248 lines
8.8 KiB
Java
248 lines
8.8 KiB
Java
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package eu.dnetlib.dhp.oa.dedup;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVENANCE_DEDUP;
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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 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.JavaSparkContext;
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import org.apache.spark.api.java.function.FlatMapFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.MapGroupsFunction;
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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.Lists;
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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.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.Identifier;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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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.util.MapDocumentUtil;
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import scala.Tuple2;
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public class SparkCreateMergeRels extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class);
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public SparkCreateMergeRels(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/createCC_parameters.json")));
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parser.parseArgument(args);
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final String isLookUpUrl = parser.get("isLookUpUrl");
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log.info("isLookupUrl {}", isLookUpUrl);
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SparkConf conf = new SparkConf();
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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 SparkCreateMergeRels(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(isLookUpUrl));
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}
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@Override
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public void run(ISLookUpService isLookUpService)
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throws ISLookUpException, DocumentException, IOException {
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final String graphBasePath = parser.get("graphBasePath");
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final String workingPath = parser.get("workingPath");
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final String isLookUpUrl = parser.get("isLookUpUrl");
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final String actionSetId = parser.get("actionSetId");
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int cut = Optional
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.ofNullable(parser.get("cutConnectedComponent"))
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.map(Integer::valueOf)
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.orElse(0);
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log.info("connected component cut: '{}'", cut);
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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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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) {
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final String subEntity = dedupConf.getWf().getSubEntityValue();
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final Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
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log.info("Creating mergerels for: '{}'", subEntity);
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final int maxIterations = dedupConf.getWf().getMaxIterations();
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log.info("Max iterations {}", maxIterations);
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final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity);
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// <hash(id), id>
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JavaPairRDD<Object, String> vertexes = createVertexes(sc, graphBasePath, subEntity, dedupConf);
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final RDD<Edge<String>> edgeRdd = spark
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.read()
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.load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity))
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.as(Encoders.bean(Relation.class))
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.javaRDD()
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.map(it -> new Edge<>(hash(it.getSource()), hash(it.getTarget()), it.getRelClass()))
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.rdd();
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Dataset<Tuple2<String, String>> rawMergeRels = spark
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.createDataset(
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GraphProcessor
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.findCCs(vertexes.rdd(), edgeRdd, maxIterations, cut)
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.toJavaRDD()
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.filter(k -> k.getIds().size() > 1)
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.flatMap(this::ccToRels)
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.rdd(),
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Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
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Dataset<Tuple2<String, OafEntity>> entities = spark
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.read()
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.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
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.map(
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(MapFunction<String, Tuple2<String, OafEntity>>) it -> {
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OafEntity entity = OBJECT_MAPPER.readValue(it, clazz);
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return new Tuple2<>(entity.getId(), entity);
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},
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Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
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Dataset<Relation> mergeRels = rawMergeRels
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.joinWith(entities, rawMergeRels.col("_2").equalTo(entities.col("_1")), "inner")
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// <tmp_source,target>,<target,entity>
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.map(
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(MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, OafEntity>>, Tuple2<String, OafEntity>>) value -> new Tuple2<>(
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value._1()._1(), value._2()._2()),
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Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)))
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// <tmp_source,entity>
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.groupByKey(
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(MapFunction<Tuple2<String, OafEntity>, String>) Tuple2::_1, Encoders.STRING())
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.mapGroups(
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(MapGroupsFunction<String, Tuple2<String, OafEntity>, ConnectedComponent>) this::generateID,
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Encoders.bean(ConnectedComponent.class))
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// <root_id, list(target)>
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.flatMap(
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(FlatMapFunction<ConnectedComponent, Relation>) cc -> ccToMergeRel(cc, dedupConf),
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Encoders.bean(Relation.class));
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mergeRels.write().mode(SaveMode.Overwrite).parquet(mergeRelPath);
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}
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}
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private <T extends OafEntity> ConnectedComponent generateID(String key, Iterator<Tuple2<String, T>> values) {
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List<Identifier<T>> identifiers = Lists.newArrayList(values).stream().map(v -> {
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T entity = v._2();
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Identifier<T> identifier = Identifier.newInstance(entity);
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return identifier;
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}).collect(Collectors.toList());
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String rootID = IdGenerator.generate(identifiers, key);
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if (Objects.equals(rootID, key))
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throw new IllegalStateException("generated default ID: " + rootID);
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return new ConnectedComponent(rootID,
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identifiers.stream().map(i -> i.getEntity().getId()).collect(Collectors.toSet()));
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}
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private JavaPairRDD<Object, String> createVertexes(JavaSparkContext sc, String graphBasePath, String subEntity,
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DedupConfig dedupConf) {
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return sc
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.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
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.mapToPair(json -> {
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String id = MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), json);
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return new Tuple2<>(hash(id), id);
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});
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}
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private Iterator<Tuple2<String, String>> ccToRels(ConnectedComponent cc) {
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return cc
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.getIds()
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.stream()
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.map(id -> new Tuple2<>(cc.getCcId(), id))
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.iterator();
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}
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private Iterator<Relation> ccToMergeRel(ConnectedComponent cc, DedupConfig dedupConf) {
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return cc
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.getIds()
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.stream()
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.flatMap(
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id -> {
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List<Relation> tmp = new ArrayList<>();
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tmp.add(rel(cc.getCcId(), id, ModelConstants.MERGES, dedupConf));
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tmp.add(rel(id, cc.getCcId(), ModelConstants.IS_MERGED_IN, dedupConf));
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return tmp.stream();
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})
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.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(ModelConstants.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_DEDUP);
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provenanceAction.setClassname(PROVENANCE_DEDUP);
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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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public static long hash(final String id) {
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return Hashing.murmur3_128().hashString(id).asLong();
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}
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}
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