2020-09-29 15:31:46 +02:00
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2020-04-02 18:37:53 +02:00
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package eu.dnetlib.dhp.oa.dedup;
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2020-04-01 18:48:31 +02:00
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2023-08-08 15:52:20 +02:00
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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.apache.spark.sql.functions.count;
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import static org.junit.jupiter.api.Assertions.*;
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import static org.mockito.Mockito.lenient;
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import java.io.File;
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import java.io.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.HashSet;
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import java.util.List;
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import java.util.Optional;
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import java.util.Set;
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import java.util.stream.Collectors;
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2020-04-03 18:32:25 +02:00
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import org.apache.commons.io.FileUtils;
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2020-04-01 18:48:31 +02:00
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import org.apache.commons.io.IOUtils;
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2020-04-03 18:32:25 +02:00
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import org.apache.spark.SparkConf;
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2020-04-20 16:49:01 +02:00
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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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2020-04-08 18:02:30 +02:00
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import org.apache.spark.api.java.JavaSparkContext;
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2020-07-13 15:28:17 +02:00
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import org.apache.spark.api.java.function.FilterFunction;
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2020-05-08 19:00:38 +02:00
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import org.apache.spark.api.java.function.MapFunction;
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2020-04-20 16:49:01 +02:00
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import org.apache.spark.api.java.function.PairFunction;
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2023-08-04 14:27:39 +02:00
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import org.apache.spark.sql.*;
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2020-10-20 12:19:46 +02:00
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import org.apache.spark.sql.Dataset;
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2020-04-03 18:32:25 +02:00
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import org.junit.jupiter.api.*;
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2020-04-02 18:37:53 +02:00
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import org.junit.jupiter.api.extension.ExtendWith;
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2020-04-01 18:48:31 +02:00
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import org.mockito.Mock;
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2020-04-02 18:37:53 +02:00
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import org.mockito.Mockito;
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2020-04-01 19:05:48 +02:00
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import org.mockito.junit.jupiter.MockitoExtension;
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2020-04-28 11:23:29 +02:00
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2023-08-08 15:52:20 +02:00
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.common.collect.Sets;
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2020-05-11 10:05:57 +02:00
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2023-08-08 15:52:20 +02:00
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.pace.util.MapDocumentUtil;
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import scala.Tuple2;
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2020-04-20 16:49:01 +02:00
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2020-04-01 19:05:48 +02:00
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@ExtendWith(MockitoExtension.class)
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2020-04-03 18:32:25 +02:00
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@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
