forked from D-Net/dnet-hadoop
Merge branch 'beta' into dedup_whitelist
This commit is contained in:
commit
7fa60e166e
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@ -12,6 +12,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.AccessRight;
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import eu.dnetlib.dhp.schema.oaf.Country;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Object>> implements Serializable {
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@ -24,17 +25,31 @@ public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Obje
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CleaningRuleMap mapping = new CleaningRuleMap();
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mapping.put(Qualifier.class, o -> cleanQualifier(vocabularies, (Qualifier) o));
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mapping.put(AccessRight.class, o -> cleanQualifier(vocabularies, (AccessRight) o));
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mapping.put(Country.class, o -> {
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final Country c = (Country) o;
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if (StringUtils.isBlank(c.getSchemeid())) {
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c.setSchemeid(ModelConstants.DNET_COUNTRY_TYPE);
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c.setSchemename(ModelConstants.DNET_COUNTRY_TYPE);
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}
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cleanQualifier(vocabularies, c);
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});
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mapping.put(Country.class, o -> cleanCountry(vocabularies, (Country) o));
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mapping.put(Relation.class, o -> cleanRelation(vocabularies, (Relation) o));
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return mapping;
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}
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private static void cleanRelation(VocabularyGroup vocabularies, Relation r) {
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if (vocabularies.vocabularyExists(ModelConstants.DNET_RELATION_SUBRELTYPE)) {
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Qualifier newValue = vocabularies.lookup(ModelConstants.DNET_RELATION_SUBRELTYPE, r.getSubRelType());
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r.setSubRelType(newValue.getClassid());
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}
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if (vocabularies.vocabularyExists(ModelConstants.DNET_RELATION_RELCLASS)) {
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Qualifier newValue = vocabularies.lookup(ModelConstants.DNET_RELATION_RELCLASS, r.getRelClass());
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r.setRelClass(newValue.getClassid());
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}
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}
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private static void cleanCountry(VocabularyGroup vocabularies, Country o) {
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final Country c = o;
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if (StringUtils.isBlank(c.getSchemeid())) {
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c.setSchemeid(ModelConstants.DNET_COUNTRY_TYPE);
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c.setSchemename(ModelConstants.DNET_COUNTRY_TYPE);
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}
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cleanQualifier(vocabularies, c);
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}
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private static <Q extends Qualifier> void cleanQualifier(VocabularyGroup vocabularies, Q q) {
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if (vocabularies.vocabularyExists(q.getSchemeid())) {
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Qualifier newValue = vocabularies.lookup(q.getSchemeid(), q.getClassid());
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@ -5,6 +5,7 @@ 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.Collection;
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import java.util.List;
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import java.util.Set;
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import java.util.stream.Stream;
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@ -16,12 +17,12 @@ 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.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
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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.CleaningFunctions;
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import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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@ -29,7 +30,8 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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@ExtendWith(MockitoExtension.class)
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public class GraphCleaningFunctionsTest {
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public static final ObjectMapper MAPPER = new ObjectMapper();
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public static final ObjectMapper MAPPER = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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@Mock
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private ISLookUpService isLookUpService;
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@ -49,6 +51,23 @@ public class GraphCleaningFunctionsTest {
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mapping = CleaningRuleMap.create(vocabularies);
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}
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@Test
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void testCleanRelations() throws Exception {
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List<String> lines = IOUtils
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.readLines(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/relation.json"));
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for (String json : lines) {
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Relation r_in = MAPPER.readValue(json, Relation.class);
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assertNotNull(r_in);
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assertFalse(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r_in.getRelClass()));
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Relation r_out = OafCleaner.apply(r_in, mapping);
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assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r_out.getRelClass()));
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assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_SUBRELTYPE).contains(r_out.getSubRelType()));
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}
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}
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@Test
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void testCleaning() throws Exception {
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@ -87,7 +106,7 @@ public class GraphCleaningFunctionsTest {
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p_out
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.getPid()
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.stream()
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.map(p -> p.getQualifier())
