[graph dedup] records stability and testing
#44
Merged
claudio.atzori
merged 9 commits from deduptesting into beta 1 year ago
@ -0,0 +1,81 @@
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package eu.dnetlib.dhp.oa.dedup;
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import java.util.Comparator;
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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 com.google.common.collect.Sets;
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import eu.dnetlib.dhp.oa.dedup.model.Identifier;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import eu.dnetlib.dhp.schema.oaf.utils.PidComparator;
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import eu.dnetlib.dhp.schema.oaf.utils.PidType;
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public class IdentifierComparator<T extends OafEntity> implements Comparator<Identifier<T>> {
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public static int compareIdentifiers(Identifier left, Identifier right) {
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return new IdentifierComparator<>().compare(left, right);
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}
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@Override
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public int compare(Identifier<T> left, Identifier<T> i) {
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// priority in comparisons: 1) pidtype, 2) collectedfrom (depending on the entity type) , 3) date 4)
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// alphabetical order of the originalID
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Set<String> lKeys = Optional
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.ofNullable(left.getCollectedFrom())
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.map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet()))
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.orElse(Sets.newHashSet());
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final Optional<List<KeyValue>> cf = Optional.ofNullable(i.getCollectedFrom());
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Set<String> rKeys = cf
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.map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet()))
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.orElse(Sets.newHashSet());
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if (left.getPidType().compareTo(i.getPidType()) == 0) { // same type
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if (left.getEntityType() == EntityType.publication) {
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if (isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID)
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&& !isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID))
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return -1;
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if (isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID)
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&& !isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID))
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return 1;
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}
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if (left.getEntityType() == EntityType.dataset) {
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if (isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID)
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&& !isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID))
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return -1;
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if (isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID)
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&& !isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID))
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return 1;
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}
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if (left.getDate().compareTo(i.getDate()) == 0) {// same date
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// we need to take the alphabetically lower id
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return left.getOriginalID().compareTo(i.getOriginalID());
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} else
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// we need to take the elder date
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return left.getDate().compareTo(i.getDate());
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} else {
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return new PidComparator<>(left.getEntity()).compare(toSP(left.getPidType()), toSP(i.getPidType()));
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}
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}
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public boolean isFromDatasourceID(Set<String> collectedFrom, String dsId) {
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return collectedFrom.contains(dsId);
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}
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private StructuredProperty toSP(PidType pidType) {
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return OafMapperUtils.structuredProperty("", pidType.toString(), pidType.toString(), "", "", new DataInfo());
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}
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}
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@ -0,0 +1,403 @@
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package eu.dnetlib.dhp.oa.dedup;
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import static java.nio.file.Files.createTempDirectory;
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import static org.apache.spark.sql.functions.count;
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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.File;
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import java.io.IOException;
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import java.io.Serializable;
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import java.net.URISyntaxException;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.util.*;
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import java.util.stream.Collectors;
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import org.apache.commons.cli.ParseException;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.*;