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2020-04-08 18:02:30 +02:00
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public class SparkDedupTest implements Serializable {
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2020-04-01 18:48:31 +02:00
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2021-10-07 15:39:55 +02:00
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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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2022-11-11 16:10:25 +01:00
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.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"));
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2021-10-07 15:39:55 +02:00
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lenient()
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.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
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2022-11-11 16:10:25 +01:00
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.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"));
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2021-10-07 15:39:55 +02:00
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lenient()
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.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
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2022-11-11 16:10:25 +01:00
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.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"));
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2021-10-07 15:39:55 +02:00
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lenient()
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.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
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2022-11-11 16:10:25 +01:00
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.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json"));
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2021-10-07 15:39:55 +02:00
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lenient()
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.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("dataset")))
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2022-11-11 16:10:25 +01:00
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.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json"));
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2021-10-07 15:39:55 +02:00
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lenient()
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.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("otherresearchproduct")))
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2022-11-11 16:10:25 +01:00
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.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json"));
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2021-10-07 15:39:55 +02:00
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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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2022-11-11 16:10:25 +01:00
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classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"));
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2021-10-07 15:39:55 +02:00
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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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2023-07-18 11:38:56 +02:00
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System.out.println("orgs_simrel = " + orgs_simrel);
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System.out.println("pubs_simrel = " + pubs_simrel);
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System.out.println("sw_simrel = " + sw_simrel);
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System.out.println("ds_simrel = " + ds_simrel);
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System.out.println("orp_simrel = " + orp_simrel);
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assertEquals(1538, orgs_simrel);
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assertEquals(3523, pubs_simrel);
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assertEquals(168, sw_simrel);
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assertEquals(221, ds_simrel);
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assertEquals(3392, orp_simrel);
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2021-10-07 15:39:55 +02:00
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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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2022-11-11 16:10:25 +01:00
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classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json"));
