merging duplicates using IdentifierComparator
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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());
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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) throws JsonProcessingException {
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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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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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@Test
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@Order(6)
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void updateEntityTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"));
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parser
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.parseArgument(
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new String[] {
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"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
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});
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new SparkUpdateEntity(parser, spark).run(isLookUpService);
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long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
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long mergedPubs = 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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.where("relClass=='merges'")
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.javaRDD()
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.map(Relation::getTarget)
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.distinct()
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.count();
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assertEquals(14, publications);
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long deletedPubs = jsc
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.textFile(testDedupGraphBasePath + "/publication")
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.filter(this::isDeletedByInference)
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.count();
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assertEquals(mergedPubs, deletedPubs);
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}
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@AfterAll
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public static void finalCleanUp() throws IOException {
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FileUtils.deleteDirectory(new File(testOutputBasePath));
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FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
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}
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public boolean isDeletedByInference(String s) {
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return s.contains("\"deletedbyinference\":true");
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}
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private static String classPathResourceAsString(String path) throws IOException {
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return IOUtils
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.toString(
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SparkDedupPublicationTest.class
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.getResourceAsStream(path));
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}
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}
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Binary file not shown.
Binary file not shown.
@ -0,0 +1,24 @@
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<RESOURCE_PROFILE>
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<HEADER>
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<RESOURCE_IDENTIFIER value=""/>
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<RESOURCE_TYPE value="DedupOrchestrationDSResourceType"/>
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<RESOURCE_KIND value="DedupOrchestrationDSResources"/>
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<RESOURCE_URI value=""/>
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<DATE_OF_CREATION value="2001-12-31T12:00:00"/>
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</HEADER>
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<BODY>
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<CONFIGURATION enabled="true">
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<DEDUPLICATION>
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<ENTITY code="20" label="Organization" name="organization"/>
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<ACTION_SET id="test-orchestrator"/>
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<SCAN_SEQUENCE>
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<SCAN id="publication"/>
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</SCAN_SEQUENCE>
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</DEDUPLICATION>
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</CONFIGURATION>
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<STATUS>
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<LAST_UPDATE value="2001-12-31T12:00:00"/>
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</STATUS>
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<SECURITY_PARAMETERS>SECURITY_PARAMETERS</SECURITY_PARAMETERS>
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</BODY>
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</RESOURCE_PROFILE>
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