SparkDedupTest updated and organization dump fixed
This commit is contained in:
miconis
parent
4da13e4570
commit
1102e32462
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@ -1,29 +1,37 @@
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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.junit.jupiter.api.Assertions.assertEquals;
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import static org.mockito.Mockito.lenient;
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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 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 eu.dnetlib.pace.util.MapDocumentUtil;
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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.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 scala.Tuple2;
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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 static java.nio.file.Files.createTempDirectory;
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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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@ExtendWith(MockitoExtension.class)
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@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
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@ -38,224 +46,164 @@ public class SparkDedupTest implements Serializable {
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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 final static String testActionSetId = "test-orchestrator";
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@BeforeAll
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private static void cleanUp() throws IOException, URISyntaxException {
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testGraphBasePath =
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Paths.get(
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SparkDedupTest.class
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.getResource("/eu/dnetlib/dhp/dedup/entities")
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.toURI())
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.toFile()
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.getAbsolutePath();
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testGraphBasePath = Paths.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath();
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testOutputBasePath =
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createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
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.toAbsolutePath()
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.toString();
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testDedupGraphBasePath =
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createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
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.toAbsolutePath()
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.toString();
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testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString();
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testDedupGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString();
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FileUtils.deleteDirectory(new File(testOutputBasePath));
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FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
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spark =
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SparkSession.builder()
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.appName(SparkCreateSimRels.class.getSimpleName())
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.master("local[*]")
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.config(new SparkConf())
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.getOrCreate();
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spark = SparkSession
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.builder()
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.appName(SparkCreateSimRels.class.getSimpleName())
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.master("local[*]")
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.config(new SparkConf())
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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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private 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.toString(
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SparkDedupTest.class.getResourceAsStream(
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"/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
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lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
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.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/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.toString(
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SparkDedupTest.class.getResourceAsStream(
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"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
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lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
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.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
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lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
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.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
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lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
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.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/sw.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.toString(
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SparkDedupTest.class.getResourceAsStream(
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"/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
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}
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@Test
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@Order(1)
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public void createSimRelsTest() throws Exception {
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ArgumentApplicationParser parser =
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new ArgumentApplicationParser(
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IOUtils.toString(
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SparkCreateSimRels.class.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
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parser.parseArgument(
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new String[] {
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"-mt", "local[*]",
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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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});
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils.toString(
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SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
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parser.parseArgument(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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new SparkCreateSimRels(parser, spark).run(isLookUpService);
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long orgs_simrel =
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spark.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
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.count();
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long pubs_simrel =
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spark.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
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.count();
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long orgs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel").count();
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long pubs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel").count();
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long sw_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_simrel").count();
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assertEquals(3288, orgs_simrel);
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assertEquals(3432, orgs_simrel);
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assertEquals(7260, pubs_simrel);
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assertEquals(344, sw_simrel);
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}
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@Test
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@Order(2)
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public void createMergeRelsTest() throws Exception {
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ArgumentApplicationParser parser =
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new ArgumentApplicationParser(
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IOUtils.toString(
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SparkCreateMergeRels.class.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
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parser.parseArgument(
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new String[] {
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"-mt", "local[*]",
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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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});
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils.toString(
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SparkCreateMergeRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
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parser.parseArgument(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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new SparkCreateMergeRels(parser, spark).run(isLookUpService);
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long orgs_mergerel =
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spark.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
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.count();
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long pubs_mergerel =
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spark.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
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.count();
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long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").count();
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long pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count();
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long sw_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel").count();
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assertEquals(1244, orgs_mergerel);
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assertEquals(1276, orgs_mergerel);
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assertEquals(1460, pubs_mergerel);
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assertEquals(288, sw_mergerel);
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}
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@Test
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@Order(3)
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public void createDedupRecordTest() throws Exception {
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ArgumentApplicationParser parser =
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new ArgumentApplicationParser(
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IOUtils.toString(
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SparkCreateDedupRecord.class.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
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parser.parseArgument(
