
|
.stream()
|
|
.findFirst();
|
|
assertTrue(opAff.isPresent());
|
|
final Field<String> affiliation = opAff.get();
|
|
assertEquals("ISTI-CNR", affiliation.getValue());
|
|
|
|
assertTrue(d.getSubject().size() > 0);
|
|
assertTrue(d.getInstance().size() > 0);
|
|
assertTrue(d.getContext().size() > 0);
|
|
assertTrue(d.getContext().get(0).getId().length() > 0);
|
|
|
|
assertNotNull(d.getInstance());
|
|
assertTrue(d.getInstance().size() > 0);
|
|
d
|
|
.getInstance()
|
|
.stream()
|
|
.forEach(i -> {
|
|
assertNotNull(i.getAccessright());
|
|
assertEquals("OPEN", i.getAccessright().getClassid());
|
|
});
|
|
assertEquals("0001", d.getInstance().get(0).getRefereed().getClassid());
|
|
|
|
assertValidId(r1.getSource());
|
|
assertValidId(r1.getTarget());
|
|
assertValidId(r2.getSource());
|
|
assertValidId(r2.getTarget());
|
|
assertNotNull(r1.getDataInfo());
|
|
assertNotNull(r2.getDataInfo());
|
|
assertNotNull(r1.getDataInfo().getTrust());
|
|
assertNotNull(r2.getDataInfo().getTrust());
|
|
assertEquals(r1.getSource(), r2.getTarget());
|
|
assertEquals(r2.getSource(), r1.getTarget());
|
|
assertTrue(StringUtils.isNotBlank(r1.getRelClass()));
|
|
assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
|
|
assertTrue(StringUtils.isNotBlank(r1.getRelType()));
|
|
assertTrue(StringUtils.isNotBlank(r2.getRelType()));
|
|
assertTrue(r1.getValidated());
|
|
assertTrue(r2.getValidated());
|
|
assertEquals(r1.getValidationDate(), "2020-01-01");
|
|
assertEquals(r2.getValidationDate(), "2020-01-01");
|
|
}
|
|
|
|
@Test
|
|
void testSoftware() throws IOException {
|
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml"));
|
|
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false).processMdRecord(xml);
|
|
|
|
assertEquals(1, list.size());
|
|
assertTrue(list.get(0) instanceof Software);
|
|
|
|
final Software s = (Software) list.get(0);
|
|
|
|
assertValidId(s.getId());
|
|
assertValidId(s.getCollectedfrom().get(0).getKey());
|
|
assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue()));
|
|
assertTrue(s.getAuthor().size() > 0);
|
|
assertTrue(s.getSubject().size() > 0);
|
|
assertTrue(s.getInstance().size() > 0);
|
|
}
|
|
|
|
// @Test
|
|
void testDataset_2() throws IOException {
|
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset_2.xml"));
|
|
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false).processMdRecord(xml);
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
}
|
|
|
|
@Test
|
|
void testClaimDedup() throws IOException {
|
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_dedup.xml"));
|
|
final List<Oaf> list = new OafToOafMapper(vocs, false).processMdRecord(xml);
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
}
|
|
|
|
@Test
|
|
void testNakala() throws IOException {
|
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_nakala.xml"));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false).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());
|
|
assertEquals(1, d.getPid().size());
|
|
assertNotNull(d.getInstance().get(0).getUrl());
|
|
}
|
|
|
|
@Test
|
|
void testClaimFromCrossref() throws IOException {
|
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_crossref.xml"));
|
|
final List<Oaf> list = new OafToOafMapper(vocs, false).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 {
|
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_record.xml"));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false).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()));
|
|
}
|
|
|
|
@Test
|
|
void testTextGrid() throws IOException {
|
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("textgrid.xml"));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false).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());
|
|
assertTrue(StringUtils.isNotBlank(p.getPid().get(0).getValue()));
|
|
assertTrue(StringUtils.isNotBlank(p.getPid().get(0).getQualifier().getClassid()));
|
|
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().get(0).getUrl().size());
|
|
// System.out.println(p.getInstance().get(0).getUrl().get(0));
|
|
// System.out.println(p.getInstance().get(0).getHostedby().getValue());
|
|
System.out.println(p.getPid().get(0).getValue());
|
|
}
|
|
|
|
@Test
|
|
void testTextGridNoAuthor() throws IOException {
|
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("textgrid-noauthor.xml"));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false).processMdRecord(xml);
|
|
|
|
System.out.println("***************");
|
|
System.out.println(new ObjectMapper().writeValueAsString(list));
|
|
System.out.println("***************");
|
|
}
|
|
|
|
@Test
|
|
void testBologna() throws IOException {
|
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf-bologna.xml"));
|
|
final List<Oaf> list = new OafToOafMapper(vocs, false).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 testEUOpenDataPortal() throws IOException {
|
|
final String xml = IOUtils.toString(getClass().getResourceAsStream("eu_odp.xml"));
|
|
final List<Oaf> list = new OdfToOafMapper(vocs, false).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(0, p.getAuthor().size());
|
|
assertEquals(1, p.getPid().size());
|
|
assertEquals("OPEN", p.getBestaccessright().getClassid());
|
|
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(
|
|
"CC_BY_4_0", p.getInstance().get(0).getLicense().getValue());
|
|
assertEquals(1, p.getInstance().get(0).getUrl().size());
|
|
assertEquals(1, p.getInstance().size());
|
|
System.out.println(p.getInstance().get(0).getUrl().get(0));
|
|
System.out.println(p.getInstance().get(0).getHostedby().getValue());
|
|
}
|
|
|
|
private void assertValidId(final String id) {
|
|
assertEquals(49, id.length());
|
|
assertEquals('|', id.charAt(2));
|
|
assertEquals(':', id.charAt(15));
|
|
assertEquals(':', id.charAt(16));
|
|
}
|
|
|
|
private List<String> vocs() throws IOException {
|
|
return IOUtils
|
|
.readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt"));
|
|
}
|
|
|
|
private List<String> synonyms() throws IOException {
|
|
return IOUtils
|
|
.readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"));
|
|
}
|
|
|
|
}
|