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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.Mockito;
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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 com.google.common.collect.Sets;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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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.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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@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
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public class SparkPublicationRootsTest implements Serializable {
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@Mock(serializable = true)
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ISLookUpService isLookUpService;
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private static SparkSession spark;
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private static String workingPath;
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private static String graphInputPath;
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private static String graphOutputPath;
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private static final String testActionSetId = "test-orchestrator";
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private static Path testBaseTmpPath;
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private static final ObjectMapper MAPPER = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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@BeforeAll
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public static void init() throws IOException, URISyntaxException {
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testBaseTmpPath = createTempDirectory(SparkPublicationRootsTest.class.getSimpleName() + "-");
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final File entitiesSources = Paths
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.get(SparkPublicationRootsTest.class.getResource("/eu/dnetlib/dhp/dedup/root").toURI())
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.toFile();
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FileUtils
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.copyDirectory(
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entitiesSources,
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testBaseTmpPath.resolve("input").toFile());
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workingPath = testBaseTmpPath.resolve("workingPath").toString();
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graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString();
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graphOutputPath = testBaseTmpPath.resolve("output").toString();
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FileUtils.deleteDirectory(new File(workingPath));
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FileUtils.deleteDirectory(new File(graphOutputPath));
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final SparkConf conf = new SparkConf();
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conf.set("spark.sql.shuffle.partitions", "10");
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spark = SparkSession
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.builder()
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.appName(SparkPublicationRootsTest.class.getSimpleName())
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.master("local[*]")
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.config(conf)
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.getOrCreate();
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}
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@BeforeEach
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public void setUp() throws IOException, ISLookUpException {
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lenient()
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.when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
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.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml"));
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lenient()
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.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
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.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"));
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}
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@AfterAll
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public static void tearDown() throws IOException {
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FileUtils.deleteDirectory(testBaseTmpPath.toFile());
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spark.close();
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}
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@Test
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@Order(1)
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void createSimRelsTest() throws Exception {
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new SparkCreateSimRels(args(
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"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json",
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new String[] {
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"--graphBasePath", graphInputPath,
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"--actionSetId", testActionSetId,
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"--isLookUpUrl", "lookupurl",
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"--workingPath", workingPath,
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"--numPartitions", "5"
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}), spark)
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.run(isLookUpService);
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long pubs_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(workingPath, testActionSetId, "publication"))
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.count();
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assertEquals(74, pubs_simrel);
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}
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@Test
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@Order(2)
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void cutMergeRelsTest() throws Exception {
