forked from D-Net/dnet-hadoop
352 lines
12 KiB
Java
352 lines
12 KiB
Java
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package eu.dnetlib.dhp.oa.graph.clean;
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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.Collection;
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import java.util.List;
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import java.util.Optional;
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import java.util.Set;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import org.apache.commons.io.IOUtils;
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import org.junit.jupiter.api.Assertions;
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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.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.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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@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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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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@Mock
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private ISLookUpService isLookUpService;
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private VocabularyGroup vocabularies;
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private CleaningRuleMap mapping;
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@BeforeEach
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public void setUp() throws ISLookUpException, IOException {
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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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vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService);
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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/graph/relation/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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assertEquals("iis", r_out.getDataInfo().getProvenanceaction().getClassid());
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assertEquals("Inferred by OpenAIRE", r_out.getDataInfo().getProvenanceaction().getClassname());
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}
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}
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@Test
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void testFilter_invisible_true() throws Exception {
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assertNotNull(vocabularies);
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assertNotNull(mapping);
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String json = IOUtils
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.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json"));
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Publication p_in = MAPPER.readValue(json, Publication.class);
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assertTrue(p_in instanceof Result);
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assertTrue(p_in instanceof Publication);
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assertEquals(true, GraphCleaningFunctions.filter(p_in));
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}
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@Test
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void testFilter_true_nothing_to_filter() throws Exception {
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assertNotNull(vocabularies);
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assertNotNull(mapping);
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String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json"));
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Publication p_in = MAPPER.readValue(json, Publication.class);
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assertTrue(p_in instanceof Result);
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assertTrue(p_in instanceof Publication);
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assertEquals(true, GraphCleaningFunctions.filter(p_in));
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}
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@Test
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void testFilter_missing_invisible() throws Exception {
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assertNotNull(vocabularies);
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assertNotNull(mapping);
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String json = IOUtils
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.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json"));
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Publication p_in = MAPPER.readValue(json, Publication.class);
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assertTrue(p_in instanceof Result);
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assertTrue(p_in instanceof Publication);
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assertEquals(true, GraphCleaningFunctions.filter(p_in));
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}
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@Test
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void testCleaning() throws Exception {
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assertNotNull(vocabularies);
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assertNotNull(mapping);
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String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json"));
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Publication p_in = MAPPER.readValue(json, Publication.class);
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assertNull(p_in.getBestaccessright());
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assertTrue(p_in instanceof Result);
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assertTrue(p_in instanceof Publication);
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Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
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assertNotNull(p_out);
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assertNotNull(p_out.getPublisher());
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assertNull(p_out.getPublisher().getValue());
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assertEquals("und", p_out.getLanguage().getClassid());
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assertEquals("Undetermined", p_out.getLanguage().getClassname());
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assertEquals("DE", p_out.getCountry().get(0).getClassid());
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assertEquals("Germany", p_out.getCountry().get(0).getClassname());
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assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid());
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assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname());
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assertEquals("0027", p_out.getInstance().get(1).getInstancetype().getClassid());
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assertEquals("Model", p_out.getInstance().get(1).getInstancetype().getClassname());
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assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassid());
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assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassname());
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assertEquals("CLOSED", p_out.getInstance().get(0).getAccessright().getClassid());
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assertEquals("Closed Access", p_out.getInstance().get(0).getAccessright().getClassname());
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Set<String> pidTerms = vocabularies.getTerms(ModelConstants.DNET_PID_TYPES);
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assertTrue(
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p_out
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.getPid()
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.stream()
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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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assertNotNull(poi);
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assertEquals(3, poi.size());
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final Instance poii = poi.get(0);
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assertNotNull(poii);
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assertNotNull(poii.getPid());
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assertEquals(2, poii.getPid().size());
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assertTrue(
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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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assertTrue(
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poii
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.getAlternateIdentifier()
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.stream()
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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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.anyMatch(s -> s.getValue().equals("10.1009/qwerty")));
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assertEquals(5, p_out.getTitle().size());
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Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
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assertEquals(3, p_cleaned.getTitle().size());
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List<String> titles = p_cleaned
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.getTitle()
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.stream()
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.map(StructuredProperty::getValue)
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.collect(Collectors.toList());
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assertTrue(titles.contains("omic"));
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assertTrue(
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titles.contains("Optical response of strained- and unstrained-silicon cold-electron bolometers test"));
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assertTrue(titles.contains("「マキャベリ的知性と心の理論の進化論」 リチャード・バーン, アンドリュー・ホワイトゥン 編/藤田和生, 山下博志, 友永雅巳 監訳"));
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assertEquals("CLOSED", p_cleaned.getBestaccessright().getClassid());
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assertNull(p_out.getPublisher());
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assertEquals("1970-10-07", p_cleaned.getDateofacceptance().getValue());
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assertEquals("0038", p_cleaned.getInstance().get(2).getInstancetype().getClassid());
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assertEquals("Other literature type", p_cleaned.getInstance().get(2).getInstancetype().getClassname());
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final List<Instance> pci = p_cleaned.getInstance();
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assertNotNull(pci);
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assertEquals(3, pci.size());
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final Instance pcii = pci.get(0);
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assertNotNull(pcii);
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assertNotNull(pcii.getPid());
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assertEquals(2, pcii.getPid().size());
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assertTrue(
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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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assertTrue(
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pcii
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.getAlternateIdentifier()
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.stream()
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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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.println(
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String
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.format(
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"%s [%s - %s]", pid.getValue(), pid.getQualifier().getClassid(),
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pid.getQualifier().getClassname()));
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});
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assertNotNull(p_cleaned.getSubject());
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List<Subject> fos_subjects = p_cleaned
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.getSubject()
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.stream()
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.filter(s -> ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))
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.collect(Collectors.toList());
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assertNotNull(fos_subjects);
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assertEquals(2, fos_subjects.size());
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assertTrue(
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fos_subjects
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.stream()
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.anyMatch(
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s -> "0101 mathematics".equals(s.getValue()) &
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ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) &
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"sysimport:crosswalk:datasetarchive"
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.equals(s.getDataInfo().getProvenanceaction().getClassid())));
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assertTrue(
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fos_subjects
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.stream()
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.anyMatch(
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s -> "0102 computer and information sciences".equals(s.getValue()) &
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ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid())));
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verify_keyword(p_cleaned, "In Situ Hybridization");
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verify_keyword(p_cleaned, "Avicennia");
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// TODO add more assertions to verity the cleaned values
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System.out.println(MAPPER.writeValueAsString(p_cleaned));
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}
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private static void verify_keyword(Publication p_cleaned, String subject) {
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Optional<Subject> s1 = p_cleaned
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.getSubject()
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.stream()
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.filter(s -> s.getValue().equals(subject))
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.findFirst();
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assertTrue(s1.isPresent());
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assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassid());
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assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassname());
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}
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private Stream<Qualifier> getAuthorPidTypes(Result pub) {
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return pub
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.getAuthor()
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.stream()
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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(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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return IOUtils
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.readLines(
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GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt"));
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}
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private List<String> synonyms() throws IOException {
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return IOUtils
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.readLines(
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GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"));
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}
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@Test
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public void testCleanDoiBoost() throws IOException {
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String json = IOUtils
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.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub.json"));
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Publication p_in = MAPPER.readValue(json, Publication.class);
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Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
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Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
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Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));
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}
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@Test
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public void testCleanDoiBoost2() throws IOException {
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String json = IOUtils
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.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub2.json"));
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Publication p_in = MAPPER.readValue(json, Publication.class);
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Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
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Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
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Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));
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}
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}
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