forked from D-Net/dnet-hadoop
682 lines
27 KiB
Java
682 lines
27 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.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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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.FileReader;
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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.List;
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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.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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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.api.java.function.PairFunction;
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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.Row;
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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.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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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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import eu.dnetlib.pace.util.MapDocumentUtil;
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import scala.Tuple2;
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@ExtendWith(MockitoExtension.class)
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@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
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public class SparkDedupTest 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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private static String whitelistPath;
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private static List<String> whiteList;
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private static String WHITELIST_SEPARATOR = "####";
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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(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI())
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.toFile()
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.getAbsolutePath();
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testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
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.toAbsolutePath()
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.toString();
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testDedupGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
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.toAbsolutePath()
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.toString();
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whitelistPath = Paths
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.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/whitelist.simrels.txt").toURI())
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.toFile()
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.getAbsolutePath();
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whiteList = IOUtils.readLines(new FileReader(whitelistPath));
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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", "200");
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spark = SparkSession
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.builder()
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.appName(SparkDedupTest.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(
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IOUtils
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.toString(
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SparkDedupTest.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
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lenient()
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.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
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.thenReturn(
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IOUtils
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.toString(
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SparkDedupTest.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
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lenient()
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.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
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.thenReturn(
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IOUtils
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.toString(
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SparkDedupTest.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
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lenient()
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.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
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.thenReturn(
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IOUtils
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.toString(
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SparkDedupTest.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
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lenient()
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.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("dataset")))
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.thenReturn(
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IOUtils
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.toString(
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SparkDedupTest.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json")));
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lenient()
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.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("otherresearchproduct")))
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.thenReturn(
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IOUtils
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.toString(
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SparkDedupTest.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/dedup/conf/orp.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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IOUtils
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.toString(
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SparkCreateSimRels.class
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.getResourceAsStream(
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"/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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"-i", testGraphBasePath,
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"-asi", testActionSetId,
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"-la", "lookupurl",
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"-w", testOutputBasePath,
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"-np", "50"
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});
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new SparkCreateSimRels(parser, spark).run(isLookUpService);
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long orgs_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
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.count();
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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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long sw_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "software"))
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.count();
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long ds_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "dataset"))
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.count();
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long orp_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct"))
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.count();
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assertEquals(3082, orgs_simrel);
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assertEquals(7036, pubs_simrel);
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assertEquals(336, sw_simrel);
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assertEquals(442, ds_simrel);
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assertEquals(6750, orp_simrel);
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}
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@Test
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@Order(2)
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void whitelistSimRelsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkWhitelistSimRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json")));
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parser
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.parseArgument(
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new String[]{
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"-i", testGraphBasePath,