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new SparkCreateMergeRels(args(
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"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json",
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new String[] {
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"--graphBasePath", graphInputPath,
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"--actionSetId", testActionSetId,
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"--isLookUpUrl", "lookupurl",
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"--workingPath", workingPath,
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"--cutConnectedComponent", "3"
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}), spark)
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.run(isLookUpService);
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long pubs_mergerel = spark
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.read()
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.load(workingPath + "/" + testActionSetId + "/publication_mergerel")
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.as(Encoders.bean(Relation.class))
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.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
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.groupBy("source")
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.agg(count("target").alias("cnt"))
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.select("source", "cnt")
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.where("cnt > 3")
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.count();
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assertEquals(0, pubs_mergerel);
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FileUtils.deleteDirectory(new File(workingPath + "/" + testActionSetId + "/publication_mergerel"));
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}
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@Test
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@Order(3)
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void createMergeRelsTest() throws Exception {
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new SparkCreateMergeRels(args(
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"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json",
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new String[] {
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"--graphBasePath", graphInputPath,
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"--actionSetId", testActionSetId,
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"--isLookUpUrl", "lookupurl",
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"--workingPath", workingPath
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}), spark)
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.run(isLookUpService);
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final Dataset<Relation> merges = spark
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.read()
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.load(workingPath + "/" + testActionSetId + "/publication_mergerel")
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.as(Encoders.bean(Relation.class));
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final List<Relation> mergeList = merges
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.filter("source == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
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.collectAsList();
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assertEquals(3, mergeList.size());
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Set<String> dups = Sets
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.newHashSet(
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"50|doi_________::3b1d0d8e8f930826665df9d6b82fbb73",
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"50|doi_________::d5021b53204e4fdeab6ff5d5bc468032",
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"50|arXiv_______::c93aeb433eb90ed7a86e29be00791b7c");
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mergeList.forEach(r -> {
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assertEquals(ModelConstants.RESULT_RESULT, r.getRelType());
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assertEquals(ModelConstants.DEDUP, r.getSubRelType());
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assertEquals(ModelConstants.MERGES, r.getRelClass());
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assertTrue(dups.contains(r.getTarget()));
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});
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final List<Relation> mergedIn = merges
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.filter("target == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
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.collectAsList();
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assertEquals(3, mergedIn.size());
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mergedIn.forEach(r -> {
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assertEquals(ModelConstants.RESULT_RESULT, r.getRelType());
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assertEquals(ModelConstants.DEDUP, r.getSubRelType());
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assertEquals(ModelConstants.IS_MERGED_IN, r.getRelClass());
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assertTrue(dups.contains(r.getSource()));
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});
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assertEquals(32, merges.count());
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}
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@Test
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@Order(4)
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void createDedupRecordTest() throws Exception {
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new SparkCreateDedupRecord(args(
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"/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json",
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new String[] {
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"--graphBasePath", graphInputPath,
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"--actionSetId", testActionSetId,
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"--isLookUpUrl", "lookupurl",
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"--workingPath", workingPath
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}), spark)
