394 lines
11 KiB
Java
394 lines
11 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.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.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.sql.Connection;
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import java.sql.DriverManager;
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import java.sql.ResultSet;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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import java.util.Properties;
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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.JavaSparkContext;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.*;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.mockito.Mock;
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import org.mockito.Mockito;
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import org.mockito.junit.jupiter.MockitoExtension;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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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 SparkOpenorgsDedupTest implements Serializable {
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private static final String dbUrl = "jdbc:h2:mem:openorgs_test;DB_CLOSE_DELAY=-1;DATABASE_TO_UPPER=false";
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private static final String dbUser = "sa";
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private static final String dbTable = "tmp_dedup_events";
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private static final String dbPwd = "";
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@Mock(serializable = true)
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ISLookUpService isLookUpService;
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protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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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-openorgs";
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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(SparkOpenorgsDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/openorgs/dedup").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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FileUtils.deleteDirectory(new File(testOutputBasePath));
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FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
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final SparkConf conf = new SparkConf();
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conf.set("spark.sql.shuffle.partitions", "200");
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spark = SparkSession
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.builder()
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.appName(SparkDedupTest.class.getSimpleName())
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.master("local[*]")
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.config(conf)
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.getOrCreate();
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jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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}
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@BeforeEach
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public void setUp() throws IOException, ISLookUpException {
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lenient()
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.when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
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.thenReturn(
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IOUtils
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.toString(
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SparkOpenorgsDedupTest.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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SparkOpenorgsDedupTest.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 createSimRelsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCreateSimRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
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parser
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.parseArgument(
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new String[] {
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"-i", testGraphBasePath,
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"-asi", testActionSetId,
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"-la", "lookupurl",
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"-w", testOutputBasePath,
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"-np", "50"
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});
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new SparkCreateSimRels(parser, spark).run(isLookUpService);
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long orgs_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
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.count();
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assertEquals(290, orgs_simrel);
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}
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@Test
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@Order(2)
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void copyOpenorgsSimRels() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCopyOpenorgsSimRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/copyOpenorgsMergeRels_parameters.json")));
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parser
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.parseArgument(
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new String[] {
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"-i", testGraphBasePath,
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"-asi", testActionSetId,
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"-w", testOutputBasePath,
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"-la", "lookupurl",
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"-np", "50"
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});
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new SparkCopyOpenorgsSimRels(parser, spark).run(isLookUpService);
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long orgs_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
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.count();
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assertEquals(326, orgs_simrel);
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}
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@Test
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@Order(3)
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void createMergeRelsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCreateMergeRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
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parser
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.parseArgument(
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new String[] {
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"-i",
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testGraphBasePath,
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"-asi",
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testActionSetId,
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"-la",
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"lookupurl",
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"-w",
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testOutputBasePath
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});
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new SparkCreateMergeRels(parser, spark).run(isLookUpService);
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long orgs_mergerel = spark
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.read()
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.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
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.count();
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assertEquals(132, orgs_mergerel);
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// verify that a DiffRel is in the mergerels (to be sure that the job supposed to remove them has something to
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// do)
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List<String> diffRels = jsc
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.textFile(DedupUtility.createEntityPath(testGraphBasePath, "relation"))
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.map(s -> OBJECT_MAPPER.readValue(s, Relation.class))
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.filter(r -> r.getRelClass().equals("isDifferentFrom"))
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.map(r -> r.getTarget())
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.collect();
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assertEquals(18, diffRels.size());
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List<String> mergeRels = 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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.toJavaRDD()
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.map(r -> r.getTarget())
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.collect();
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assertFalse(Collections.disjoint(mergeRels, diffRels));
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}
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@Test
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@Order(4)
