forked from D-Net/dnet-hadoop
minor changes
This commit is contained in:
miconis
parent
1a85020572
commit
98854b0124
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@ -68,12 +68,9 @@ public class SparkCopyOpenorgs extends AbstractSparkAction {
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log.info("Copying openorgs to the working dir");
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final String outputPath = DedupUtility.createDedupRecordPath(workingPath, actionSetId, subEntity);
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removeOutputDir(spark, outputPath);
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final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity);
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final Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
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filterOpenorgs(spark, entityPath)
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.write()
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.mode(SaveMode.Overwrite)
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@ -95,9 +92,13 @@ public class SparkCopyOpenorgs extends AbstractSparkAction {
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.rdd(),
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Encoders.bean(Organization.class));
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entities.show();
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log.info("Number of organization entities processed: {}", entities.count());
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return entities.filter(entities.col("id").contains("openorgs____"));
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entities = entities.filter(entities.col("id").contains("openorgs____"));
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log.info("Number of Openorgs organization entities: {}", entities.count());
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return entities;
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}
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}
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@ -74,8 +74,6 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
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final String outputPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, "organization");
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removeOutputDir(spark, outputPath);
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final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation");
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DedupConfig dedupConf = getConfigurations(isLookUpService, actionSetId).get(0);
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@ -85,11 +83,13 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
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.textFile(relationPath)
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.map(patchRelFn(), Encoders.bean(Relation.class))
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.toJavaRDD()
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.filter(this::isOpenorgs) // takes only relations coming from openorgs
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.filter(this::filterOpenorgsRels) // takes only isSimilarTo relations between organizations from openorgs
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.filter(this::excludeOpenorgsMesh) // excludes relations between an organization and an openorgsmesh
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.filter(this::isOpenorgs)
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.filter(this::filterOpenorgsRels)
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.filter(this::excludeOpenorgsMesh)
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.filter(this::excludeNonOpenorgs); // excludes relations with no openorgs id involved
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log.info("Number of raw Openorgs Relations collected: {}", rawRels.count());
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// turn openorgs isSimilarTo relations into mergerels
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JavaRDD<Relation> mergeRelsRDD = rawRels.flatMap(rel -> {
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List<Relation> mergerels = new ArrayList<>();
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@ -103,6 +103,8 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
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return mergerels.iterator();
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});
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log.info("Number of Openorgs Merge Relations created: {}", mergeRelsRDD.count());
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spark
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.createDataset(
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mergeRelsRDD.rdd(),
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@ -134,7 +136,7 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
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if (rel.getCollectedfrom() != null) {
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for (KeyValue k : rel.getCollectedfrom()) {
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if (k.getValue().equals("OpenOrgs Database")) {
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if (k.getValue() != null && k.getValue().equals("OpenOrgs Database")) {
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return true;
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}
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}
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@ -144,7 +146,7 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
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private boolean excludeOpenorgsMesh(Relation rel) {
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if (rel.getSource().equals("openorgsmesh") || rel.getTarget().equals("openorgsmesh")) {
