forked from D-Net/dnet-hadoop
101 lines
4.8 KiB
Java
101 lines
4.8 KiB
Java
package eu.dnetlib.dhp.dedup;
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import com.google.common.hash.Hashing;
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import eu.dnetlib.dhp.dedup.graph.ConnectedComponent;
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import eu.dnetlib.dhp.dedup.graph.GraphProcessor;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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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 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.FlatMapFunction;
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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.SparkSession;
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import org.dom4j.DocumentException;
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import scala.Tuple2;
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import java.util.ArrayList;
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import java.util.List;
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public class SparkCreateConnectedComponent {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/createCC_parameters.json")));
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parser.parseArgument(args);
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new SparkCreateConnectedComponent().run(parser);
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}
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private void run(ArgumentApplicationParser parser) throws ISLookUpException, DocumentException {
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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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try (SparkSession spark = getSparkSession(parser)) {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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for (DedupConfig dedupConf: DedupUtility.getConfigurations(isLookUpUrl, 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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final JavaPairRDD<Object, String> vertexes = sc.textFile(graphBasePath + "/" + subEntity)
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.map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s))
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.mapToPair((PairFunction<String, Object, String>)
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s -> new Tuple2<Object, String>(getHashcode(s), s)
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);
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final Dataset<Relation> similarityRelations = spark.read().load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)).as(Encoders.bean(Relation.class));
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final RDD<Edge<String>> edgeRdd = similarityRelations.javaRDD().map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass())).rdd();
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final JavaRDD<ConnectedComponent> cc = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, dedupConf.getWf().getMaxIterations()).toJavaRDD();
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final Dataset<Relation> mergeRelation = spark.createDataset(cc.filter(k -> k.getDocIds().size() > 1).flatMap((FlatMapFunction<ConnectedComponent, Relation>) c ->
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c.getDocIds()
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.stream()
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.flatMap(id -> {
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List<Relation> tmp = new ArrayList<>();
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Relation r = new Relation();
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r.setSource(c.getCcId());
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r.setTarget(id);
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r.setRelClass("merges");
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tmp.add(r);
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r = new Relation();
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r.setTarget(c.getCcId());
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r.setSource(id);
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r.setRelClass("isMergedIn");
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tmp.add(r);
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return tmp.stream();
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}).iterator()).rdd(), Encoders.bean(Relation.class));
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mergeRelation.write().mode("overwrite").save(DedupUtility.createMergeRelPath(workingPath, actionSetId, entity));
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}
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}
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}
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public static long getHashcode(final String id) {
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return Hashing.murmur3_128().hashString(id).asLong();
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}
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private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
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SparkConf conf = new SparkConf();
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return SparkSession
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.builder()
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.appName(SparkCreateSimRels.class.getSimpleName())
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.master(parser.get("master"))
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.config(conf)
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.enableHiveSupport()
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.getOrCreate();
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}
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}
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