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void prepareOrgRelsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkPrepareOrgRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/prepareOrgRels_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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"-du",
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dbUrl,
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"-dusr",
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dbUser,
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"-t",
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dbTable,
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"-dpwd",
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dbPwd
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});
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new SparkPrepareOrgRels(parser, spark).run(isLookUpService);
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final Properties connectionProperties = new Properties();
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connectionProperties.put("user", dbUser);
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connectionProperties.put("password", dbPwd);
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Connection connection = DriverManager.getConnection(dbUrl, connectionProperties);
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ResultSet resultSet = connection
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.prepareStatement("SELECT COUNT(*) as total_rels FROM " + dbTable)
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.executeQuery();
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if (resultSet.next()) {
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int total_rels = resultSet.getInt("total_rels");
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assertEquals(32, total_rels);
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} else
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fail("No result in the sql DB");
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resultSet.close();
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// verify the number of organizations with duplicates
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ResultSet resultSet2 = connection
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.prepareStatement("SELECT COUNT(DISTINCT(local_id)) as total_orgs FROM " + dbTable)
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.executeQuery();
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if (resultSet2.next()) {
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int total_orgs = resultSet2.getInt("total_orgs");
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assertEquals(6, total_orgs);
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} else
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fail("No result in the sql DB");
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resultSet2.close();
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// verify that no DiffRel is in the DB
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List<String> diffRels = jsc
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.textFile(DedupUtility.createEntityPath(testGraphBasePath, "relation"))
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.map(s -> OBJECT_MAPPER.readValue(s, Relation.class))
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.filter(r -> r.getRelClass().equals("isDifferentFrom"))
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.map(r -> r.getSource() + "@@@" + r.getTarget())
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.collect();
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List<String> dbRels = new ArrayList<>();
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ResultSet resultSet3 = connection
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.prepareStatement("SELECT local_id, oa_original_id FROM " + dbTable)
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.executeQuery();
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while (resultSet3.next()) {
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String source = OafMapperUtils.createOpenaireId("organization", resultSet3.getString("local_id"), true);
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String target = OafMapperUtils
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.createOpenaireId("organization", resultSet3.getString("oa_original_id"), true);
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dbRels.add(source + "@@@" + target);
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}
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resultSet3.close();
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assertTrue(Collections.disjoint(dbRels, diffRels));
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connection.close();
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}
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@Test
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@Order(5)
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void prepareNewOrgsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkPrepareNewOrgs.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/prepareNewOrgs_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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"-du",
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dbUrl,
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"-dusr",
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dbUser,
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"-t",
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dbTable,
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"-dpwd",
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dbPwd
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});
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new SparkPrepareNewOrgs(parser, spark).run(isLookUpService);
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final Properties connectionProperties = new Properties();
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connectionProperties.put("user", dbUser);
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connectionProperties.put("password", dbPwd);
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long orgs_in_diffrel = jsc
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.textFile(DedupUtility.createEntityPath(testGraphBasePath, "relation"))
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.map(s -> OBJECT_MAPPER.readValue(s, Relation.class))
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.filter(r -> r.getRelClass().equals("isDifferentFrom"))
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.map(r -> r.getTarget())
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.distinct()
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.count();
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Connection connection = DriverManager.getConnection(dbUrl, connectionProperties);
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jsc
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.textFile(DedupUtility.createEntityPath(testGraphBasePath, "relation"))
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.map(s -> OBJECT_MAPPER.readValue(s, Relation.class))
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.filter(r -> r.getRelClass().equals("isDifferentFrom"))
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.map(r -> r.getTarget())
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.distinct()
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.foreach(s -> System.out.println("difforgs = " + s));
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ResultSet resultSet0 = connection
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.prepareStatement("SELECT oa_original_id FROM " + dbTable + " WHERE local_id = ''")
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.executeQuery();
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while (resultSet0.next())
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System.out
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.println(
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"dborgs = " + OafMapperUtils.createOpenaireId(20, resultSet0.getString("oa_original_id"), true));
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resultSet0.close();
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ResultSet resultSet = connection
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.prepareStatement("SELECT COUNT(*) as total_new_orgs FROM " + dbTable + " WHERE local_id = ''")
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.executeQuery();
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if (resultSet.next()) {
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int total_new_orgs = resultSet.getInt("total_new_orgs");
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assertEquals(orgs_in_diffrel + 1, total_new_orgs);
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} else
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fail("No result in the sql DB");
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resultSet.close();
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}
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@AfterAll
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public static void finalCleanUp() throws IOException {
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FileUtils.deleteDirectory(new File(testOutputBasePath));
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FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
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}
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}
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