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if (rel.getSource().contains("openorgsmesh") || rel.getTarget().contains("openorgsmesh")) {
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return false;
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}
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return true;
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@ -152,7 +154,7 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
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private boolean excludeNonOpenorgs(Relation rel) {
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if (rel.getSource().equals("openorgs____") || rel.getTarget().equals("openorgs____")) {
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if (rel.getSource().contains("openorgs____") || rel.getTarget().contains("openorgs____")) {
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return true;
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}
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return false;
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@ -33,7 +33,7 @@ import scala.Tuple2;
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public class SparkCopyRelationsNoOpenorgs extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkUpdateEntity.class);
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private static final Logger log = LoggerFactory.getLogger(SparkCopyRelationsNoOpenorgs.class);
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public SparkCopyRelationsNoOpenorgs(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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@ -52,7 +52,7 @@ public class SparkCopyRelationsNoOpenorgs extends AbstractSparkAction {
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.registerKryoClasses(ModelSupport.getOafModelClasses());
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new SparkUpdateEntity(parser, getSparkSession(conf))
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new SparkCopyRelationsNoOpenorgs(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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@ -69,14 +69,14 @@ public class SparkCopyRelationsNoOpenorgs extends AbstractSparkAction {
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final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation");
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final String outputPath = DedupUtility.createEntityPath(dedupGraphPath, "relation");
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removeOutputDir(spark, outputPath);
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JavaRDD<Relation> simRels = spark
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.read()
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.textFile(relationPath)
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.map(patchRelFn(), Encoders.bean(Relation.class))
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.toJavaRDD()
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.filter(this::excludeOpenorgsRels);
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.filter(x -> !isOpenorgs(x));
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log.info("Number of non-Openorgs relations collected: {}", simRels.count());
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spark
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.createDataset(simRels.rdd(), Encoders.bean(Relation.class))
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@ -96,15 +96,15 @@ public class SparkCopyRelationsNoOpenorgs extends AbstractSparkAction {
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};
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}
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private boolean excludeOpenorgsRels(Relation rel) {
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private boolean isOpenorgs(Relation rel) {
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if (rel.getCollectedfrom() != null) {
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for (KeyValue k : rel.getCollectedfrom()) {
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if (k.getValue().equals("OpenOrgs Database")) {
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return false;
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}
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}
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}
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if (k.getValue() != null && k.getValue().equals("OpenOrgs Database")) {
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return true;
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}
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}
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}
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return false;
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}
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}
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@ -1,281 +0,0 @@
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package eu.dnetlib.dhp.oa.dedup;
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import static eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels.DNET_PROVENANCE_ACTIONS;
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import static eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels.PROVENANCE_ACTION_CLASS;
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import static eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels.hash;
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import java.io.IOException;
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import java.util.*;
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import java.util.stream.Collectors;
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import java.util.stream.StreamSupport;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.PairFunction;
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import org.apache.spark.graphx.Edge;