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.run(isLookUpService);
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final Dataset<Publication> roots = spark
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.read()
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.textFile(workingPath + "/" + testActionSetId + "/publication_deduprecord")
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.map(asEntity(Publication.class), Encoders.bean(Publication.class));
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assertEquals(3, roots.count());
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final Dataset<Publication> pubs = spark
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.read()
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.textFile(DedupUtility.createEntityPath(graphInputPath, "publication"))
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.map(asEntity(Publication.class), Encoders.bean(Publication.class));
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verifyRoot_case_1(roots, pubs);
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verifyRoot_case_2(roots, pubs);
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verifyRoot_case_3(roots, pubs);
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}
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private static void verifyRoot_case_1(Dataset<Publication> roots, Dataset<Publication> pubs) {
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Publication root = roots
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.filter("id = '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
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.first();
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assertNotNull(root);
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Publication crossref_duplicate = pubs
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.filter("id = '50|doi_________::d5021b53204e4fdeab6ff5d5bc468032'")
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.collectAsList()
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.get(0);
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assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName());
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assertEquals(crossref_duplicate.getJournal().getIssnPrinted(), root.getJournal().getIssnPrinted());
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assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue());
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Set<String> rootPids = root
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.getPid()
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.stream()
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.map(StructuredProperty::getValue)
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.collect(Collectors.toCollection(HashSet::new));
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Set<String> dupPids = crossref_duplicate
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.getPid()
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.stream()
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.map(StructuredProperty::getValue)
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.collect(Collectors.toCollection(HashSet::new));
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assertFalse(Sets.intersection(rootPids, dupPids).isEmpty());
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assertTrue(rootPids.contains("10.1109/jstqe.2022.3205716"));
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Optional<Instance> instance_cr = root
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.getInstance()
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.stream()
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.filter(i -> i.getCollectedfrom().getValue().equals("Crossref"))
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.findFirst();
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assertTrue(instance_cr.isPresent());
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assertEquals("OPEN", instance_cr.get().getAccessright().getClassid());
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assertEquals("Open Access", instance_cr.get().getAccessright().getClassname());
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assertEquals(OpenAccessRoute.hybrid, instance_cr.get().getAccessright().getOpenAccessRoute());
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assertEquals(
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"IEEE Journal of Selected Topics in Quantum Electronics", instance_cr.get().getHostedby().getValue());
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assertEquals("0001", instance_cr.get().getInstancetype().getClassid());
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assertEquals("Article", instance_cr.get().getInstancetype().getClassname());
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}
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private void verifyRoot_case_2(Dataset<Publication> roots, Dataset<Publication> pubs) {
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Publication root = roots
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.filter("id = '50|doi_dedup___::18aff3b55fb6876466a5d4bd82434885'")
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.first();
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assertNotNull(root);
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Publication crossref_duplicate = pubs
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.filter("id = '50|doi_________::18aff3b55fb6876466a5d4bd82434885'")
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.first();
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// System.err.println(new ObjectMapper().writeValueAsString(root));
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assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName());
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assertEquals(crossref_duplicate.getJournal().getIssnOnline(), root.getJournal().getIssnOnline());
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assertEquals(crossref_duplicate.getJournal().getVol(), root.getJournal().getVol());
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assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue());
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Set<String> dups_cf = pubs
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.collectAsList()
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.stream()
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.flatMap(p -> p.getCollectedfrom().stream())
