forked from antonis.lempesis/dnet-hadoop
implemented test for sparkcreatesimrels
This commit is contained in:
miconis
parent
a61763d149
commit
53fd624c34
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@ -2,18 +2,15 @@ package eu.dnetlib.dhp.oa.dedup;
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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.utils.ISLookupClientFactory;
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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.config.DedupConfig;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.sql.SparkSession;
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.Element;
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import org.dom4j.io.SAXReader;
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import scala.xml.Elem;
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import java.io.IOException;
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import java.io.Serializable;
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@ -24,15 +21,15 @@ import java.util.List;
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abstract class AbstractSparkAction implements Serializable {
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public ArgumentApplicationParser parser; //parameters for the spark action
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public ISLookUpService isLookUpService; //lookup service to take dedupconfig
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public SparkSession spark; //the spark session
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public AbstractSparkAction(ArgumentApplicationParser parser, ISLookUpService isLookUpService) throws Exception {
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public AbstractSparkAction(ArgumentApplicationParser parser, SparkSession spark) throws Exception {
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this.parser = parser;
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this.isLookUpService = isLookUpService;
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this.spark = spark;
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}
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public List<DedupConfig> getConfigurations(String orchestrator) throws ISLookUpException, DocumentException, IOException {
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public List<DedupConfig> getConfigurations(ISLookUpService isLookUpService, String orchestrator) throws ISLookUpException, DocumentException, IOException {
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final String xquery = String.format("/RESOURCE_PROFILE[.//DEDUPLICATION/ACTION_SET/@id = '%s']", orchestrator);
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@ -51,7 +48,7 @@ abstract class AbstractSparkAction implements Serializable {
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return configurations;
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}
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public DedupConfig loadConfig(final ISLookUpService isLookUpService, final String actionSetId, final Object o)
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private DedupConfig loadConfig(final ISLookUpService isLookUpService, final String actionSetId, final Object o)
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throws ISLookUpException, IOException {
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final Element s = (Element) o;
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final String configProfileId = s.attributeValue("id");
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@ -68,9 +65,9 @@ abstract class AbstractSparkAction implements Serializable {
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return dedupConfig;
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}
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abstract void run() throws DocumentException, IOException, ISLookUpException;
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abstract void run(ISLookUpService isLookUpService) throws DocumentException, IOException, ISLookUpException;
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protected SparkSession getSparkSession(ArgumentApplicationParser parser) {
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protected static SparkSession getSparkSession(ArgumentApplicationParser parser) {
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SparkConf conf = new SparkConf();
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return SparkSession
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@ -38,8 +38,8 @@ public class SparkCreateSimRels extends AbstractSparkAction {
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private static final Log log = LogFactory.getLog(SparkCreateSimRels.class);
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public SparkCreateSimRels(ArgumentApplicationParser parser, ISLookUpService isLookUpService) throws Exception {
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super(parser, isLookUpService);
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public SparkCreateSimRels(ArgumentApplicationParser parser, SparkSession spark) throws Exception {
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super(parser, spark);
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}
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public static void main(String[] args) throws Exception {
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@ -48,11 +48,11 @@ public class SparkCreateSimRels extends AbstractSparkAction {
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SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
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parser.parseArgument(args);
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new SparkCreateSimRels(parser, ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))).run();
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new SparkCreateSimRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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@Override
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public void run() throws DocumentException, IOException, ISLookUpException {
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public void run(ISLookUpService isLookUpService) throws DocumentException, IOException, ISLookUpException {
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//read oozie parameters
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final String graphBasePath = parser.get("graphBasePath");
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@ -65,34 +65,32 @@ public class SparkCreateSimRels extends AbstractSparkAction {
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System.out.println(String.format("actionSetId: '%s'", actionSetId));
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System.out.println(String.format("workingPath: '%s'", workingPath));
