404 lines
13 KiB
Java
404 lines
13 KiB
Java
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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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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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Publication pivot_duplicate = pubs
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.filter("id = '50|od_______166::31ca734cc22181b704c4aa8fd050062a'")
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.first();
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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()
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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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new SparkUpdateEntity(args(
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"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json",
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new String[] {
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"--graphBasePath", graphInputPath,
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"--workingPath", workingPath,
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"--dedupGraphPath", graphOutputPath
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}), spark)
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.run(isLookUpService);
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long publications = spark.read().textFile(graphOutputPath + "/publication").count();
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long mergedPubs = 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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.where("relClass=='merges'")
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.map((MapFunction<Relation, String>) Relation::getTarget, Encoders.STRING())
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.distinct()
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.count();
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assertEquals(19, publications); // 16 originals + 3 roots
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long deletedPubs = spark
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.read()
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.textFile(graphOutputPath + "/publication")
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.map(asEntity(Publication.class), Encoders.bean(Publication.class))
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.filter("datainfo.deletedbyinference == true")
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.map((MapFunction<Publication, String>) OafEntity::getId, Encoders.STRING())
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.distinct()
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.count();
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assertEquals(mergedPubs, deletedPubs);
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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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SparkPublicationRootsTest.class
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.getResourceAsStream(path));
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}
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private static <T extends OafEntity> MapFunction<String, T> asEntity(Class<T> clazz) {
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return value -> MAPPER.readValue(value, clazz);
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}
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private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs));
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parser.parseArgument(args);
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return parser;
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}
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}
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