merging duplicates using IdentifierComparator
This commit is contained in:
parent
5af5a8ae42
commit
ddff0e8999
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@ -1,12 +1,12 @@
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package eu.dnetlib.dhp.oa.dedup;
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import java.util.Collection;
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import java.util.Comparator;
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import java.util.Iterator;
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import java.util.List;
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import java.lang.reflect.InvocationTargetException;
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import java.util.*;
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import java.util.stream.Collectors;
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import org.apache.commons.beanutils.BeanUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.MapGroupsFunction;
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import org.apache.spark.sql.Dataset;
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@ -15,14 +15,12 @@ import org.apache.spark.sql.SparkSession;
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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.Iterators;
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import com.google.common.collect.Lists;
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import eu.dnetlib.dhp.oa.dedup.model.Identifier;
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import eu.dnetlib.dhp.oa.merge.AuthorMerger;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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import scala.Tuple2;
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public class DedupRecordFactory {
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@ -79,23 +77,25 @@ public class DedupRecordFactory {
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public static <T extends OafEntity> T entityMerger(
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String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz)
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throws IllegalAccessException, InstantiationException {
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throws IllegalAccessException, InstantiationException, InvocationTargetException {
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T entity = clazz.newInstance();
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entity.setDataInfo(dataInfo);
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final Comparator<Identifier<T>> idComparator = new IdentifierComparator<>();
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final Collection<String> dates = Lists.newArrayList();
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final List<List<Author>> authors = Lists.newArrayList();
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final Comparator<Identifier<T>> idComparator = new IdentifierComparator<T>().reversed();
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final List<T> entityList = Lists
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final LinkedList<T> entityList = Lists
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.newArrayList(entities)
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.stream()
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.map(t -> Identifier.newInstance(t._2()))
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.sorted(idComparator)
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.map(Identifier::getEntity)
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.collect(Collectors.toList());
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.collect(Collectors.toCollection(LinkedList::new));
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final T entity = clazz.newInstance();
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final T first = entityList.removeFirst();
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BeanUtils.copyProperties(entity, first);
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final Collection<String> dates = Lists.newArrayList();
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final List<List<Author>> authors = Lists.newArrayList();
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entityList
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.forEach(
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@ -103,12 +103,11 @@ public class DedupRecordFactory {
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entity.mergeFrom(duplicate);
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if (ModelSupport.isSubClass(duplicate, Result.class)) {
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Result r1 = (Result) duplicate;
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if (r1.getAuthor() != null && !r1.getAuthor().isEmpty())
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if (r1.getAuthor() != null && StringUtils.isNotBlank(r1.getDateofacceptance().getValue()))
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authors.add(r1.getAuthor());
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if (r1.getDateofacceptance() != null)
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dates.add(r1.getDateofacceptance().getValue());
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}
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});
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// set authors and date
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@ -7,6 +7,7 @@ import java.io.BufferedReader;
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import java.io.FileReader;
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import java.io.IOException;
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import java.io.Serializable;
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import java.lang.reflect.InvocationTargetException;
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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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@ -54,7 +55,7 @@ class EntityMergerTest implements Serializable {
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}
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@Test
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void softwareMergerTest() throws InstantiationException, IllegalAccessException {
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void softwareMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException {
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List<Tuple2<String, Software>> softwares = readSample(
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testEntityBasePath + "/software_merge.json", Software.class);
