minor changes
miconis
3 years ago
parent
1a85020572
commit
98854b0124
@ -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);
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info.setInferenceprovenance(dedupConf.getWf().getConfigurationId());
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Qualifier provenanceAction = new Qualifier();
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provenanceAction.setClassid(PROVENANCE_ACTION_CLASS);
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provenanceAction.setClassname(PROVENANCE_ACTION_CLASS);
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provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS);
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provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS);
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info.setProvenanceaction(provenanceAction);
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// TODO calculate the trust value based on the similarity score of the elements in the CC
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// info.setTrust();
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r.setDataInfo(info);
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return r;
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}
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}
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