|
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.map(KeyValue::getValue)
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.collect(Collectors.toCollection(HashSet::new));
|
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|
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Set<String> root_cf = root
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.getCollectedfrom()
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.stream()
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.map(KeyValue::getValue)
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.collect(Collectors.toCollection(HashSet::new));
|
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assertTrue(Sets.difference(root_cf, dups_cf).isEmpty());
|
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}
|
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private void verifyRoot_case_3(Dataset<Publication> roots, Dataset<Publication> pubs) {
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Publication root = roots
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.filter("id = '50|dedup_wf_001::31ca734cc22181b704c4aa8fd050062a'")
|
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.first();
|
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assertNotNull(root);
|
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|
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Publication pivot_duplicate = pubs
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.filter("id = '50|od_______166::31ca734cc22181b704c4aa8fd050062a'")
|
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.first();
|
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|
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assertEquals(pivot_duplicate.getPublisher().getValue(), root.getPublisher().getValue());
|
||||
|
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Set<String> dups_cf = pubs
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.collectAsList()
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||||
.stream()
|
||||
.flatMap(p -> p.getCollectedfrom().stream())
|
||||
.map(KeyValue::getValue)
|
||||
.collect(Collectors.toCollection(HashSet::new));
|
||||
|
||||
Set<String> root_cf = root
|
||||
.getCollectedfrom()
|
||||
.stream()
|
||||
.map(KeyValue::getValue)
|
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.collect(Collectors.toCollection(HashSet::new));
|
||||
|
||||
assertTrue(Sets.difference(root_cf, dups_cf).isEmpty());
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(6)
|
||||
void updateEntityTest() throws Exception {
|
||||
new SparkUpdateEntity(args(
|
||||
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json",
|
||||
new String[] {
|
||||
"--graphBasePath", graphInputPath,
|
||||
"--workingPath", workingPath,
|
||||
"--dedupGraphPath", graphOutputPath
|
||||
}), spark)
|
||||
.run(isLookUpService);
|
||||
|
||||
long publications = spark.read().textFile(graphOutputPath + "/publication").count();
|
||||
|
||||
long mergedPubs = spark
|
||||
.read()
|
||||
.load(workingPath + "/" + testActionSetId + "/publication_mergerel")
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.where("relClass=='merges'")
|
||||
.map((MapFunction<Relation, String>) Relation::getTarget, Encoders.STRING())
|
||||
.distinct()
|
||||
.count();
|
||||
|
||||
assertEquals(19, publications); // 16 originals + 3 roots
|
||||
|
||||
long deletedPubs = spark
|
||||
.read()
|
||||
.textFile(graphOutputPath + "/publication")
|
||||
.map(asEntity(Publication.class), Encoders.bean(Publication.class))
|
||||
.filter("datainfo.deletedbyinference == true")
|
||||
.map((MapFunction<Publication, String>) OafEntity::getId, Encoders.STRING())
|
||||
.distinct()
|
||||
.count();
|
||||
|
||||
assertEquals(mergedPubs, deletedPubs);
|
||||
}
|
||||
|
||||
private static String classPathResourceAsString(String path) throws IOException {
|
||||
return IOUtils
|
||||
.toString(
|
||||
SparkPublicationRootsTest.class
|
||||
.getResourceAsStream(path));
|
||||
}
|
||||
|
||||
private static <T extends OafEntity> MapFunction<String, T> asEntity(Class<T> clazz) {
|
||||
return value -> MAPPER.readValue(value, clazz);
|
||||
}
|
||||
|
||||
private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs));
|
||||
parser.parseArgument(args);
|
||||
return parser;
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,251 @@
|
||||
|
||||
package eu.dnetlib.dhp.oa.dedup;
|
||||
|
||||
import static java.nio.file.Files.createTempDirectory;
|
||||
|
||||
import static org.apache.spark.sql.functions.count;
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.IOException;
|
||||
import java.io.Serializable;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Path;
|
||||
import java.nio.file.Paths;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.cli.ParseException;
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.*;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.Mockito;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.google.common.collect.Sets;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
|
||||
public class SparkPublicationRootsTest2 implements Serializable {
|
||||
|
||||
@Mock(serializable = true)
|
||||
ISLookUpService isLookUpService;
|
||||
private static SparkSession spark;
|
||||
|
||||
private static String workingPath;
|
||||
|
||||
private static String graphInputPath;
|
||||
|
||||
private static String graphOutputPath;
|
||||
|
||||
private static final String testActionSetId = "test-orchestrator";
|
||||
|
||||
private static Path testBaseTmpPath;
|
||||
|
||||
private static final ObjectMapper MAPPER = new ObjectMapper()
|
||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
|
||||
@BeforeAll
|
||||
public static void init() throws IOException, URISyntaxException {
|
||||
|
||||
testBaseTmpPath = createTempDirectory(SparkPublicationRootsTest2.class.getSimpleName() + "-");
|
||||
|
||||
final File entitiesSources = Paths
|
||||
.get(SparkPublicationRootsTest2.class.getResource("/eu/dnetlib/dhp/dedup/root").toURI())
|
||||
.toFile();
|
||||
|
||||
FileUtils
|
||||
.copyDirectory(
|
||||
entitiesSources,
|
||||
testBaseTmpPath.resolve("input").toFile());
|
||||
|
||||
FileUtils
|
||||
.copyFileToDirectory(
|
||||
Paths
|
||||
.get(
|
||||
SparkPublicationRootsTest2.class
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/dedup/root/alterations/publication/publication_1.gz")
|
||||
.toURI())
|
||||
.toFile(),
|
||||
testBaseTmpPath.resolve("input").resolve("entities").resolve("publication").toFile());
|
||||
|
||||
