2021-02-26 10:19:28 +01:00
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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.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 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.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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2021-03-19 16:57:40 +01:00
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import org.apache.spark.api.java.function.ForeachFunction;
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2021-02-26 10:19:28 +01:00
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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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2021-03-19 16:57:40 +01:00
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import org.apache.spark.sql.Row;
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2021-02-26 10:19:28 +01:00
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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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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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 jdk.nashorn.internal.ir.annotations.Ignore;
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@ExtendWith(MockitoExtension.class)
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public class SparkOpenorgsTest 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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protected static final ObjectMapper OBJECT_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 cleanUp() throws IOException, URISyntaxException {
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testGraphBasePath = Paths
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.get(SparkOpenorgsTest.class.getResource("/eu/dnetlib/dhp/dedup/openorgs").toURI())
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.toFile()
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.getAbsolutePath();
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testOutputBasePath = createTempDirectory(SparkOpenorgsTest.class.getSimpleName() + "-")
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.toAbsolutePath()
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.toString();
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testDedupGraphBasePath = createTempDirectory(SparkOpenorgsTest.class.getSimpleName() + "-")
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.toAbsolutePath()
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.toString();
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2021-03-19 16:57:40 +01:00
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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_openorgs.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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}
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2021-03-29 10:07:12 +02:00
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@Disabled
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@Test
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public void copyOpenorgsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCopyOpenorgs.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/copyOpenorgs_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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"-w", testOutputBasePath,
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"-np", "50"
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});
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new SparkCopyOpenorgs(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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assertEquals(100, orgs_deduprecord);
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}
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@Test
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public void copyOpenorgsMergeRels() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCopyOpenorgsMergeRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/copyOpenorgsMergeRels_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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"-w", testOutputBasePath,
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"-la", "lookupurl",
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"-np", "50"
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});
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new SparkCopyOpenorgsMergeRels(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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assertEquals(384, orgs_mergerel);
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}
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@Test
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public void copyOpenorgsSimRels() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCopyOpenorgsSimRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/copyOpenorgsMergeRels_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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"-w", testOutputBasePath,
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"-la", "lookupurl",
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"-np", "50"
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});
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new SparkCopyOpenorgsSimRels(parser, spark).run(isLookUpService);
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long orgs_simrel = spark
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.read()
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.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
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.count();
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assertEquals(73, orgs_simrel);
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}
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@Test
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public void copyRelationsNoOpenorgsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCopyRelationsNoOpenorgs.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,
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"-w", testOutputBasePath,
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"-o", testDedupGraphBasePath
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});
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new SparkCopyRelationsNoOpenorgs(parser, spark).run(isLookUpService);
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long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
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assertEquals(400, relations);
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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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private static MapFunction<String, Relation> patchRelFn() {
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return value -> {
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final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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return rel;
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};
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}
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}
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