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try (SparkSession spark = getSparkSession(parser)) {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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//for each dedup configuration
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for (DedupConfig dedupConf: getConfigurations(actionSetId)) {
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final String entity = dedupConf.getWf().getEntityType();
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final String subEntity = dedupConf.getWf().getSubEntityValue();
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//for each dedup configuration
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for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) {
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final String entity = dedupConf.getWf().getEntityType();
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final String subEntity = dedupConf.getWf().getSubEntityValue();
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JavaPairRDD<String, MapDocument> mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
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.mapToPair((PairFunction<String, String, MapDocument>) s -> {
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MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
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return new Tuple2<String, MapDocument>(d.getIdentifier(), d);
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});
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JavaPairRDD<String, MapDocument> mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
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.mapToPair((PairFunction<String, String, MapDocument>) s -> {
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MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
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return new Tuple2<String, MapDocument>(d.getIdentifier(), d);
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});
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//create blocks for deduplication
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JavaPairRDD<String, List<MapDocument>> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf);
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//create blocks for deduplication
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JavaPairRDD<String, List<MapDocument>> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf);
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//create relations by comparing only elements in the same group
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final JavaPairRDD<String, String> dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf);
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//create relations by comparing only elements in the same group
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final JavaPairRDD<String, String> dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf);
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JavaRDD<Relation> relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity));
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JavaRDD<Relation> relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity));
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//save the simrel in the workingdir
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spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class))
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.write()
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.mode("overwrite")
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.save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity));
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}
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//save the simrel in the workingdir
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spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class))
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.write()
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.mode("overwrite")
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.save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity));
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}
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}
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@ -1,43 +1,54 @@
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package eu.dnetlib.dhp.oa.dedup;
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import com.google.common.collect.Lists;
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import com.google.common.hash.HashFunction;
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import com.google.common.hash.Hashing;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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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.config.DedupConfig;
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import net.bytebuddy.utility.RandomString;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.sql.SparkSession;
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import org.dom4j.DocumentException;
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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.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Disabled;
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import org.junit.jupiter.api.Test;
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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 java.io.File;
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import java.io.IOException;
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import java.util.List;
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import java.net.URISyntaxException;
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import java.nio.file.Paths;
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import static org.mockito.ArgumentMatchers.anyString;
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import static org.mockito.Mockito.mock;
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import static org.mockito.Mockito.when;
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import static org.mockito.Mockito.withSettings;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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@ExtendWith(MockitoExtension.class)
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@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
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public class SparkDedupTest {
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ISLookUpService isLookUpService = mock(ISLookUpService.class, withSettings().serializable());
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@Mock
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ISLookUpService isLookUpService;
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SparkSession spark;
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static String testGraphBasePath;