workingPath = testBaseTmpPath.resolve("workingPath").toString();
|
||||
graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString();
|
||||
graphOutputPath = testBaseTmpPath.resolve("output").toString();
|
||||
|
||||
final SparkConf conf = new SparkConf();
|
||||
conf.set("spark.sql.shuffle.partitions", "10");
|
||||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(SparkPublicationRootsTest2.class.getSimpleName())
|
||||
.master("local[*]")
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@BeforeEach
|
||||
public void setUp() throws IOException, ISLookUpException {
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
|
||||
.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml"));
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
|
||||
.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"));
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void tearDown() throws IOException {
|
||||
FileUtils.deleteDirectory(testBaseTmpPath.toFile());
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(7)
|
||||
void dedupAlteredDatasetTest() throws Exception {
|
||||
|
||||
new SparkCreateSimRels(args(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json",
|
||||
new String[] {
|
||||
"--graphBasePath", graphInputPath,
|
||||
"--actionSetId", testActionSetId,
|
||||
"--isLookUpUrl", "lookupurl",
|
||||
"--workingPath", workingPath,
|
||||
"--numPartitions", "5"
|
||||
}), spark)
|
||||
.run(isLookUpService);
|
||||
|
||||
new SparkCreateMergeRels(args(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json",
|
||||
new String[] {
|
||||
"--graphBasePath", graphInputPath,
|
||||
"--actionSetId", testActionSetId,
|
||||
"--isLookUpUrl", "lookupurl",
|
||||
"--workingPath", workingPath
|
||||
}), spark)
|
||||
.run(isLookUpService);
|
||||
|
||||
final Dataset<Relation> merges = spark
|
||||
.read()
|
||||
.load(workingPath + "/" + testActionSetId + "/publication_mergerel")
|
||||
.as(Encoders.bean(Relation.class));
|
||||
|
||||
assertEquals(
|
||||
3, merges
|
||||
.filter("relclass == 'isMergedIn'")
|
||||
.map((MapFunction<Relation, String>) Relation::getTarget, Encoders.STRING())
|
||||
.distinct()
|
||||
.count());
|
||||
assertEquals(
|
||||
4, merges
|
||||
.filter("source == '50|doi_dedup___::b3aec7985136e36827176aaa1dd5082d'")
|
||||
.count());
|
||||
|
||||
new SparkCreateDedupRecord(args(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json",
|
||||
new String[] {
|
||||
"--graphBasePath", graphInputPath,
|
||||
"--actionSetId", testActionSetId,
|
||||
"--isLookUpUrl", "lookupurl",
|
||||
"--workingPath", workingPath
|
||||
}), spark)
|
||||
.run(isLookUpService);
|
||||
|
||||
final Dataset<Publication> roots = spark
|
||||
.read()
|
||||
.textFile(workingPath + "/" + testActionSetId + "/publication_deduprecord")
|
||||
.map(asEntity(Publication.class), Encoders.bean(Publication.class));
|
||||
|
||||
assertEquals(3, roots.count());
|
||||
|
||||
final Dataset<Publication> pubs = spark
|
||||
.read()
|
||||
.textFile(DedupUtility.createEntityPath(graphInputPath, "publication"))
|
||||
.map(asEntity(Publication.class), Encoders.bean(Publication.class));
|
||||
|
||||
Publication root = roots
|
||||
.filter("id = '50|doi_dedup___::b3aec7985136e36827176aaa1dd5082d'")
|
||||
.first();
|
||||
assertNotNull(root);
|
||||
|
||||
Publication crossref_duplicate = pubs
|
||||
.filter("id = '50|doi_________::b3aec7985136e36827176aaa1dd5082d'")
|
||||
.collectAsList()
|
||||
.get(0);
|
||||
|
||||
assertEquals(crossref_duplicate.getDateofacceptance().getValue(), root.getDateofacceptance().getValue());
|
||||
assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName());
|
||||
assertEquals(crossref_duplicate.getJournal().getIssnPrinted(), root.getJournal().getIssnPrinted());
|
||||
assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue());
|
||||
|
||||
Set<String> rootPids = root
|
||||
.getPid()
|
||||
.stream()
|
||||
.map(StructuredProperty::getValue)
|
||||
.collect(Collectors.toCollection(HashSet::new));
|
||||
Set<String> dupPids = crossref_duplicate
|
||||
.getPid()
|
||||
.stream()
|
||||
.map(StructuredProperty::getValue)
|
||||
.collect(Collectors.toCollection(HashSet::new));
|
||||
|
||||
assertFalse(Sets.intersection(rootPids, dupPids).isEmpty());
|
||||
assertTrue(rootPids.contains("10.1109/jstqe.2022.3205716"));
|
||||
assertTrue(rootPids.contains("10.1109/jstqe.2023.9999999"));
|
||||
|
||||
Optional<Instance> instance_cr = root
|
||||
.getInstance()
|
||||
.stream()
|
||||
.filter(i -> i.getCollectedfrom().getValue().equals("Crossref"))
|
||||
.findFirst();
|
||||
assertTrue(instance_cr.isPresent());
|
||||
assertEquals("OPEN", instance_cr.get().getAccessright().getClassid());
|
||||
assertEquals("Open Access", instance_cr.get().getAccessright().getClassname());
|
||||
assertEquals(OpenAccessRoute.hybrid, instance_cr.get().getAccessright().getOpenAccessRoute());
|
||||
assertEquals(
|
||||
"IEEE Journal of Selected Topics in Quantum Electronics", instance_cr.get().getHostedby().getValue());
|
||||
assertEquals("0001", instance_cr.get().getInstancetype().getClassid());
|
||||
assertEquals("Article", instance_cr.get().getInstancetype().getClassname());
|
||||
|
||||
}
|
||||
|
||||
private static String classPathResourceAsString(String path) throws IOException {
|
||||
return IOUtils
|
||||
.toString(
|
||||
SparkPublicationRootsTest2.class
|
||||
.getResourceAsStream(path));
|
||||
}
|
||||
|
||||
private static <T extends OafEntity> MapFunction<String, T> asEntity(Class<T> clazz) {
|
||||
return value -> MAPPER.readValue(value, clazz);
|
||||
}
|
||||
|
||||
private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs));
|
||||
parser.parseArgument(args);
|
||||
return parser;
|
||||
}
|
||||
|
||||
}
|
||||
Binary file not shown.
@ -0,0 +1,24 @@
|
||||
<RESOURCE_PROFILE>
|
||||
<HEADER>
|
||||
<RESOURCE_IDENTIFIER value=""/>
|
||||
<RESOURCE_TYPE value="DedupOrchestrationDSResourceType"/>
|
||||
<RESOURCE_KIND value="DedupOrchestrationDSResources"/>
|
||||
<RESOURCE_URI value=""/>
|
||||
<DATE_OF_CREATION value="2001-12-31T12:00:00"/>
|
||||
</HEADER>
|
||||
<BODY>
|
||||
<CONFIGURATION enabled="true">
|
||||
<DEDUPLICATION>
|
||||
<ENTITY code="20" label="Organization" name="organization"/>
|
||||
<ACTION_SET id="test-orchestrator"/>
|
||||
<SCAN_SEQUENCE>
|
||||
<SCAN id="publication"/>
|
||||
</SCAN_SEQUENCE>
|
||||
</DEDUPLICATION>
|
||||
</CONFIGURATION>
|
||||
<STATUS>
|
||||
<LAST_UPDATE value="2001-12-31T12:00:00"/>
|
||||
</STATUS>
|
||||
<SECURITY_PARAMETERS>SECURITY_PARAMETERS</SECURITY_PARAMETERS>
|
||||
</BODY>
|
||||
</RESOURCE_PROFILE>
|
||||
Binary file not shown.