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2021-10-07 15:39:55 +02:00
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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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2023-07-18 11:38:56 +02:00
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assertEquals(1538, orgs_simrel);
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assertEquals(3523, pubs_simrel);
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assertEquals(221, ds_simrel);
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assertEquals(3392, orp_simrel);
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2022-03-15 16:33:03 +01:00
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// System.out.println("orgs_simrel = " + orgs_simrel);
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// System.out.println("pubs_simrel = " + pubs_simrel);
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// System.out.println("ds_simrel = " + ds_simrel);
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// System.out.println("orp_simrel = " + orp_simrel);
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2021-10-07 15:39:55 +02:00
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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(
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sw_simrel
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.as(Encoders.bean(Relation.class))
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.toJavaRDD()
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.filter(
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rel -> rel.getSource().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[0])
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&& rel.getTarget().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[1]))
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.count() > 0);
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// check if the second relation in the whitelist exists
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assertTrue(
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sw_simrel
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.as(Encoders.bean(Relation.class))
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.toJavaRDD()
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.filter(
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rel -> rel.getSource().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[0])
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&& rel.getTarget().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[1]))
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.count() > 0);
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2023-07-18 11:38:56 +02:00
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assertEquals(170, sw_simrel.count());
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2022-03-15 16:33:03 +01:00
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// System.out.println("sw_simrel = " + sw_simrel.count());
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2021-10-07 15:39:55 +02:00
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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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2022-11-11 16:10:25 +01:00
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classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"));
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2021-10-07 15:39:55 +02:00
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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()
|
|
|
|
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
|
|
|
|
.as(Encoders.bean(Relation.class))
|
|
|
|
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
|
|
|
|
.groupBy("source")
|
|
|
|
.agg(count("target").alias("cnt"))
|
|
|
|
.select("source", "cnt")
|
|
|
|
.where("cnt > 3")
|
|
|
|
.count();
|
|
|
|
|
|
|
|
long ds_mergerel = spark
|
|
|
|
.read()
|
|
|
|
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
|
|
|
|
.as(Encoders.bean(Relation.class))
|
|
|
|
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
|
|
|
|
.groupBy("source")
|
|
|
|
.agg(count("target").alias("cnt"))
|
|
|
|
.select("source", "cnt")
|
|
|
|
.where("cnt > 3")
|
|
|
|
.count();
|
|
|
|
|
|
|
|
long orp_mergerel = spark
|
|
|
|
.read()
|
|
|
|
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
|
|
|
|
.as(Encoders.bean(Relation.class))
|
|
|
|
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
|
|
|
|
.groupBy("source")
|
|
|
|
.agg(count("target").alias("cnt"))
|
|
|
|
.select("source", "cnt")
|
|
|
|
.where("cnt > 3")
|
|
|
|
.count();
|
|
|
|
|
|
|
|
assertEquals(0, orgs_mergerel);
|
|
|
|
assertEquals(0, pubs_mergerel);
|
|
|
|
assertEquals(0, sw_mergerel);
|
|
|
|
assertEquals(0, ds_mergerel);
|
|
|
|
assertEquals(0, orp_mergerel);
|
|
|
|
|
|
