106 lines
3.7 KiB
Java
106 lines
3.7 KiB
Java
package eu.dnetlib.jobs;
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import eu.dnetlib.Deduper;
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import eu.dnetlib.graph.JavaGraphProcessor;
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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 eu.dnetlib.pace.utils.Utility;
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import eu.dnetlib.support.ArgumentApplicationParser;
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import eu.dnetlib.support.ConnectedComponent;
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import eu.dnetlib.support.Relation;
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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.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.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import scala.Tuple2;
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import java.io.IOException;
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import java.util.Optional;
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import static eu.dnetlib.Deduper.hash;
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public class SparkCreateMergeRels extends AbstractSparkJob {
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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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Utility.readResource("/jobs/parameters/createMergeRels_parameters.json", SparkCreateMergeRels.class)
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);
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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new SparkCreateMergeRels(
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parser,
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getSparkSession(conf)
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).run();
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}
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@Override
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public void run() throws IOException {
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// read oozie parameters
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final String entitiesPath = parser.get("entitiesPath");
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final String workingPath = parser.get("workingPath");
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final String dedupConfPath = parser.get("dedupConfPath");
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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("entitiesPath: '{}'", entitiesPath);
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log.info("workingPath: '{}'", workingPath);
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log.info("dedupConfPath: '{}'", dedupConfPath);
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log.info("numPartitions: '{}'", numPartitions);
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DedupConfig dedupConf = DedupConfig.load(readFileFromHDFS(dedupConfPath));
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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final JavaPairRDD<Object, String> vertexes = sc
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.textFile(entitiesPath)
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.map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s))
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.mapToPair((PairFunction<String, Object, String>) s -> new Tuple2<>(hash(s), s));
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final JavaRDD<Edge<String>> edgeRdd = spark
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.read()
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.load(workingPath + "/simrels")
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.as(Encoders.bean(Relation.class))
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.javaRDD()
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.map(Relation::toEdgeRdd);
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JavaRDD<ConnectedComponent> ccs = JavaGraphProcessor
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.findCCs(vertexes, edgeRdd, dedupConf.getWf().getMaxIterations())
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.toJavaRDD();
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JavaRDD<Relation> mergeRel = ccs
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.filter(k -> k.getDocs().size() > 1)
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.flatMap(cc -> Deduper.ccToMergeRel(cc, dedupConf))
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.map(it -> new Relation(it._1(), it._2(), "mergeRel"));
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final Dataset<Relation> mergeRels = spark
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.createDataset(
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mergeRel.rdd(),
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Encoders.bean(Relation.class));
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mergeRels.write().mode(SaveMode.Overwrite).parquet(workingPath + "/mergerels");
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}
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}
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