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@ -69,7 +70,7 @@ class EntityMergerTest implements Serializable {
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}
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@Test
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void publicationMergerTest() throws InstantiationException, IllegalAccessException {
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void publicationMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException {
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Publication pub_merged = DedupRecordFactory
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.entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class);
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@ -134,7 +135,7 @@ class EntityMergerTest implements Serializable {
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}
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@Test
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void publicationMergerTest2() throws InstantiationException, IllegalAccessException {
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void publicationMergerTest2() throws InstantiationException, IllegalAccessException, InvocationTargetException {
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Publication pub_merged = DedupRecordFactory
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.entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class);
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@ -146,7 +147,7 @@ class EntityMergerTest implements Serializable {
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}
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@Test
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void publicationMergerTest3() throws InstantiationException, IllegalAccessException {
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void publicationMergerTest3() throws InstantiationException, IllegalAccessException, InvocationTargetException {
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Publication pub_merged = DedupRecordFactory
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.entityMerger(dedupId, publications3.iterator(), 0, dataInfo, Publication.class);
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@ -156,7 +157,8 @@ class EntityMergerTest implements Serializable {
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}
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@Test
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void publicationMergerTest4() throws InstantiationException, IllegalStateException, IllegalAccessException {
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void publicationMergerTest4()
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throws InstantiationException, IllegalStateException, IllegalAccessException, InvocationTargetException {
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Publication pub_merged = DedupRecordFactory
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.entityMerger(dedupId, publications4.iterator(), 0, dataInfo, Publication.class);
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@ -166,7 +168,8 @@ class EntityMergerTest implements Serializable {
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}
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@Test
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void publicationMergerTest5() throws InstantiationException, IllegalStateException, IllegalAccessException {
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void publicationMergerTest5()
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throws InstantiationException, IllegalStateException, IllegalAccessException, InvocationTargetException {
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System.out
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.println(
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@ -0,0 +1,389 @@
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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.Paths;
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import java.util.*;
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import java.util.stream.Collectors;
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import com.fasterxml.jackson.core.JsonProcessingException;
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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.FlatMapFunction;
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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 SparkDedupPublicationTest 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 JavaSparkContext jsc;
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private static String testGraphBasePath;
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private static String testOutputBasePath;
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private static String testDedupGraphBasePath;
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private static final String testActionSetId = "test-orchestrator";
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@BeforeAll
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public static void cleanUp() throws IOException, URISyntaxException {
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testGraphBasePath = Paths
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.get(SparkDedupPublicationTest.class.getResource("/eu/dnetlib/dhp/dedup/entities2").toURI())
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.toFile()
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.getAbsolutePath();
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testOutputBasePath = createTempDirectory(SparkDedupPublicationTest.class.getSimpleName() + "-")
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.toAbsolutePath()
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.toString();
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testDedupGraphBasePath = createTempDirectory(SparkDedupPublicationTest.class.getSimpleName() + "-")
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.toAbsolutePath()
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.toString();
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FileUtils.deleteDirectory(new File(testOutputBasePath));
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FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
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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(SparkDedupPublicationTest.class.getSimpleName())
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.master("local[*]")
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.config(conf)
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.getOrCreate();