Binary file not shown.
@ -0,0 +1,47 @@
|
||||
# Root logger option
|
||||
log4j.rootLogger=DEBUG, stdout
|
||||
|
||||
# Direct log messages to stdout
|
||||
log4j.appender.stdout=org.apache.log4j.ConsoleAppender
|
||||
log4j.appender.stdout.Target=System.out
|
||||
log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
|
||||
log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n
|
||||
|
||||
# Change this to set Spark log level
|
||||
log4j.logger.org.apache.spark=ERROR
|
||||
log4j.rootCategory=WARN
|
||||
|
||||
# Silence akka remoting
|
||||
log4j.logger.Remoting=WARN
|
||||
|
||||
# Ignore messages below warning level from Jetty, because it's a bit verbose
|
||||
log4j.logger.org.eclipse.jetty=WARN
|
||||
|
||||
log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitterFactory=WARN
|
||||
log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitter=WARN
|
||||
#log4j.logger.org.apache.parquet.hadoop.ParquetOutputFormat=WARN
|
||||
#log4j.logger.org.apache.parquet.hadoop.InternalParquetRecordWriter=WARN
|
||||
log4j.logger.org.apache.hadoop.io.compress.CodecPool=WARN
|
||||
#log4j.logger.org.apache.hadoop.io.compress=WARN
|
||||
#log4j.logger.org.apache.parquet.hadoop.codec.CodecConfig=WARN
|
||||
log4j.logger.parquet.hadoop.ColumnChunkPageWriteStore=ERROR
|
||||
log4j.logger.com.jayway.jsonpath.internal.path.CompiledPath=WARN
|
||||
log4j.logger.org.apache.parquet.hadoop.ParquetRecordReader=ERROR
|
||||
log4j.logger.parquet.hadoop=WARN
|
||||
log4j.logger.org.eclipse.jetty.server.handler.ContextHandlerCollection=WARN
|
||||
log4j.logger.org.spark_project.jetty.util.component.ContainerLifeCycle=WARN
|
||||
log4j.logger.org.apache.hadoop.mapred.FileInputFormat=WARN
|
||||
log4j.logger.org.spark_project.jetty.servlet.ServletHandler=WARN
|
||||
log4j.logger.org.apache.commons.beanutils.converters.BooleanConverter=WARN
|
||||
log4j.logger.org.apache.commons.beanutils.converters.StringConverter=WARN
|
||||
log4j.logger.org.apache.commons.beanutils.converters.LongConverter=WARN
|
||||
log4j.logger.org.apache.commons.beanutils.converters.ArrayConverter=WARN
|
||||
log4j.logger.org.apache.commons.beanutils.converters.FloatConverter=WARN
|
||||
log4j.logger.org.apache.commons.beanutils.converters.IntegerConverter=WARN
|
||||
log4j.logger.org.apache.commons.beanutils.converters.DoubleConverter=WARN
|
||||
log4j.logger.org.apache.commons.beanutils.converters.CharacterConverter=WARN
|
||||
log4j.logger.org.apache.commons.beanutils.converters.ByteConverter=WARN
|
||||
log4j.logger.org.apache.commons.beanutils.converters.BigIntegerConverter=WARN
|
||||
log4j.logger.org.apache.commons.beanutils.converters.BigDecimalConverter=WARN
|
||||
log4j.logger.org.apache.commons.beanutils.converters.ShortConverter=WARN
|
||||
log4j.logger.org.apache.commons.beanutils.BeanUtils=WARN
|
||||
Loading…
Reference in New Issue