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.map(StructuredProperty::getQualifier)
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.allMatch(q -> pidTerms.contains(q.getClassid())));
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List<Instance> poi = p_out.getInstance();
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@ -101,8 +120,8 @@ public class GraphCleaningFunctionsTest {
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assertEquals(2, poii.getPid().size());
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assertTrue(
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poii.getPid().stream().filter(s -> s.getValue().equals("10.1007/s109090161569x")).findFirst().isPresent());
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assertTrue(poii.getPid().stream().filter(s -> s.getValue().equals("10.1008/abcd")).findFirst().isPresent());
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poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x")));
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assertTrue(poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd")));
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assertNotNull(poii.getAlternateIdentifier());
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assertEquals(2, poii.getAlternateIdentifier().size());
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@ -111,16 +130,12 @@ public class GraphCleaningFunctionsTest {
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poii
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.getAlternateIdentifier()
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.stream()
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.filter(s -> s.getValue().equals("10.1007/s109090161569x"))
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.findFirst()
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.isPresent());
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.anyMatch(s -> s.getValue().equals("10.1007/s109090161569x")));
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assertTrue(
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poii
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.getAlternateIdentifier()
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.stream()
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.filter(s -> s.getValue().equals("10.1009/qwerty"))
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.findFirst()
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.isPresent());
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.anyMatch(s -> s.getValue().equals("10.1009/qwerty")));
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Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out);
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@ -142,8 +157,8 @@ public class GraphCleaningFunctionsTest {
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assertEquals(2, pcii.getPid().size());
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assertTrue(
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pcii.getPid().stream().filter(s -> s.getValue().equals("10.1007/s109090161569x")).findFirst().isPresent());
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assertTrue(pcii.getPid().stream().filter(s -> s.getValue().equals("10.1008/abcd")).findFirst().isPresent());
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pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x")));
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assertTrue(pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd")));
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assertNotNull(pcii.getAlternateIdentifier());
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assertEquals(1, pcii.getAlternateIdentifier().size());
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@ -151,9 +166,7 @@ public class GraphCleaningFunctionsTest {
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pcii
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.getAlternateIdentifier()
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.stream()
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.filter(s -> s.getValue().equals("10.1009/qwerty"))
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.findFirst()
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.isPresent());
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.anyMatch(s -> s.getValue().equals("10.1009/qwerty")));
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getAuthorPids(p_cleaned).forEach(pid -> {
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System.out
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@ -172,17 +185,17 @@ public class GraphCleaningFunctionsTest {
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return pub
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.getAuthor()
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.stream()
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.map(a -> a.getPid())
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.flatMap(p -> p.stream())
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.map(s -> s.getQualifier());
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.map(Author::getPid)
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.flatMap(Collection::stream)
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.map(StructuredProperty::getQualifier);
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}
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private Stream<StructuredProperty> getAuthorPids(Result pub) {
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return pub
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.getAuthor()
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.stream()
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.map(a -> a.getPid())
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.flatMap(p -> p.stream());
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.map(Author::getPid)
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.flatMap(Collection::stream);
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}
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private List<String> vocs() throws IOException {
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@ -0,0 +1,10 @@
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{"relType":"resultResult","subRelType":"citation","relClass":"cites","source":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","target":"50|openaire____::007a4870b31056f89b768cf508e1538e"}
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{"relType":"resultResult","subRelType":"citation","relClass":"isCitedBy","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
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{"relType":"resultResult","subRelType":"supplement","relClass":"isSupplementTo","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
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{"relType":"resultResult","subRelType":"supplement","relClass":"isSupplementedBy","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
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{"relType":"resultResult","subRelType":"part","relClass":"isPartOf","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
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{"relType":"resultResult","subRelType":"part","relClass":"hasPart","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
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{"relType":"resultResult","subRelType":"review","relClass":"isReviewedBy","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
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{"relType":"resultResult","subRelType":"review","relClass":"reviews","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