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jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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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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@Test
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@Order(1)
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void createSimRelsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"));
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parser
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.parseArgument(
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new String[] {
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"--graphBasePath", testGraphBasePath,
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"--actionSetId", testActionSetId,
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"--isLookUpUrl", "lookupurl",
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"--workingPath", testOutputBasePath,
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"--numPartitions", "5"
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});
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new SparkCreateSimRels(parser, spark).run(isLookUpService);
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long pubs_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "publication"))
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.count();
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assertEquals(62, 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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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"));
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parser
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.parseArgument(
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new String[] {
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"--graphBasePath", testGraphBasePath,
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"--actionSetId", testActionSetId,
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"--isLookUpUrl", "lookupurl",
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"--workingPath", testOutputBasePath,
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"--cutConnectedComponent", "3"
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});
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new SparkCreateMergeRels(parser, spark).run(isLookUpService);
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long pubs_mergerel = spark
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.read()
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.load(testOutputBasePath + "/" + 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(testOutputBasePath + "/" + 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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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"));
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parser
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.parseArgument(
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new String[] {
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"--graphBasePath", testGraphBasePath,
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"--actionSetId", testActionSetId,
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"--isLookUpUrl", "lookupurl",
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"--workingPath", testOutputBasePath
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});
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new SparkCreateMergeRels(parser, spark).run(isLookUpService);
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final Dataset<Relation> pubs = spark
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.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
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.as(Encoders.bean(Relation.class));
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final List<Relation> merges = pubs
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.filter("source == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
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.collectAsList();
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assertEquals(3, merges.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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merges.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 = pubs
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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(24, pubs.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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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"));
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parser
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.parseArgument(
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new String[] {
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"--graphBasePath", testGraphBasePath,
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"--actionSetId", testActionSetId,
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"--isLookUpUrl", "lookupurl",
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"--workingPath", testOutputBasePath
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});
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new SparkCreateDedupRecord(parser, spark).run(isLookUpService);
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final ObjectMapper mapper = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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final Dataset<Publication> roots = spark
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.read()
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.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord")
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.map(
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(MapFunction<String, Publication>) value -> mapper.readValue(value, Publication.class),
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Encoders.bean(Publication.class));
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assertEquals(2, roots.count());
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final Dataset<Publication> pubs = spark
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.read()
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.textFile(DedupUtility.createEntityPath(testGraphBasePath, "publication"))
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.map(
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(MapFunction<String, Publication>) value -> mapper.readValue(value, Publication.class),