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static String testOutputBasePath;
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String testActionSetId = "test-orchestrator";
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@BeforeEach
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public void setUp() throws IOException, ISLookUpException, DocumentException {
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public void setUp() throws IOException, ISLookUpException, DocumentException, URISyntaxException {
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withSettings().serializable();
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testGraphBasePath = Paths.get(getClass().getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath();
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testOutputBasePath = "/tmp/" + RandomString.make(5).toLowerCase();
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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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when(isLookUpService.getResourceProfileByQuery(Mockito.contains("test-orchestrator")))
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when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
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.thenReturn(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
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when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
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@ -48,6 +59,7 @@ public class SparkDedupTest {
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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 = new ArgumentApplicationParser(
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@ -55,12 +67,19 @@ public class SparkDedupTest {
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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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"-mt", "local[*]",
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"-i", "/Users/miconis/dumps",
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"-asi", "test-orchestrator",
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"-i", testGraphBasePath,
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"-asi", testActionSetId,
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"-la", "lookupurl",
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"-w", "workingPath"});
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"-w", testOutputBasePath});
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new SparkCreateSimRels(parser, isLookUpService).run();
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new SparkCreateSimRels(parser, spark).run(isLookUpService);
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//test number of simrels
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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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assertEquals(918, orgs_simrel);
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assertEquals(0, pubs_simrel);
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}
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@ -90,26 +109,31 @@ public class SparkDedupTest {
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// @Disabled("must be parametrized to run locally")
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// public void printConfiguration() throws Exception {
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// System.out.println(ArgumentApplicationParser.compressArgument(configuration));
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// }
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//
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// @Disabled("must be parametrized to run locally")
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// public void testHashCode() {
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// final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f";
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// final String s2 = "20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46";
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//
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// final HashFunction hashFunction = Hashing.murmur3_128();
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//
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// System.out.println(s1.hashCode());
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// System.out.println(hashFunction.hashString(s1).asLong());
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// System.out.println(s2.hashCode());
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// System.out.println(hashFunction.hashString(s2).asLong());
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// }
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//
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// public List<DedupConfig> prepareConfigurations() throws IOException {
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//
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// return Lists.newArrayList(
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// DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))),
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// DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")))
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// );
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// }
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@Disabled("must be parametrized to run locally")
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public void testHashCode() {
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final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f";
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final String s2 = "20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46";
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final HashFunction hashFunction = Hashing.murmur3_128();
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System.out.println(s1.hashCode());
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System.out.println(hashFunction.hashString(s1).asLong());
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System.out.println(s2.hashCode());
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System.out.println(hashFunction.hashString(s2).asLong());
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}
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public List<DedupConfig> prepareConfigurations() throws IOException {
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return Lists.newArrayList(
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DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))),
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DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")))
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);