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import org.apache.spark.rdd.RDD;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.dom4j.DocumentException;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.google.common.collect.Iterables;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent;
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import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor;
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import eu.dnetlib.dhp.oa.dedup.model.Block;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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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 eu.dnetlib.pace.model.MapDocument;
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import eu.dnetlib.pace.util.MapDocumentUtil;
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import scala.Tuple2;
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public class SparkRemoveDiffRels extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkRemoveDiffRels.class);
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public SparkRemoveDiffRels(ArgumentApplicationParser parser, SparkSession spark) {
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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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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.parseArgument(args);
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SparkConf conf = new SparkConf();
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new SparkCreateSimRels(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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@Override
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public void run(ISLookUpService isLookUpService)
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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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final String isLookUpUrl = parser.get("isLookUpUrl");
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final String actionSetId = parser.get("actionSetId");
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final String workingPath = parser.get("workingPath");
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final int numPartitions = Optional
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.ofNullable(parser.get("numPartitions"))
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.map(Integer::valueOf)
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.orElse(NUM_PARTITIONS);
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log.info("numPartitions: '{}'", numPartitions);
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log.info("graphBasePath: '{}'", graphBasePath);
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log.info("isLookUpUrl: '{}'", isLookUpUrl);
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log.info("actionSetId: '{}'", actionSetId);
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log.info("workingPath: '{}'", workingPath);
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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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log.info("Removing diffrels for: '{}'", subEntity);
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final String mergeRelsPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity);
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final String relationPath = DedupUtility.createEntityPath(graphBasePath, subEntity);
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final String openorgsMergeRelsPath = DedupUtility
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.createOpenorgsMergeRelsPath(workingPath, actionSetId, subEntity);
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final int maxIterations = dedupConf.getWf().getMaxIterations();
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log.info("Max iterations {}", maxIterations);
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JavaRDD<Relation> mergeRelsRDD = spark
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.read()
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.load(mergeRelsPath)
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.as(Encoders.bean(Relation.class))
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.where("relClass == 'merges'")
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.toJavaRDD();
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System.out.println("mergeRelsRDD = " + mergeRelsRDD.count());
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// JavaRDD<Tuple2<Tuple2<String, String>, String>> diffRelsRDD = spark
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// .read()
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// .textFile(relationPath)
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// .map(patchRelFn(), Encoders.bean(Relation.class))
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// .toJavaRDD()
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// .filter(r -> filterRels(r, entity))
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// .map(rel -> {
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// if (rel.getSource().compareTo(rel.getTarget()) < 0)
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// return new Tuple2<>(new Tuple2<>(rel.getSource(), rel.getTarget()), "diffRel");
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// else
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// return new Tuple2<>(new Tuple2<>(rel.getTarget(), rel.getSource()), "diffRel");
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// });
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// THIS IS FOR TESTING PURPOSE
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JavaRDD<Tuple2<Tuple2<String, String>, String>> diffRelsRDD = spark
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.read()
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.load(mergeRelsPath)
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.as(Encoders.bean(Relation.class))
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.toJavaRDD()