|
|
FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel"));
|
|
|
|
FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel"));
|
|
|
|
FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/software_mergerel"));
|
|
|
|
FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel"));
|
|
|
|
FileUtils
|
|
|
|
.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel"));
|
|
|
|
}
|
|
|
|
|
|
|
|
@Test
|
|
|
|
@Order(4)
|
|
|
|
void createMergeRelsTest() throws Exception {
|
|
|
|
|
|
|
|
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
2022-11-11 16:10:25 +01:00
|
|
|
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"));
|
2021-10-07 15:39:55 +02:00
|
|
|
|
|
|
|
parser
|
|
|
|
.parseArgument(
|
|
|
|
new String[] {
|
|
|
|
"-i",
|
|
|
|
testGraphBasePath,
|
|
|
|
"-asi",
|
|
|
|
testActionSetId,
|
|
|
|
"-la",
|
|
|
|
"lookupurl",
|
|
|
|
"-w",
|
|
|
|
testOutputBasePath
|
|
|
|
});
|
|
|
|
|
|
|
|
new SparkCreateMergeRels(parser, spark).run(isLookUpService);
|
|
|
|
|
|
|
|
long orgs_mergerel = spark
|
|
|
|
.read()
|
|
|
|
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
|
|
|
|
.count();
|
2022-11-11 16:10:25 +01:00
|
|
|
final Dataset<Relation> pubs = spark
|
2021-10-07 15:39:55 +02:00
|
|
|
.read()
|
|
|
|
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
|
2022-11-11 16:10:25 +01:00
|
|
|
.as(Encoders.bean(Relation.class));
|
2021-10-07 15:39:55 +02:00
|
|
|
long sw_mergerel = spark
|
|
|
|
.read()
|
|
|
|
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
|
|
|
|
.count();
|
|
|
|
long ds_mergerel = spark
|
|
|
|
.read()
|
|
|
|
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
|
|
|
|
.count();
|
|
|
|
|
|
|
|
long orp_mergerel = spark
|
|
|
|
.read()
|
|
|
|
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
|
|
|
|
.count();
|
|
|
|
|
2022-11-11 16:10:25 +01:00
|
|
|
final List<Relation> merges = pubs
|
|
|
|
.filter("source == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
|
|
|
|
.collectAsList();
|
|
|
|
assertEquals(3, merges.size());
|
|
|
|
Set<String> dups = Sets
|
|
|
|
.newHashSet(
|
|
|
|
"50|doi_________::3b1d0d8e8f930826665df9d6b82fbb73",
|
|
|
|
"50|doi_________::d5021b53204e4fdeab6ff5d5bc468032",
|
|
|
|
"50|arXiv_______::c93aeb433eb90ed7a86e29be00791b7c");
|
|
|
|
merges.forEach(r -> {
|
|
|
|
assertEquals(ModelConstants.RESULT_RESULT, r.getRelType());
|
|
|
|
assertEquals(ModelConstants.DEDUP, r.getSubRelType());
|
|
|
|
assertEquals(ModelConstants.MERGES, r.getRelClass());
|
|
|
|
assertTrue(dups.contains(r.getTarget()));
|
|
|
|
});
|
|
|
|
|
|
|
|
final List<Relation> mergedIn = pubs
|
|
|
|
.filter("target == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
|
|
|
|
.collectAsList();
|
|
|
|
assertEquals(3, mergedIn.size());
|
|
|
|
mergedIn.forEach(r -> {
|
|
|
|
assertEquals(ModelConstants.RESULT_RESULT, r.getRelType());
|
|
|
|
assertEquals(ModelConstants.DEDUP, r.getSubRelType());
|
|
|
|
assertEquals(ModelConstants.IS_MERGED_IN, r.getRelClass());
|
|
|
|
assertTrue(dups.contains(r.getSource()));
|
|
|
|
});
|
|
|
|
|
2022-03-15 16:33:03 +01:00
|
|
|
assertEquals(1268, orgs_mergerel);
|
2022-11-11 16:10:25 +01:00
|
|
|
assertEquals(1450, pubs.count());
|
2021-10-07 15:39:55 +02:00
|
|
|
assertEquals(286, sw_mergerel);
|
|
|
|
assertEquals(472, ds_mergerel);
|
2022-03-15 16:33:03 +01:00
|
|
|
assertEquals(738, orp_mergerel);
|
|
|
|
// System.out.println("orgs_mergerel = " + orgs_mergerel);
|
|
|
|
// System.out.println("pubs_mergerel = " + pubs_mergerel);
|
|
|
|
// System.out.println("sw_mergerel = " + sw_mergerel);
|
|
|
|
// System.out.println("ds_mergerel = " + ds_mergerel);
|
|
|
|
// System.out.println("orp_mergerel = " + orp_mergerel);
|
2021-10-07 15:39:55 +02:00
|
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
@Test
|
|
|
|
@Order(5)
|
|
|
|
void createDedupRecordTest() throws Exception {
|
|
|
|
|
|
|
|
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
2022-11-11 16:10:25 +01:00
|
|
|
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"));
|
2021-10-07 15:39:55 +02:00
|
|
|
parser
|
|
|
|
.parseArgument(
|
|
|
|
new String[] {
|
|
|
|
"-i",
|
|
|
|
testGraphBasePath,
|
|
|
|
"-asi",
|
|
|
|
testActionSetId,
|
|
|
|
"-la",
|
|
|
|
"lookupurl",
|
|
|
|
"-w",
|
|
|
|
testOutputBasePath
|
|
|
|
});
|
|
|
|
|
|
|
|
new SparkCreateDedupRecord(parser, spark).run(isLookUpService);
|
|
|
|
|
2022-11-11 16:10:25 +01:00
|
|
|
final ObjectMapper mapper = new ObjectMapper()
|
|
|
|
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
|
|
|
|
|
|
|
final Dataset<Publication> pubs = spark
|
|
|
|
.read()
|
|
|
|
.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord")
|
|
|
|
.map(
|
|
|
|
(MapFunction<String, Publication>) value -> mapper.readValue(value, Publication.class),
|
|
|
|
Encoders.bean(Publication.class));
|
2021-10-07 15:39:55 +02:00
|
|
|
long orgs_deduprecord = jsc
|
|
|
|