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"-asi", testActionSetId,
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"-la", "lookupurl",
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"-w", testOutputBasePath,
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"-np", "50",
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"-wl", whitelistPath
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});
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new SparkWhitelistSimRels(parser, spark).run(isLookUpService);
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long orgs_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
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.count();
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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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long ds_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "dataset"))
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.count();
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long orp_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct"))
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.count();
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//entities simrels supposed to be equal to the number of previous step (no rels in whitelist)
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assertEquals(3082, orgs_simrel);
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assertEquals(7036, pubs_simrel);
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assertEquals(442, ds_simrel);
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assertEquals(6750, orp_simrel);
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//entities simrels to be different from the number of previous step (new simrels in the whitelist)
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Dataset<Row> sw_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "software"));
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//check if the first relation in the whitelist exists
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assertTrue(sw_simrel
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.as(Encoders.bean(Relation.class))
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.toJavaRDD()
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.filter(rel ->
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rel.getSource().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[0]) && rel.getTarget().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[1])).count() > 0);
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//check if the second relation in the whitelist exists
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assertTrue(sw_simrel
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.as(Encoders.bean(Relation.class))
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.toJavaRDD()
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.filter(rel ->
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rel.getSource().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[0]) && rel.getTarget().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[1])).count() > 0);
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assertEquals(338, sw_simrel.count());
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}
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@Test
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@Order(3)
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void cutMergeRelsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCreateMergeRels.class
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.getResourceAsStream(
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"/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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"-i",
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testGraphBasePath,
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"-asi",
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testActionSetId,
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"-la",
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"lookupurl",
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"-w",
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testOutputBasePath,
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"-cc",
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"3"
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});
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new SparkCreateMergeRels(parser, spark).run(isLookUpService);
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long orgs_mergerel = spark
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.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/organization_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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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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long sw_mergerel = spark
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.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/software_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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long ds_mergerel = spark
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.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/dataset_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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long orp_mergerel = spark
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.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_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, orgs_mergerel);
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assertEquals(0, pubs_mergerel);
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assertEquals(0, sw_mergerel);
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assertEquals(0, ds_mergerel);
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assertEquals(0, orp_mergerel);
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FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel"));
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FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel"));
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FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/software_mergerel"));
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FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel"));
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FileUtils
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.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel"));
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}
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@Test
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@Order(4)
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void createMergeRelsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCreateMergeRels.class
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.getResourceAsStream(
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"/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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"-i",
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testGraphBasePath,
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"-asi",
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testActionSetId,
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"-la",
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"lookupurl",
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"-w",
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testOutputBasePath
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});
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new SparkCreateMergeRels(parser, spark).run(isLookUpService);
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long orgs_mergerel = spark
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.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
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.count();
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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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.count();
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long sw_mergerel = spark
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.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
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.count();
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long ds_mergerel = spark
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.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
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.count();
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long orp_mergerel = spark
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.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
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.count();