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.map(rel -> {
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if (rel.getSource().compareTo(rel.getTarget()) < 0)
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return new Tuple2<>(new Tuple2<>(rel.getSource(), rel.getTarget()), "diffRel");
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else
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return new Tuple2<>(new Tuple2<>(rel.getTarget(), rel.getSource()), "diffRel");
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})
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.distinct();
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System.out.println("diffRelsRDD = " + diffRelsRDD.count());
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// JavaRDD<Tuple2<Tuple2<String, String>, String>> flatMergeRels = mergeRelsRDD
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// .mapToPair(rel -> new Tuple2<>(rel.getSource(), rel.getTarget()))
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// .groupByKey()
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// .flatMap(g -> {
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// List<Tuple2<Tuple2<String, String>, String>> rels = new ArrayList<>();
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//
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// List<String> ids = StreamSupport
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// .stream(g._2().spliterator(), false)
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// .collect(Collectors.toList());
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//
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// for (int i = 0; i < ids.size(); i++) {
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// for (int j = i + 1; j < ids.size(); j++) {
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// if (ids.get(i).compareTo(ids.get(j)) < 0)
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// rels.add(new Tuple2<>(new Tuple2<>(ids.get(i), ids.get(j)), g._1()));
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// else
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// rels.add(new Tuple2<>(new Tuple2<>(ids.get(j), ids.get(i)), g._1()));
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// }
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// }
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// return rels.iterator();
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//
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// });
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JavaRDD<Tuple2<Tuple2<String, String>, String>> mergeRels = mergeRelsRDD
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.map(rel -> {
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if (rel.getSource().compareTo(rel.getTarget()) < 0)
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return new Tuple2<>(new Tuple2<>(rel.getSource(), rel.getTarget()), "mergeRel");
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else
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return new Tuple2<>(new Tuple2<>(rel.getTarget(), rel.getSource()), "mergeRel");
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});
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System.out.println("mergeRelsProcessed = " + mergeRels.count());
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// JavaRDD<Relation> purgedMergeRels = flatMergeRels
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// .union(diffRelsRDD)
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// .mapToPair(rel -> new Tuple2<>(rel._1(), Arrays.asList(rel._2())))
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// .reduceByKey((a, b) -> {
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// List<String> list = new ArrayList<String>();
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// list.addAll(a);
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// list.addAll(b);
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// return list;
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// })
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// .filter(rel -> rel._2().size() == 1)
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// .mapToPair(rel -> new Tuple2<>(rel._2().get(0), rel._1()))
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// .flatMap(rel -> {
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// List<Tuple2<String, String>> rels = new ArrayList<>();
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// String source = rel._1();
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// rels.add(new Tuple2<>(source, rel._2()._1()));
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// rels.add(new Tuple2<>(source, rel._2()._2()));
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// return rels.iterator();
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// })
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// .distinct()
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// .flatMap(rel -> tupleToMergeRel(rel, dedupConf));
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JavaRDD<Relation> purgedMergeRels = mergeRels
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.union(diffRelsRDD)
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.mapToPair(t -> new Tuple2<>(t._1()._1() + "|||" + t._1()._2(), t._2()))
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.groupByKey()
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.filter(g -> Iterables.size(g._2()) == 1)
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.flatMap(
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t -> tupleToMergeRel(
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new Tuple2<>(t._1().split("\\|\\|\\|")[0], t._1().split("\\|\\|\\|")[1]),
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dedupConf));
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System.out.println("purgedMergeRels = " + purgedMergeRels.count());
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spark