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new String[] {
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"-mt", "local[*]",
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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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});
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils.toString(
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SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
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parser.parseArgument(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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new SparkCreateDedupRecord(parser, spark).run(isLookUpService);
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long orgs_deduprecord =
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jsc.textFile(
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testOutputBasePath
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+ "/"
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+ testActionSetId
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+ "/organization_deduprecord")
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.count();
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long pubs_deduprecord =
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jsc.textFile(
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testOutputBasePath
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+ "/"
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+ testActionSetId
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+ "/publication_deduprecord")
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.count();
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long orgs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count();
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long pubs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count();
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long sw_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord").count();
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assertEquals(82, orgs_deduprecord);
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assertEquals(66, pubs_deduprecord);
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assertEquals(51, sw_deduprecord);
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}
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@Test
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@Order(4)
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public void updateEntityTest() throws Exception {
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ArgumentApplicationParser parser =
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new ArgumentApplicationParser(
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IOUtils.toString(
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SparkUpdateEntity.class.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
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parser.parseArgument(
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new String[] {
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"-mt", "local[*]",
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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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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils.toString(
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SparkUpdateEntity.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
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parser.parseArgument(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 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();
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long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count();
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long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count();
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long mergedOrgs =
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spark.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
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.as(Encoders.bean(Relation.class))
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.where("relClass=='merges'")
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.javaRDD()
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.map(Relation::getTarget)
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.distinct()
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.count();
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long mergedOrgs = spark
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.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").as(Encoders.bean(Relation.class))
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.where("relClass=='merges'")
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.javaRDD()
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.map(Relation::getTarget)
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.distinct().count();
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long mergedPubs =
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spark.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
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.as(Encoders.bean(Relation.class))
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.where("relClass=='merges'")
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.javaRDD()
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.map(Relation::getTarget)
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.distinct()
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.count();
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long mergedPubs = spark
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.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").as(Encoders.bean(Relation.class))
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.where("relClass=='merges'")
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.javaRDD()
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.map(Relation::getTarget)
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.distinct().count();
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assertEquals(897, publications);
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assertEquals(831, publications);
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assertEquals(835, organizations);
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assertEquals(100, projects);
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assertEquals(100, datasource);
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assertEquals(200, softwares);
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long deletedOrgs =
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jsc.textFile(testDedupGraphBasePath + "/organization")
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.filter(this::isDeletedByInference)
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.count();
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long deletedPubs =
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jsc.textFile(testDedupGraphBasePath + "/publication")
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.filter(this::isDeletedByInference)
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.count();
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long deletedOrgs = jsc.textFile(testDedupGraphBasePath + "/organization")
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.filter(this::isDeletedByInference).count();
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long deletedPubs = jsc.textFile(testDedupGraphBasePath + "/publication")
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.filter(this::isDeletedByInference).count();
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assertEquals(mergedOrgs, deletedOrgs);
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assertEquals(mergedPubs, deletedPubs);
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@ -265,24 +213,42 @@ public class SparkDedupTest implements Serializable {
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@Order(5)
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public void propagateRelationTest() throws Exception {
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ArgumentApplicationParser parser =
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new ArgumentApplicationParser(
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IOUtils.toString(
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SparkPropagateRelation.class.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
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parser.parseArgument(
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new String[] {
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"-mt", "local[*]",
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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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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils.toString(
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SparkPropagateRelation.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
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parser.parseArgument(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 SparkPropagateRelation(parser, spark).run(isLookUpService);
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long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
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assertEquals(826, relations);
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//check deletedbyinference
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final Dataset<Relation> mergeRels = spark.read().load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*")).as(Encoders.bean(Relation.class));
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final JavaPairRDD<String, String> mergedIds = mergeRels
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.where("relClass == 'merges'")
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.select(mergeRels.col("target"))
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.distinct()
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.toJavaRDD()
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.mapToPair((PairFunction<Row, String, String>) r -> new Tuple2<String, String>(r.getString(0), "d"));
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JavaRDD<String> toCheck = jsc.textFile(testDedupGraphBasePath + "/relation")
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.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json))
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.join(mergedIds)
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.map(t -> t._2()._1())
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.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json))
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.join(mergedIds)
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.map(t -> t._2()._1());
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long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
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long updated = toCheck.count();
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assertEquals(updated, deletedbyinference);
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}
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@AfterAll
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@ -292,6 +258,6 @@ public class SparkDedupTest implements Serializable {
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}
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public boolean isDeletedByInference(String s) {
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return s.contains("\"deletedbyinference\":true");
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return s.contains("\"deletedbyinference\":true");
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}
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}
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}
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