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{"relType":"resultResult","subRelType":"relationship","relClass":"isRelatedTo","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
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{"relType":"resultResult","subRelType":"publicationDataset","relClass":"isRelatedTo","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
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@ -1231,4 +1231,14 @@ dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-学術雑誌論文（査
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dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-紀要論文（査読有り）
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dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-雑誌記事（査読有り）
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dnet:review_levels @=@ 0001 @=@ 原著論文（査読有り）
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dnet:review_levels @=@ 0001 @=@ 査読論文
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dnet:review_levels @=@ 0001 @=@ 査読論文
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dnet:relation_relClass @=@ Cites @=@ cites
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dnet:relation_relClass @=@ IsCitedBy @=@ isCitedBy
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dnet:relation_relClass @=@ HasPart @=@ hasPart
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dnet:relation_relClass @=@ IsPartOf @=@ isPartOf
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dnet:relation_relClass @=@ IsReviewedBy @=@ isReviewedBy
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dnet:relation_relClass @=@ Reviews @=@ reviews
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dnet:relation_relClass @=@ IsSupplementTo @=@ isSupplementTo
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dnet:relation_relClass @=@ IsSupplementedBy @=@ isSupplementedBy
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dnet:relation_relClass @=@ IsRelatedTo @=@ isRelatedTo
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dnet:relation_subRelType @=@ relationship @=@ publicationDataset
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@ -1079,4 +1079,41 @@ dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_SUPPLEMENTED
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dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/AUTHOR/ORCID @=@ An Open Researcher and Contributor ID (ORCID) that can be associated to an author of your publications
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dnet:review_levels @=@ dnet:review_levels @=@ 0000 @=@ Unknown
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dnet:review_levels @=@ dnet:review_levels @=@ 0002 @=@ nonPeerReviewed
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dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed
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dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ Cites @=@ Cites
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsCitedBy @=@ IsCitedBy
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ HasPart @=@ HasPart
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsPartOf @=@ IsPartOf
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsReviewedBy @=@ IsReviewedBy
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ Reviews @=@ Reviews
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsSupplementTo @=@ IsSupplementTo
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsSupplementedBy @=@ IsSupplementedBy
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsRelatedTo @=@ IsRelatedTo
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ Compiles @=@ Compiles
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ Continues @=@ Continues
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ Documents @=@ Documents
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ HasAmongTopNSimilarDocuments @=@ HasAmongTopNSimilarDocuments
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ HasVersion @=@ HasVersion
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsAmongTopNSimilarDocuments @=@ IsAmongTopNSimilarDocuments
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsCompiledBy @=@ IsCompiledBy
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsContinuedBy @=@ IsContinuedBy
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsDerivedFrom @=@ IsDerivedFrom
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsDocumentedBy @=@ IsDocumentedBy
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsNewVersionOf @=@ IsNewVersionOf
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsObsoletedBy @=@ IsObsoletedBy
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsOriginalFormOf @=@ IsOriginalFormOf
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsPreviousVersionOf @=@ IsPreviousVersionOf
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsSourceOf @=@ IsSourceOf
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dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsVariantFormOf @=@ IsVariantFormOf
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dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ affiliation @=@ affiliation
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dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ citation @=@ citation
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dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ dedup @=@ dedup
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dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ outcome @=@ outcome
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dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ part @=@ part
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dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ participation @=@ participation
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dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ provision @=@ provision
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dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ relationship @=@ relationship
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dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ review @=@ review
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dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ similarity @=@ similarity
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dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ supplement @=@ supplement
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dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ version @=@ version
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2
pom.xml
2
pom.xml
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@ -753,7 +753,7 @@
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<mockito-core.version>3.3.3</mockito-core.version>
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<mongodb.driver.version>3.4.2</mongodb.driver.version>
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<vtd.version>[2.12,3.0)</vtd.version>
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<dhp-schemas.version>[2.7.17]</dhp-schemas.version>
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<dhp-schemas.version>[2.7.18]</dhp-schemas.version>
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<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
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<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
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<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
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|
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