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.createDataset(purgedMergeRels.rdd(), Encoders.bean(Relation.class))
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.write()
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.mode(SaveMode.Overwrite)
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.json(openorgsMergeRelsPath);
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}
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}
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private static MapFunction<String, Relation> patchRelFn() {
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return value -> {
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final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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return rel;
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};
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}
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private boolean filterRels(Relation rel, String entityType) {
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switch (entityType) {
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case "result":
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if (rel.getRelClass().equals("isDifferentFrom") && rel.getRelType().equals("resultResult")
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&& rel.getSubRelType().equals("dedup"))
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return true;
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break;
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case "organization":
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if (rel.getRelClass().equals("isDifferentFrom") && rel.getRelType().equals("organizationOrganization")
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&& rel.getSubRelType().equals("dedup"))
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return true;
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break;
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default:
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return false;
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}
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return false;
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}
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public Iterator<Relation> tupleToMergeRel(Tuple2<String, String> rel, DedupConfig dedupConf) {
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List<Relation> rels = new ArrayList<>();
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rels.add(rel(rel._1(), rel._2(), "merges", dedupConf));
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rels.add(rel(rel._2(), rel._1(), "isMergedIn", dedupConf));
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return rels.iterator();
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}
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private Relation rel(String source, String target, String relClass, DedupConfig dedupConf) {
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String entityType = dedupConf.getWf().getEntityType();
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Relation r = new Relation();
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r.setSource(source);
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r.setTarget(target);
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r.setRelClass(relClass);
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r.setRelType(entityType + entityType.substring(0, 1).toUpperCase() + entityType.substring(1));
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r.setSubRelType("dedup");
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DataInfo info = new DataInfo();
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info.setDeletedbyinference(false);
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info.setInferred(true);
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info.setInvisible(false);
|
||||
info.setInferenceprovenance(dedupConf.getWf().getConfigurationId());
|
||||
Qualifier provenanceAction = new Qualifier();
|
||||
provenanceAction.setClassid(PROVENANCE_ACTION_CLASS);
|
||||
provenanceAction.setClassname(PROVENANCE_ACTION_CLASS);
|
||||
provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS);
|
||||
provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS);
|
||||
info.setProvenanceaction(provenanceAction);
|
||||
|
||||
// TODO calculate the trust value based on the similarity score of the elements in the CC
|
||||
// info.setTrust();
|
||||
|
||||
r.setDataInfo(info);
|
||||
return r;
|
||||
}
|
||||
}
|
||||
|
|
@ -87,8 +87,8 @@
|
|||
|
||||
<action name="resetOrgSimRels">
|
||||
<fs>
|
||||
<delete path="${workingPath}/${actionSetId}/organization_simrel"/>
|
||||
<delete path="${workingPath}/${actionSetId}/organization_mergerel"/>
|
||||
<delete path="${workingPath}/${actionSetIdOpenorgs}/organization_simrel"/>
|
||||
<delete path="${workingPath}/${actionSetIdOpenorgs}/organization_mergerel"/>
|
||||
</fs>
|
||||
<ok to="CreateSimRels"/>
|
||||
<error to="Kill"/>
|
||||
|
|
@ -113,7 +113,7 @@
|
|||
</spark-opts>
|
||||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetIdOpenorgs}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--numPartitions</arg><arg>8000</arg>
|
||||
</spark>
|
||||
|
|
@ -142,7 +142,7 @@
|
|||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetIdOpenorgs}</arg>
|
||||
<arg>--numPartitions</arg><arg>8000</arg>
|
||||
</spark>
|
||||
<ok to="CreateMergeRels"/>
|
||||
|
|
@ -169,7 +169,7 @@
|
|||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetIdOpenorgs}</arg>
|
||||
<arg>--cutConnectedComponent</arg><arg>${cutConnectedComponent}</arg>
|
||||
</spark>
|
||||
<ok to="PrepareOrgRels"/>
|
||||
|
|
@ -196,7 +196,7 @@
|
|||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetIdOpenorgs}</arg>
|
||||
<arg>--dbUrl</arg><arg>${dbUrl}</arg>
|
||||
<arg>--dbTable</arg><arg>${dbTable}</arg>
|
||||
<arg>--dbUser</arg><arg>${dbUser}</arg>
|
||||
|
|
@ -227,7 +227,7 @@