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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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}
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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());
|
||||
assertEquals("Article", instance_cr.get().getInstancetype().getClassname());
|
||||
}
|
||||
|
||||
private void verifyRoot_case_2(Dataset<Publication> roots, Dataset<Publication> pubs) throws JsonProcessingException {
|
||||
Publication root = roots
|
||||
.filter("id = '50|doi_dedup___::18aff3b55fb6876466a5d4bd82434885'")
|
||||
.first();
|
||||
assertNotNull(root);
|
||||
|
||||
Publication crossref_duplicate = pubs
|
||||
.filter("id = '50|doi_________::18aff3b55fb6876466a5d4bd82434885'")
|
||||
.first();
|
||||
|
||||
//System.err.println(new ObjectMapper().writeValueAsString(root));
|
||||
|
||||
assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName());
|
||||
assertEquals(crossref_duplicate.getJournal().getIssnOnline(), root.getJournal().getIssnOnline());
|
||||
assertEquals(crossref_duplicate.getJournal().getVol(), root.getJournal().getVol());
|
||||
|
||||
assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue());
|
||||
|
||||
Set<String> dups_cf = pubs
|
||||
.collectAsList()
|
||||
.stream()
|
||||
.flatMap(p -> p.getCollectedfrom().stream())
|
||||
.map(KeyValue::getValue)
|
||||
.collect(Collectors.toCollection(HashSet::new));
|
||||
|
||||
Set<String> root_cf = root
|
||||
.getCollectedfrom()
|
||||
.stream()
|
||||
.map(KeyValue::getValue)
|
||||
.collect(Collectors.toCollection(HashSet::new));
|
||||
|
||||
assertTrue(Sets.difference(root_cf, dups_cf).isEmpty());
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(6)
|
||||
void updateEntityTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
|
||||
});
|
||||
|
||||
new SparkUpdateEntity(parser, spark).run(isLookUpService);
|
||||
|
||||
long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
|
||||
|
||||
long mergedPubs = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.where("relClass=='merges'")
|
||||
.javaRDD()
|
||||
.map(Relation::getTarget)
|
||||
.distinct()
|
||||
.count();
|
||||
|
||||
assertEquals(14, publications);
|
||||
|
||||
long deletedPubs = jsc
|
||||
.textFile(testDedupGraphBasePath + "/publication")
|
||||
.filter(this::isDeletedByInference)
|
||||
.count();
|
||||
|
||||
assertEquals(mergedPubs, deletedPubs);
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void finalCleanUp() throws IOException {
|
||||
FileUtils.deleteDirectory(new File(testOutputBasePath));
|
||||
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
|
||||
}
|
||||
|
||||
public boolean isDeletedByInference(String s) {
|
||||
return s.contains("\"deletedbyinference\":true");
|
||||
}
|
||||
|
||||
private static String classPathResourceAsString(String path) throws IOException {
|
||||
return IOUtils
|
||||
.toString(
|
||||
SparkDedupPublicationTest.class
|
||||
.getResourceAsStream(path));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -4,8 +4,7 @@ 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.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
import java.io.File;
|
||||
|
|
@ -14,7 +13,11 @@ import java.io.IOException;
|
|||
import java.io.Serializable;
|
||||
import java.net.URISyntaxException;
|
||||
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.io.FileUtils;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
|
|
@ -35,10 +38,13 @@ 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.oaf.Relation;
|
||||
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;
|
||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||
|
|
@ -105,57 +111,27 @@ public class SparkDedupTest implements Serializable {
|
|||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
|
||||
.thenReturn(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkDedupTest.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
|
||||
.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"));
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
|
||||
.thenReturn(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkDedupTest.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
|
||||
.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"));
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
|
||||
.thenReturn(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkDedupTest.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
|
||||
.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"));
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
|
||||
.thenReturn(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkDedupTest.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
|
||||
.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json"));
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("dataset")))
|
||||
.thenReturn(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkDedupTest.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json")));
|
||||
.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json"));
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("otherresearchproduct")))
|
||||
.thenReturn(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkDedupTest.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json")));
|
||||
.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json"));
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -163,11 +139,7 @@ public class SparkDedupTest implements Serializable {
|
|||
void createSimRelsTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateSimRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"));
|
||||
|
||||
parser
|
||||
.parseArgument(
|
||||
|
|
@ -207,7 +179,7 @@ public class SparkDedupTest implements Serializable {
|
|||
.count();
|
||||
|
||||
assertEquals(3076, orgs_simrel);
|
||||
assertEquals(7040, pubs_simrel);
|
||||
assertEquals(7046, pubs_simrel);
|
||||
assertEquals(336, sw_simrel);
|
||||
assertEquals(442, ds_simrel);
|
||||
assertEquals(6784, orp_simrel);
|
||||
|
|
@ -223,11 +195,7 @@ public class SparkDedupTest implements Serializable {
|
|||
void whitelistSimRelsTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkWhitelistSimRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json")));
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json"));
|
||||
|
||||
parser
|
||||
.parseArgument(
|
||||
|
|
@ -264,7 +232,7 @@ public class SparkDedupTest implements Serializable {
|
|||
|
||||
// entities simrels supposed to be equal to the number of previous step (no rels in whitelist)
|
||||
assertEquals(3076, orgs_simrel);
|
||||
assertEquals(7040, pubs_simrel);
|
||||
assertEquals(7046, pubs_simrel);
|
||||
assertEquals(442, ds_simrel);
|
||||
assertEquals(6784, orp_simrel);
|
||||
// System.out.println("orgs_simrel = " + orgs_simrel);
|
||||
|
|
@ -306,11 +274,7 @@ public class SparkDedupTest implements Serializable {
