forked from D-Net/dnet-hadoop
282 lines
8.0 KiB
Java
282 lines
8.0 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.col;
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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.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 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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@ExtendWith(MockitoExtension.class)
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@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
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public class SparkOpenorgsProvisionTest 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 testGraphBasePath;
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private static String testOutputBasePath;
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private static String testDedupGraphBasePath;
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private static String testConsistencyGraphBasePath;
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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(SparkOpenorgsProvisionTest.class.getResource("/eu/dnetlib/dhp/dedup/openorgs/provision").toURI())
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.toFile()
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.getAbsolutePath();
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testOutputBasePath = createTempDirectory(SparkOpenorgsProvisionTest.class.getSimpleName() + "-")
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.toAbsolutePath()
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.toString();
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testDedupGraphBasePath = createTempDirectory(SparkOpenorgsProvisionTest.class.getSimpleName() + "-")
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.toAbsolutePath()
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.toString();
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testConsistencyGraphBasePath = createTempDirectory(SparkOpenorgsProvisionTest.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", "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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}
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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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FileUtils.deleteDirectory(new File(testConsistencyGraphBasePath));
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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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@Test
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@Order(1)
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void copyOpenorgsMergeRelTest() 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",
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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 SparkCopyOpenorgsMergeRels(parser, spark).run(isLookUpService);
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long orgs_mergerel = spark
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.read()
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.load(DedupUtility.createMergeRelPath(testOutputBasePath, testActionSetId, "organization"))
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.count();
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assertEquals(140, orgs_mergerel);
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}
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@Test
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@Order(2)
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void createOrgsDedupRecordTest() 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/copyOpenorgs_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 SparkCreateOrgsDedupRecord(parser, spark).run(isLookUpService);
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long orgs_deduprecord = spark
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.read()
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.json(DedupUtility.createDedupRecordPath(testOutputBasePath, testActionSetId, "organization"))
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.count();
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assertEquals(10, orgs_deduprecord);
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}
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@Test
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@Order(3)
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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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Dataset<Row> organizations = spark.read().json(testDedupGraphBasePath + "/organization");
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Dataset<Row> mergedOrgs = spark
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.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
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.where("relClass=='merges'")
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.select("target")
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.distinct();
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assertEquals(80, organizations.count());
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Dataset<Row> deletedOrgs = organizations
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.filter("dataInfo.deletedbyinference = TRUE");
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assertEquals(mergedOrgs.count(), deletedOrgs.count());
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}
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@Test
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@Order(4)
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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, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
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});
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new SparkCopyRelationsNoOpenorgs(parser, spark).run(isLookUpService);
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final Dataset<Row> outputRels = spark.read().text(testDedupGraphBasePath + "/relation");
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assertEquals(2382, outputRels.count());
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}
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@Test
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@Order(5)
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void propagateRelationsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkPropagateRelation.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
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parser
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.parseArgument(
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new String[] {
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"-i", testDedupGraphBasePath, "-w", testOutputBasePath, "-o", testConsistencyGraphBasePath
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});
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new SparkPropagateRelation(parser, spark).run(isLookUpService);
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final Dataset<Relation> mergeRels = spark
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.read()
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.load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*"))
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.as(Encoders.bean(Relation.class));
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Dataset<Row> inputRels = spark
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.read()
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.json(testDedupGraphBasePath + "/relation");
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Dataset<Row> outputRels = spark
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.read()
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.json(testConsistencyGraphBasePath + "/relation");
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final Dataset<Row> mergedIds = mergeRels
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.where("relClass == 'merges'")
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.select(col("target").as("id"))
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.distinct();
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Dataset<Row> toUpdateRels = inputRels
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.as("rel")
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.join(mergedIds.as("s"), col("rel.source").equalTo(col("s.id")), "left_outer")
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.join(mergedIds.as("t"), col("rel.target").equalTo(col("t.id")), "left_outer")
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.filter("s.id IS NOT NULL OR t.id IS NOT NULL")
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.distinct();
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Dataset<Row> updatedRels = inputRels
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.select("source", "target", "relClass")
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.except(outputRels.select("source", "target", "relClass"));
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assertEquals(toUpdateRels.count(), updatedRels.count());
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assertEquals(140, outputRels.count());
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}
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}
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