|
|||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetIdOpenorgs}</arg>
|
||||
<arg>--apiUrl</arg><arg>${apiUrl}</arg>
|
||||
<arg>--dbUrl</arg><arg>${dbUrl}</arg>
|
||||
<arg>--dbTable</arg><arg>${dbTable}</arg>
|
||||
|
|
|
|||
|
|
@ -92,11 +92,23 @@
|
|||
<action name="resetWorkingPath">
|
||||
<fs>
|
||||
<delete path="${workingPath}"/>
|
||||
<delete path="${dedupGraphPath}"/>
|
||||
</fs>
|
||||
<ok to="CreateSimRel"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<!--<action name="testOpenorgs">-->
|
||||
<!--<fs>-->
|
||||
<!--<delete path="${workingPath}/${actionSetIdOpenorgs}/organization_simrel"/>-->
|
||||
<!--<delete path="${workingPath}/${actionSetIdOpenorgs}/organization_mergerel"/>-->
|
||||
<!--<delete path="${workingPath}/${actionSetIdOpenorgs}/organization_deduprecord"/>-->
|
||||
<!--<delete path="${dedupGraphPath}"/>-->
|
||||
<!--</fs>-->
|
||||
<!--<ok to="CopyOpenorgsMergeRels"/>-->
|
||||
<!--<error to="Kill"/>-->
|
||||
<!--</action>-->
|
||||
|
||||
<action name="CreateSimRel">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
|
|
@ -182,7 +194,7 @@
|
|||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Copy Merge Relations</name>
|
||||
<name>Copy Openorgs Merge Relations</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.SparkCopyOpenorgsMergeRels</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
|
|
@ -201,7 +213,7 @@
|
|||
<arg>--actionSetId</arg><arg>${actionSetIdOpenorgs}</arg>
|
||||
<arg>--numPartitions</arg><arg>8000</arg>
|
||||
</spark>
|
||||
<ok to="CopyEntities"/>
|
||||
<ok to="CopyOpenorgs"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
|
@ -210,7 +222,7 @@
|
|||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Copy Entities</name>
|
||||
<name>Copy Openorgs Entities</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.SparkCopyOpenorgs</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
|
|
@ -225,7 +237,6 @@
|
|||
</spark-opts>
|
||||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetIdOpenorgs}</arg>
|
||||
</spark>
|
||||
<ok to="UpdateEntity"/>
|
||||
|
|
@ -262,7 +273,7 @@
|
|||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Update Entity</name>
|
||||
<name>Copy Non-Openorgs Relations</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.SparkCopyRelationsNoOpenorgs</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
|
|
|
|||
|
|
@ -19,9 +19,11 @@ import org.apache.spark.SparkConf;
|
|||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.ForeachFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.*;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
|
|
@ -61,7 +63,7 @@ public class SparkOpenorgsTest implements Serializable {
|
|||
public static void cleanUp() throws IOException, URISyntaxException {
|
||||
|
||||
testGraphBasePath = Paths
|
||||
.get(SparkOpenorgsTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI())
|
||||
.get(SparkOpenorgsTest.class.getResource("/eu/dnetlib/dhp/dedup/openorgs").toURI())
|
||||
.toFile()
|
||||
.getAbsolutePath();
|
||||
testOutputBasePath = createTempDirectory(SparkOpenorgsTest.class.getSimpleName() + "-")
|
||||
|
|
@ -71,9 +73,8 @@ public class SparkOpenorgsTest implements Serializable {
|
|||
.toAbsolutePath()
|
||||
.toString();
|
||||
|
||||
// FileUtils.deleteDirectory(new File(testOutputBasePath));
|
||||
FileUtils.deleteDirectory(new File(testOutputBasePath));
|
||||
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
|
||||
FileUtils.deleteDirectory(new File("/tmp/test-orchestrator/organization_openorgs_mergerels"));
|
||||
|
||||
final SparkConf conf = new SparkConf();
|
||||
conf.set("spark.sql.shuffle.partitions", "200");
|
||||
|
|
@ -133,7 +134,7 @@ public class SparkOpenorgsTest implements Serializable {
|
|||
.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord")
|
||||
.count();
|
||||
|
||||
assertEquals(0, orgs_deduprecord);
|
||||
assertEquals(100, orgs_deduprecord);
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -161,7 +162,7 @@ public class SparkOpenorgsTest implements Serializable {
|
|||
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
|
||||
.count();
|
||||
|
||||
assertEquals(0, orgs_mergerel);
|
||||
assertEquals(6, orgs_mergerel);
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -190,67 +191,7 @@ public class SparkOpenorgsTest implements Serializable {
|
|||
.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
|
||||
.count();
|
||||
|
||||
System.out.println("orgs_simrel = " + orgs_simrel);
|
||||
}
|
||||
|
||||
@Test
|
||||
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[] {
|
||||
"-i", testGraphBasePath,
|
||||
"-asi", testActionSetId,
|
||||
"-la", "lookupurl",
|
||||
"-w", "/tmp",
|
||||
"-np", "50"
|
||||
});
|
||||
|
||||
new SparkCreateSimRels(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_simrel = spark
|
||||
.read()
|
||||
.textFile("/tmp/" + testActionSetId + "/organization_simrel")
|
||||
.count();
|
||||
|
||||
assertEquals(3082, orgs_simrel);
|
||||
}
|
||||
|
||||
@Test
|
||||
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[] {
|
||||
"-i",
|
||||
testGraphBasePath,
|
||||
"-asi",
|
||||
testActionSetId,
|
||||
"-la",
|
||||
"lookupurl",
|
||||
"-w",
|
||||
"/tmp"
|
||||
});
|
||||
|
||||
new SparkCreateMergeRels(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_mergerel = spark
|
||||
.read()
|
||||
.load("/tmp/" + testActionSetId + "/organization_mergerel")
|
||||
.count();
|
||||
assertEquals(1272, orgs_mergerel);
|
||||
assertEquals(96, orgs_simrel);
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -273,9 +214,7 @@ public class SparkOpenorgsTest implements Serializable {
|
|||
|
||||
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
|
||||
|
||||
// Dataset<Relation> relsRDD = spark.read().textFile(testDedupGraphBasePath + "/relation").map(patchRelFn(), Encoders.bean(Relation.class));
|
||||
|
||||
assertEquals(500, relations);
|
||||
assertEquals(400, relations);
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
|
|
|
|||
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Reference in New Issue