|
|||
void cutMergeRelsTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateMergeRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"));
|
||||
|
||||
parser
|
||||
.parseArgument(
|
||||
|
|
@ -402,11 +366,7 @@ public class SparkDedupTest implements Serializable {
|
|||
void createMergeRelsTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateMergeRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"));
|
||||
|
||||
parser
|
||||
.parseArgument(
|
||||
|
|
@ -427,10 +387,10 @@ public class SparkDedupTest implements Serializable {
|
|||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
|
||||
.count();
|
||||
long pubs_mergerel = spark
|
||||
final Dataset<Relation> pubs = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
|
||||
.count();
|
||||
.as(Encoders.bean(Relation.class));
|
||||
long sw_mergerel = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
|
||||
|
|
@ -445,8 +405,35 @@ public class SparkDedupTest implements Serializable {
|
|||
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
|
||||
.count();
|
||||
|
||||
final List<Relation> merges = pubs
|
||||
.filter("source == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
|
||||
.collectAsList();
|
||||
assertEquals(3, merges.size());
|
||||
Set<String> dups = Sets
|
||||
.newHashSet(
|
||||
"50|doi_________::3b1d0d8e8f930826665df9d6b82fbb73",
|
||||
"50|doi_________::d5021b53204e4fdeab6ff5d5bc468032",
|
||||
"50|arXiv_______::c93aeb433eb90ed7a86e29be00791b7c");
|
||||
merges.forEach(r -> {
|
||||
assertEquals(ModelConstants.RESULT_RESULT, r.getRelType());
|
||||
assertEquals(ModelConstants.DEDUP, r.getSubRelType());
|
||||
assertEquals(ModelConstants.MERGES, r.getRelClass());
|
||||
assertTrue(dups.contains(r.getTarget()));
|
||||
});
|
||||
|
||||
final List<Relation> mergedIn = pubs
|
||||
.filter("target == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
|
||||
.collectAsList();
|
||||
assertEquals(3, mergedIn.size());
|
||||
mergedIn.forEach(r -> {
|
||||
assertEquals(ModelConstants.RESULT_RESULT, r.getRelType());
|
||||
assertEquals(ModelConstants.DEDUP, r.getSubRelType());
|
||||
assertEquals(ModelConstants.IS_MERGED_IN, r.getRelClass());
|
||||
assertTrue(dups.contains(r.getSource()));
|
||||
});
|
||||
|
||||
assertEquals(1268, orgs_mergerel);
|
||||
assertEquals(1444, pubs_mergerel);
|
||||
assertEquals(1450, pubs.count());
|
||||
assertEquals(286, sw_mergerel);
|
||||
assertEquals(472, ds_mergerel);
|
||||
assertEquals(738, orp_mergerel);
|
||||
|
|
@ -463,11 +450,7 @@ public class SparkDedupTest implements Serializable {
|
|||
void createDedupRecordTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateDedupRecord.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
|
|
@ -483,12 +466,18 @@ public class SparkDedupTest implements Serializable {
|
|||
|
||||
new SparkCreateDedupRecord(parser, spark).run(isLookUpService);
|
||||
|
||||
final ObjectMapper mapper = new ObjectMapper()
|
||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
|
||||
final Dataset<Publication> pubs = spark
|
||||
.read()
|
||||
.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord")
|
||||
.map(
|
||||
(MapFunction<String, Publication>) value -> mapper.readValue(value, Publication.class),
|
||||
Encoders.bean(Publication.class));
|
||||
long orgs_deduprecord = jsc
|
||||
.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord")
|
||||
.count();
|
||||
long pubs_deduprecord = jsc
|
||||
.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord")
|
||||
.count();
|
||||
long sw_deduprecord = jsc
|
||||
.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord")
|
||||
.count();
|
||||
|
|
@ -499,11 +488,13 @@ public class SparkDedupTest implements Serializable {
|
|||
.count();
|
||||
|
||||
assertEquals(86, orgs_deduprecord);
|
||||
assertEquals(67, pubs_deduprecord);
|
||||
assertEquals(68, pubs.count());
|
||||
assertEquals(49, sw_deduprecord);
|
||||
assertEquals(97, ds_deduprecord);
|
||||
assertEquals(92, orp_deduprecord);
|
||||
|
||||
verifyRoot_1(mapper, pubs);
|
||||
|
||||
// System.out.println("orgs_deduprecord = " + orgs_deduprecord);
|
||||
// System.out.println("pubs_deduprecord = " + pubs_deduprecord);
|
||||
// System.out.println("sw_deduprecord = " + sw_deduprecord);
|
||||
|
|
@ -511,16 +502,63 @@ public class SparkDedupTest implements Serializable {
|
|||
// System.out.println("orp_deduprecord = " + orp_deduprecord);
|
||||
}
|
||||
|
||||
private static void verifyRoot_1(ObjectMapper mapper, Dataset<Publication> pubs) {
|
||||
Publication root = pubs
|
||||
.filter("id = '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
|
||||
.first();
|
||||
assertNotNull(root);
|
||||
|
||||
final Dataset<String> publication = spark
|
||||
.read()
|
||||
.textFile(DedupUtility.createEntityPath(testGraphBasePath, "publication"));
|
||||
|
||||
Publication crossref_duplicate = publication
|
||||
.map(
|
||||
(MapFunction<String, Publication>) value -> mapper.readValue(value, Publication.class),
|
||||
Encoders.bean(Publication.class))
|
||||
.filter("id = '50|doi_________::d5021b53204e4fdeab6ff5d5bc468032'")
|
||||
.collectAsList()
|
||||
.get(0);
|
||||
|
||||
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"));
|
||||
|
||||
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());
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(6)
|
||||
void updateEntityTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkUpdateEntity.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
|
|
@ -587,7 +625,7 @@ public class SparkDedupTest implements Serializable {
|
|||
.distinct()
|
||||
.count();
|
||||
|
||||
assertEquals(898, publications);
|
||||
assertEquals(902, publications);
|
||||
assertEquals(839, organizations);
|
||||
assertEquals(100, projects);
|
||||
assertEquals(100, datasource);
|
||||
|
|
@ -640,11 +678,7 @@ public class SparkDedupTest implements Serializable {
|
|||
void propagateRelationTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkPropagateRelation.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
|
|
@ -714,4 +748,12 @@ public class SparkDedupTest implements Serializable {
|
|||
public boolean isDeletedByInference(String s) {
|
||||
return s.contains("\"deletedbyinference\":true");
|
||||
}
|
||||
|
||||
private static String classPathResourceAsString(String path) throws IOException {
|
||||
return IOUtils
|
||||
.toString(
|
||||
SparkDedupTest.class
|
||||
.getResourceAsStream(path));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Binary file not shown.
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>
|
||||
|
|
@ -19,7 +19,29 @@ 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.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.parquet.hadoop.codec.CodecConfig=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