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@AfterAll
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public static void cleanUp() throws IOException {
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FileUtils.deleteDirectory(new File(testOutputBasePath));
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}
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}
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@ -144,10 +144,10 @@
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}
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},
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"model" : [
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{ "name" : "country", "type" : "String", "path" : "$.country.classid"},
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{ "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"},
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{ "name" : "legalname", "type" : "String", "path" : "$.legalname.value" },
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{ "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" },
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{ "name" : "country", "type" : "String", "path" : "$.organization.metadata.country.classid"},
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{ "name" : "legalshortname", "type" : "String", "path" : "$.organization.metadata.legalshortname.value"},
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{ "name" : "legalname", "type" : "String", "path" : "$.organization.metadata.legalname.value" },
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{ "name" : "websiteurl", "type" : "URL", "path" : "$.organization.metadata.websiteurl.value" },
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{ "name" : "gridid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='grid')].value"},
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{ "name" : "originalId", "type" : "String", "path" : "$.id" }
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],
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@ -0,0 +1,257 @@
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{"dateoftransformation":"2018-11-12","originalId":["opendoar____::Humboldt_State_University"],"collectedfrom":[{"value":"OpenDOAR","key":"10|openaire____::47ce9e9f4fad46e732cff06419ecaabb"}],"organization":{"metadata":{"eclegalbody":{"value":"false"},"eclegalperson":{"value":"false"},"ecinternationalorganization":{"value":"false"},"ecresearchorganization":{"value":"false"},"ecnonprofit":{"value":"false"},"ecenterprise":{"value":"false"},"websiteurl":{"value":"http://www.humboldt.edu/"},"ecnutscode":{"value":"false"},"ecinternationalorganizationeurinterests":{"value":"false"},"legalname":{"value":"Humboldt State University"},"country":{"classid":"US","classname":"United States","schemename":"dnet:countries","schemeid":"dnet:countries"},"echighereducation":{"value":"false"},"ecsmevalidated":{"value":"false"}}},"dateofcollection":"2018-11-12","type":20,"id":"20|opendoar____::9c3522c59aef0edab19b8a3f0aeb39ed"}
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{"dateoftransformation":"2019-05-19","originalId":["rcuk________::9758583A-FF1E-41C4-9176-B875E8FAC110"],"collectedfrom":[{"value":"Research Councils UK","key":"10|openaire____::ab2d3310741ea80d3b8726f651502858"}],"organization":{"metadata":{"eclegalbody":{"value":"false"},"eclegalperson":{"value":"false"},"ecinternationalorganization":{"value":"false"},"ecnonprofit":{"value":"false"},"ecresearchorganization":{"value":"false"},"ecenterprise":{"value":"false"},"ecnutscode":{"value":"false"},"ecinternationalorganizationeurinterests":{"value":"false"},"legalname":{"value":"Humboldt State University"},"echighereducation":{"value":"false"},"ecsmevalidated":{"value":"false"}}},"dateofcollection":"2017-11-04","type":20,"id":"20|rcuk________::7715018b4838eaf1d57242c788e222d4"}
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{"dateoftransformation":"2018-09-13","originalId":["opendoar____::Humboldt-Universität_zu_Berlin"],"collectedfrom":[{"value":"OpenDOAR","key":"10|openaire____::47ce9e9f4fad46e732cff06419ecaabb"}],"organization":{"metadata":{"eclegalbody":{"value":"false"},"eclegalperson":{"value":"false"},"ecinternationalorganization":{"value":"false"},"legalshortname":{"value":"HU"},"ecresearchorganization":{"value":"false"},"ecnonprofit":{"value":"false"},"ecenterprise":{"value":"false"},"websiteurl":{"value":"https://www.hu-berlin.de/"},"ecnutscode":{"value":"false"},"ecinternationalorganizationeurinterests":{"value":"false"},"legalname":{"value":"Humboldt-Universität zu Berlin"},"country":{"classid":"DE","classname":"Germany","schemename":"dnet:countries","schemeid":"dnet:countries"},"echighereducation":{"value":"false"},"ecsmevalidated":{"value":"false"}}},"dateofcollection":"2015-08-24","type":20,"id":"20|opendoar____::13ab9ef517038d3751f4b0e31aea9ac7"}
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{"dateoftransformation":"2018-09-27","originalId":["re3data_____::678d9d5a712331f6e2fce7b7b764090f"],"collectedfrom":[{"value":"Registry of Research Data Repository","key":"10|openaire____::21f8a223b9925c2f87c404096080b046"}],"organization":{"metadata":{"eclegalbody":{"value":"false"},"eclegalperson":{"value":"false"},"ecinternationalorganization":{"value":"false"},"ecresearchorganization":{"value":"false"},"ecnonprofit":{"value":"true"},"ecenterprise":{"value":"false"},"websiteurl":{"value":"https://www.hu-berlin.de/de/"},"ecnutscode":{"value":"false"},"ecinternationalorganizationeurinterests":{"value":"false"},"legalname":{"value":"Humboldt-Universität Berlin"},"country":{"classid":"DE","classname":"Germany","schemename":"dnet:countries","schemeid":"dnet:countries"},"echighereducation":{"value":"false"},"ecsmevalidated":{"value":"false"}}},"dateofcollection":"2018-09-27","type":20,"id":"20|re3data_____::aeb488fd15eb1be77b998b5602450910"}
|
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{"dateoftransformation":"2018-11-12","originalId":["opendoar____::Netherlands_Aerospace_Centre"],"collectedfrom":[{"value":"OpenDOAR","key":"10|openaire____::47ce9e9f4fad46e732cff06419ecaabb"}],"organization":{"metadata":{"eclegalbody":{"value":"false"},"eclegalperson":{"value":"false"},"ecinternationalorganization":{"value":"false"},"legalshortname":{"value":"NLR"},"ecresearchorganization":{"value":"false"},"ecnonprofit":{"value":"false"},"ecenterprise":{"value":"false"},"websiteurl":{"value":"http://www.nlr.nl/"},"ecnutscode":{"value":"false"},"ecinternationalorganizationeurinterests":{"value":"false"},"legalname":{"value":"Netherlands Aerospace Centre"},"country":{"classid":"NL","classname":"Netherlands","schemename":"dnet:countries","schemeid":"dnet:countries"},"echighereducation":{"value":"false"},"ecsmevalidated":{"value":"false"}}},"dateofcollection":"2018-11-12","type":20,"id":"20|opendoar____::ce12359dec61a8e00837c3e507918812"}
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||||
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