.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord")
|
|
|
|
.count();
|
|
|
|
long sw_deduprecord = jsc
|
|
|
|
.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord")
|
|
|
|
.count();
|
|
|
|
long ds_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_deduprecord").count();
|
|
|
|
long orp_deduprecord = jsc
|
|
|
|
.textFile(
|
|
|
|
testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_deduprecord")
|
|
|
|
.count();
|
|
|
|
|
2022-03-15 16:33:03 +01:00
|
|
|
assertEquals(86, orgs_deduprecord);
|
2022-11-11 16:10:25 +01:00
|
|
|
assertEquals(68, pubs.count());
|
2021-10-07 15:39:55 +02:00
|
|
|
assertEquals(49, sw_deduprecord);
|
|
|
|
assertEquals(97, ds_deduprecord);
|
2022-03-15 16:33:03 +01:00
|
|
|
assertEquals(92, orp_deduprecord);
|
|
|
|
|
2022-11-11 16:10:25 +01:00
|
|
|
verifyRoot_1(mapper, pubs);
|
|
|
|
|
2022-03-15 16:33:03 +01:00
|
|
|
// System.out.println("orgs_deduprecord = " + orgs_deduprecord);
|
|
|
|
// System.out.println("pubs_deduprecord = " + pubs_deduprecord);
|
|
|
|
// System.out.println("sw_deduprecord = " + sw_deduprecord);
|
|
|
|
// System.out.println("ds_deduprecord = " + ds_deduprecord);
|
|
|
|
// System.out.println("orp_deduprecord = " + orp_deduprecord);
|
2021-10-07 15:39:55 +02:00
|
|
|
}
|
|
|
|
|
2022-11-11 16:10:25 +01:00
|
|
|
private static void verifyRoot_1(ObjectMapper mapper, Dataset<Publication> pubs) {
|
|
|
|
Publication root = pubs
|
|
|
|
.filter("id = '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
|
|
|
|
.first();
|
|
|
|
assertNotNull(root);
|
|
|
|
|
|
|
|
final Dataset<String> publication = spark
|
|
|
|
.read()
|
|
|
|
.textFile(DedupUtility.createEntityPath(testGraphBasePath, "publication"));
|
|
|
|
|
|
|
|
Publication crossref_duplicate = publication
|
|
|
|
.map(
|
|
|
|
(MapFunction<String, Publication>) value -> mapper.readValue(value, Publication.class),
|
|
|
|
Encoders.bean(Publication.class))
|
|
|
|
.filter("id = '50|doi_________::d5021b53204e4fdeab6ff5d5bc468032'")
|
|
|
|
.collectAsList()
|
|
|
|
.get(0);
|
|
|
|
|
|
|
|
assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName());
|
|
|
|
assertEquals(crossref_duplicate.getJournal().getIssnPrinted(), root.getJournal().getIssnPrinted());
|
|
|
|
assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue());
|
|
|
|
|
|
|
|
Set<String> rootPids = root
|
|
|
|
.getPid()
|
|
|
|
.stream()
|
|
|
|
.map(StructuredProperty::getValue)
|
|
|
|
.collect(Collectors.toCollection(HashSet::new));
|
|
|
|
Set<String> dupPids = crossref_duplicate
|
|
|
|
.getPid()
|
|
|
|
.stream()
|
|
|
|
.map(StructuredProperty::getValue)
|
|
|
|
.collect(Collectors.toCollection(HashSet::new));
|
|
|
|
|
|
|
|
assertFalse(Sets.intersection(rootPids, dupPids).isEmpty());
|
|
|
|
assertTrue(rootPids.contains("10.1109/jstqe.2022.3205716"));
|
|
|
|
|
|
|
|
Optional<Instance> instance_cr = root
|
|
|
|
.getInstance()
|
|
|
|
.stream()
|
|
|
|
.filter(i -> i.getCollectedfrom().getValue().equals("Crossref"))
|
|
|
|
.findFirst();
|
|
|
|
assertTrue(instance_cr.isPresent());
|
|
|
|
assertEquals("OPEN", instance_cr.get().getAccessright().getClassid());
|
|
|
|
assertEquals("Open Access", instance_cr.get().getAccessright().getClassname());
|
|
|
|
assertEquals(OpenAccessRoute.hybrid, instance_cr.get().getAccessright().getOpenAccessRoute());
|
|
|
|
assertEquals(
|
|
|
|
"IEEE Journal of Selected Topics in Quantum Electronics", instance_cr.get().getHostedby().getValue());
|
|
|
|
assertEquals("0001", instance_cr.get().getInstancetype().getClassid());
|
|
|
|
assertEquals("Article", instance_cr.get().getInstancetype().getClassname());
|
|
|
|
}
|
|
|
|
|
2021-10-07 15:39:55 +02:00
|
|
|
@Test
|
|
|
|
@Order(6)
|
|
|
|
void updateEntityTest() throws Exception {
|
|
|
|
|
|
|
|
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
2022-11-11 16:10:25 +01:00
|
|
|
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"));
|
2021-10-07 15:39:55 +02:00
|
|
|
parser
|
|
|
|
.parseArgument(
|
|
|
|
new String[] {
|
|
|
|
"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
|
|
|
|
});
|
|
|
|
|
|
|
|
new SparkUpdateEntity(parser, spark).run(isLookUpService);
|
|
|
|
|
|
|
|
long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
|
|
|
|
long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
|
|
|
|
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();
|
|
|
|
|
2022-11-11 16:10:25 +01:00
|
|
|
assertEquals(902, publications);
|
2022-03-15 16:33:03 +01:00
|
|
|
assertEquals(839, organizations);
|
2021-10-07 15:39:55 +02:00
|
|
|
assertEquals(100, projects);
|
|
|
|
assertEquals(100, datasource);
|
|
|
|
assertEquals(198, softwares);
|
|
|
|
assertEquals(389, dataset);
|
2022-03-15 16:33:03 +01:00
|
|
|
assertEquals(520, otherresearchproduct);
|
|
|
|
|
|
|
|
// System.out.println("publications = " + publications);
|
|
|
|
// System.out.println("organizations = " + organizations);
|
|
|
