dnet-hadoop/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java

package eu.dnetlib.dhp.oa.dedup;

import static java.nio.file.Files.createTempDirectory;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.Mockito.lenient;

import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import java.io.File;
import java.io.IOException;
import java.io.Serializable;
import java.net.URISyntaxException;
import java.nio.file.Paths;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension;

@ExtendWith(MockitoExtension.class)
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
public class SparkDedupTest implements Serializable {

    @Mock(serializable = true)
    ISLookUpService isLookUpService;

    private static SparkSession spark;
    private static JavaSparkContext jsc;

    private static String testGraphBasePath;
    private static String testOutputBasePath;
    private static String testDedupGraphBasePath;
    private static final String testActionSetId = "test-orchestrator";

    @BeforeAll
    private static void cleanUp() throws IOException, URISyntaxException {

        testGraphBasePath =
                Paths.get(
                                SparkDedupTest.class
                                        .getResource("/eu/dnetlib/dhp/dedup/entities")
                                        .toURI())
                        .toFile()
                        .getAbsolutePath();

        testOutputBasePath =
                createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
                        .toAbsolutePath()
                        .toString();
        testDedupGraphBasePath =
                createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
                        .toAbsolutePath()
                        .toString();

        FileUtils.deleteDirectory(new File(testOutputBasePath));
        FileUtils.deleteDirectory(new File(testDedupGraphBasePath));

        spark =
                SparkSession.builder()
                        .appName(SparkCreateSimRels.class.getSimpleName())
                        .master("local[*]")
                        .config(new SparkConf())
                        .getOrCreate();

        jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
    }

    @BeforeEach
    private void setUp() throws IOException, ISLookUpException {

        lenient()
                .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
                .thenReturn(
                        IOUtils.toString(
                                SparkDedupTest.class.getResourceAsStream(
                                        "/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));

        lenient()
                .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
                .thenReturn(
                        IOUtils.toString(
                                SparkDedupTest.class.getResourceAsStream(
                                        "/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));

        lenient()
                .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
                .thenReturn(
                        IOUtils.toString(
                                SparkDedupTest.class.getResourceAsStream(
                                        "/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
    }

    @Test
    @Order(1)
    public void createSimRelsTest() throws Exception {

        ArgumentApplicationParser parser =
                new ArgumentApplicationParser(
                        IOUtils.toString(
                                SparkCreateSimRels.class.getResourceAsStream(
                                        "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
        parser.parseArgument(
                new String[] {
                    "-mt", "local[*]",
                    "-i", testGraphBasePath,
                    "-asi", testActionSetId,
                    "-la", "lookupurl",
                    "-w", testOutputBasePath
                });

        new SparkCreateSimRels(parser, spark).run(isLookUpService);

        long orgs_simrel =
                spark.read()
                        .load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
                        .count();
        long pubs_simrel =
                spark.read()
                        .load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
                        .count();

        assertEquals(3288, orgs_simrel);
        assertEquals(7260, pubs_simrel);
    }

    @Test
    @Order(2)
    public void createMergeRelsTest() throws Exception {

        ArgumentApplicationParser parser =
                new ArgumentApplicationParser(
                        IOUtils.toString(
                                SparkCreateMergeRels.class.getResourceAsStream(
                                        "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
        parser.parseArgument(
                new String[] {
                    "-mt", "local[*]",
                    "-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();
        long pubs_mergerel =
                spark.read()
                        .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
                        .count();

        assertEquals(1244, orgs_mergerel);
        assertEquals(1460, pubs_mergerel);
    }

    @Test
    @Order(3)
    public void createDedupRecordTest() throws Exception {

        ArgumentApplicationParser parser =
                new ArgumentApplicationParser(
                        IOUtils.toString(
                                SparkCreateDedupRecord.class.getResourceAsStream(
                                        "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
        parser.parseArgument(
                new String[] {
                    "-mt", "local[*]",
                    "-i", testGraphBasePath,
                    "-asi", testActionSetId,
                    "-la", "lookupurl",
                    "-w", testOutputBasePath
                });

        new SparkCreateDedupRecord(parser, spark).run(isLookUpService);

        long orgs_deduprecord =
                jsc.textFile(
                                testOutputBasePath
                                        + "/"
                                        + testActionSetId
                                        + "/organization_deduprecord")
                        .count();
        long pubs_deduprecord =
                jsc.textFile(
                                testOutputBasePath
                                        + "/"
                                        + testActionSetId
                                        + "/publication_deduprecord")
                        .count();

        assertEquals(82, orgs_deduprecord);
        assertEquals(66, pubs_deduprecord);
    }

    @Test
    @Order(4)
    public void updateEntityTest() throws Exception {

        ArgumentApplicationParser parser =
                new ArgumentApplicationParser(
                        IOUtils.toString(
                                SparkUpdateEntity.class.getResourceAsStream(
                                        "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
        parser.parseArgument(
                new String[] {
                    "-mt", "local[*]",
                    "-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 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();

        assertEquals(897, publications);
        assertEquals(835, organizations);

        long deletedOrgs =
                jsc.textFile(testDedupGraphBasePath + "/organization")
                        .filter(this::isDeletedByInference)
                        .count();
        long deletedPubs =
                jsc.textFile(testDedupGraphBasePath + "/publication")
                        .filter(this::isDeletedByInference)
                        .count();

        assertEquals(mergedOrgs, deletedOrgs);
        assertEquals(mergedPubs, deletedPubs);
    }

    @Test
    @Order(5)
    public void propagateRelationTest() throws Exception {

        ArgumentApplicationParser parser =
                new ArgumentApplicationParser(
                        IOUtils.toString(
                                SparkPropagateRelation.class.getResourceAsStream(
                                        "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
        parser.parseArgument(
                new String[] {
                    "-mt", "local[*]",
                    "-i", testGraphBasePath,
                    "-w", testOutputBasePath,
                    "-o", testDedupGraphBasePath
                });

        new SparkPropagateRelation(parser, spark).run(isLookUpService);

        long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();

        assertEquals(826, relations);
    }

    @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");
    }
}