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assertEquals(1272, orgs_mergerel);
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assertEquals(1438, pubs_mergerel);
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assertEquals(286, sw_mergerel);
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assertEquals(472, ds_mergerel);
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assertEquals(718, orp_mergerel);
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}
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@Test
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@Order(5)
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void createDedupRecordTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCreateDedupRecord.class
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.getResourceAsStream(
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"/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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"-i",
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testGraphBasePath,
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"-asi",
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testActionSetId,
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"-la",
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"lookupurl",
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"-w",
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testOutputBasePath
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});
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new SparkCreateDedupRecord(parser, spark).run(isLookUpService);
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long orgs_deduprecord = jsc
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.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord")
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.count();
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long pubs_deduprecord = jsc
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.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord")
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.count();
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long sw_deduprecord = jsc
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.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord")
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.count();
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long ds_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_deduprecord").count();
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long orp_deduprecord = jsc
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.textFile(
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testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_deduprecord")
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.count();
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assertEquals(85, orgs_deduprecord);
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assertEquals(65, pubs_deduprecord);
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assertEquals(49, sw_deduprecord);
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assertEquals(97, ds_deduprecord);
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assertEquals(89, orp_deduprecord);
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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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IOUtils
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.toString(
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SparkUpdateEntity.class
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.getResourceAsStream(
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"/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 organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
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long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
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long projects = jsc.textFile(testDedupGraphBasePath + "/project").count();
|
|
long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count();
|
|
long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count();
|
|
long dataset = jsc.textFile(testDedupGraphBasePath + "/dataset").count();
|
|
long otherresearchproduct = jsc.textFile(testDedupGraphBasePath + "/otherresearchproduct").count();
|
|
|
|
long mergedOrgs = spark
|
|
.read()
|
|
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
|
|
.as(Encoders.bean(Relation.class))
|
|
.where("relClass=='merges'")
|
|
.javaRDD()
|
|
.map(Relation::getTarget)
|
|
.distinct()
|
|
.count();
|
|
|
|
long mergedPubs = spark
|
|
.read()
|
|
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
|
|
.as(Encoders.bean(Relation.class))
|
|
.where("relClass=='merges'")
|
|
.javaRDD()
|
|
.map(Relation::getTarget)
|
|
.distinct()
|
|
.count();
|
|
|
|
long mergedSw = spark
|
|
.read()
|
|
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
|
|
.as(Encoders.bean(Relation.class))
|
|
.where("relClass=='merges'")
|
|
.javaRDD()
|
|
.map(Relation::getTarget)
|
|
.distinct()
|
|
.count();
|
|
|
|
long mergedDs = spark
|
|
.read()
|
|
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
|
|
.as(Encoders.bean(Relation.class))
|
|
.where("relClass=='merges'")
|
|
.javaRDD()
|
|
.map(Relation::getTarget)
|
|
.distinct()
|
|
.count();
|
|
|
|
long mergedOrp = spark
|
|
.read()
|
|
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
|
|
.as(Encoders.bean(Relation.class))
|
|
.where("relClass=='merges'")
|
|
.javaRDD()
|
|
.map(Relation::getTarget)
|
|
.distinct()
|
|
.count();
|
|
|
|
assertEquals(896, publications);
|
|
assertEquals(838, organizations);
|
|
assertEquals(100, projects);
|
|
assertEquals(100, datasource);
|
|
assertEquals(198, softwares);
|
|
assertEquals(389, dataset);
|
|
assertEquals(517, otherresearchproduct);
|
|
|
|
long deletedOrgs = jsc
|
|
.textFile(testDedupGraphBasePath + "/organization")
|
|
.filter(this::isDeletedByInference)
|
|
.count();
|
|
|
|
long deletedPubs = jsc
|
|
.textFile(testDedupGraphBasePath + "/publication")
|
|
.filter(this::isDeletedByInference)
|
|
.count();
|
|
|
|
long deletedSw = jsc
|
|
.textFile(testDedupGraphBasePath + "/software")
|
|
.filter(this::isDeletedByInference)
|
|
.count();
|
|
|
|
long deletedDs = jsc
|
|
.textFile(testDedupGraphBasePath + "/dataset")
|
|
.filter(this::isDeletedByInference)
|
|
.count();
|
|
|
|
long deletedOrp = jsc
|
|
.textFile(testDedupGraphBasePath + "/otherresearchproduct")
|
|
.filter(this::isDeletedByInference)
|
|
.count();
|
|
|
|
assertEquals(mergedOrgs, deletedOrgs);
|
|
assertEquals(mergedPubs, deletedPubs);
|
|
assertEquals(mergedSw, deletedSw);
|
|
assertEquals(mergedDs, deletedDs);
|
|
assertEquals(mergedOrp, deletedOrp);
|
|
}
|
|
|
|
@Test
|
|
@Order(7)
|
|
void propagateRelationTest() throws Exception {
|
|
|
|
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
|
IOUtils
|
|
.toString(
|
|
SparkPropagateRelation.class
|
|
.getResourceAsStream(
|
|
"/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
|
|
parser
|
|
.parseArgument(
|
|
new String[]{
|
|
"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
|
|
});
|
|
|
|
new SparkPropagateRelation(parser, spark).run(isLookUpService);
|
|
|
|
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
|
|
|
|
assertEquals(4860, relations);
|
|
|
|
// check deletedbyinference
|
|
final Dataset<Relation> mergeRels = spark
|
|
.read()
|
|
.load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*"))
|
|
.as(Encoders.bean(Relation.class));
|
|
final JavaPairRDD<String, String> mergedIds = mergeRels
|
|
.where("relClass == 'merges'")
|
|
.select(mergeRels.col("target"))
|
|
.distinct()
|
|
.toJavaRDD()
|
|
.mapToPair(
|
|
(PairFunction<Row, String, String>) r -> new Tuple2<String, String>(r.getString(0), "d"));
|
|
|
|
JavaRDD<String> toCheck = jsc
|
|
.textFile(testDedupGraphBasePath + "/relation")
|
|
.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json))
|
|
.join(mergedIds)
|
|
.map(t -> t._2()._1())
|
|
.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json))
|
|
.join(mergedIds)
|
|
.map(t -> t._2()._1());
|
|
|
|
long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
|
|
long updated = toCheck.count();
|
|
|
|
assertEquals(updated, deletedbyinference);
|
|
}
|
|
|
|
@Test
|
|
@Order(8)
|
|
void testRelations() throws Exception {
|
|
testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_1.json", 12, 10);
|
|
testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_2.json", 10, 2);
|
|
}
|
|
|
|
private void testUniqueness(String path, int expected_total, int expected_unique) {
|
|
Dataset<Relation> rel = spark
|
|
.read()
|
|
.textFile(getClass().getResource(path).getPath())
|
|
.map(
|
|
(MapFunction<String, Relation>) s -> new ObjectMapper().readValue(s, Relation.class),
|
|
Encoders.bean(Relation.class));
|
|
|
|
assertEquals(expected_total, rel.count());
|
|
assertEquals(expected_unique, rel.distinct().count());
|
|
}
|
|
|
|
@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");
|
|
}
|
|
}
|