|
// System.out.println("projects = " + projects);
|
|
|
|
// System.out.println("datasource = " + datasource);
|
|
|
|
// System.out.println("software = " + softwares);
|
|
|
|
// System.out.println("dataset = " + dataset);
|
|
|
|
// System.out.println("otherresearchproduct = " + otherresearchproduct);
|
2021-10-07 15:39:55 +02:00
|
|
|
|
|
|
|
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(
|
2022-11-11 16:10:25 +01:00
|
|
|
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"));
|
2023-08-04 14:27:39 +02:00
|
|
|
String outputRelPath = testDedupGraphBasePath + "/propagaterelation";
|
2021-10-07 15:39:55 +02:00
|
|
|
parser
|
|
|
|
.parseArgument(
|
|
|
|
new String[] {
|
2023-08-04 14:27:39 +02:00
|
|
|
"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", outputRelPath
|
2021-10-07 15:39:55 +02:00
|
|
|
});
|
|
|
|
|
|
|
|
new SparkPropagateRelation(parser, spark).run(isLookUpService);
|
|
|
|
|
2023-08-04 14:27:39 +02:00
|
|
|
long relations = jsc.textFile(outputRelPath + "/relation").count();
|
2021-10-07 15:39:55 +02:00
|
|
|
|
2022-03-15 16:33:03 +01:00
|
|
|
// assertEquals(4860, relations);
|
|
|
|
System.out.println("relations = " + relations);
|
2021-10-07 15:39:55 +02:00
|
|
|
|
|
|
|
// 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
|
2023-08-04 14:27:39 +02:00
|
|
|
.textFile(outputRelPath + "/relation")
|
2021-10-07 15:39:55 +02:00
|
|
|
.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)
|
2023-08-04 14:27:39 +02:00
|
|
|
void testCleanBaseRelations() throws Exception {
|
|
|
|
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
2023-08-08 15:52:20 +02:00
|
|
|
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json"));
|
2023-08-04 14:27:39 +02:00
|
|
|
|
|
|
|
// append dangling relations to be cleaned up
|
2023-08-08 15:52:20 +02:00
|
|
|
Dataset<Row> df_before = spark
|
|
|
|
.read()
|
|
|
|
.schema(Encoders.bean(Relation.class).schema())
|
|
|
|
.json(testGraphBasePath + "/relation");
|
|
|
|
Dataset<Row> df_input = df_before
|
|
|
|
.unionByName(df_before.drop("source").withColumn("source", functions.lit("n/a")))
|
|
|
|
.unionByName(df_before.drop("target").withColumn("target", functions.lit("n/a")));
|
2023-08-04 14:27:39 +02:00
|
|
|
df_input.write().mode(SaveMode.Overwrite).json(testOutputBasePath + "_tmp");
|
|
|
|
|
|
|
|
parser
|
2023-08-08 15:52:20 +02:00
|
|
|
.parseArgument(
|
|
|
|
new String[] {
|
|
|
|
"--graphBasePath", testGraphBasePath,
|
|
|
|
"--inputPath", testGraphBasePath + "/relation",
|
|
|
|
"--outputPath", testDedupGraphBasePath + "/relation"
|
|
|
|
});
|
2023-08-04 14:27:39 +02:00
|
|
|
|
|
|
|
new SparkCleanRelation(parser, spark).run(isLookUpService);
|
|
|
|
|
2023-08-08 15:52:20 +02:00
|
|
|
Dataset<Row> df_after = spark
|
|
|
|
.read()
|
|
|
|
.schema(Encoders.bean(Relation.class).schema())
|
|
|
|
.json(testDedupGraphBasePath + "/relation");
|
2023-08-04 14:27:39 +02:00
|
|
|
|
|
|
|
assertNotEquals(df_before.count(), df_input.count());
|
|
|
|
assertNotEquals(df_input.count(), df_after.count());
|
|
|
|
assertEquals(5, df_after.count());
|
|
|
|
}
|
|
|
|
|
|
|
|
@Test
|
|
|
|
@Order(9)
|
|
|
|
void testCleanDedupedRelations() throws Exception {
|
|
|
|
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
2023-08-08 15:52:20 +02:00
|
|
|
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json"));
|
2023-08-04 14:27:39 +02:00
|
|
|
|
|
|
|
String inputRelPath = testDedupGraphBasePath + "/propagaterelation/relation";
|
|
|
|
|
|
|
|
// append dangling relations to be cleaned up
|
|
|
|
Dataset<Row> df_before = spark.read().schema(Encoders.bean(Relation.class).schema()).json(inputRelPath);
|
|
|
|
|
|
|
|
df_before.filter(col("dataInfo.deletedbyinference").notEqual(true)).show(50, false);
|
|
|
|
|
|
|
|
parser
|
2023-08-08 15:52:20 +02:00
|
|
|
.parseArgument(
|
|
|
|
new String[] {
|
|
|
|
"--graphBasePath", testGraphBasePath,
|
|
|
|
"--inputPath", inputRelPath,
|
|
|
|
"--outputPath", testDedupGraphBasePath + "/relation"
|
|
|
|
});
|
2023-08-04 14:27:39 +02:00
|
|
|
|
|
|
|
new SparkCleanRelation(parser, spark).run(isLookUpService);
|
|
|
|
|
2023-08-08 15:52:20 +02:00
|
|
|
Dataset<Row> df_after = spark
|
|
|
|
.read()
|
|
|
|
.schema(Encoders.bean(Relation.class).schema())
|
|
|
|
.json(testDedupGraphBasePath + "/relation");
|
2023-08-04 14:27:39 +02:00
|
|
|
|
|
|
|
assertNotEquals(df_before.count(), df_after.count());
|
|
|
|
assertEquals(0, df_after.count());
|
|
|
|
}
|
|
|
|
|
|
|
|
@Test
|
|
|
|
@Order(10)
|
2021-10-07 15:39:55 +02:00
|
|
|
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");
|
|
|
|
}
|
2022-11-11 16:10:25 +01:00
|
|
|
|
|
|
|
private static String classPathResourceAsString(String path) throws IOException {
|
|
|
|
return IOUtils
|
|
|
|
.toString(
|
|
|
|
SparkDedupTest.class
|
|
|
|
.getResourceAsStream(path));
|
|
|
|
}
|
|
|
|
|
2020-04-20 18:44:06 +02:00
|
|
|
}
|