95 lines
3.5 KiB
Java
95 lines
3.5 KiB
Java
package eu.dnetlib.jobs;
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import eu.dnetlib.Deduper;
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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 eu.dnetlib.pace.utils.Utility;
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import eu.dnetlib.support.ArgumentApplicationParser;
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import eu.dnetlib.support.Block;
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import eu.dnetlib.support.Relation;
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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.PairFunction;
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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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public class SparkCreateSimRels extends AbstractSparkJob {
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private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class);
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public SparkCreateSimRels(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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readResource("/jobs/parameters/createSimRels_parameters.json", SparkCreateSimRels.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 SparkCreateSimRels(
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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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final boolean useTree = Boolean.parseBoolean(parser.get("useTree"));
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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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log.info("useTree: '{}'", useTree);
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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DedupConfig dedupConfig = loadDedupConfig(dedupConfPath);
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JavaPairRDD<String, MapDocument> mapDocuments = sc
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.textFile(entitiesPath)
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.mapToPair(
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(PairFunction<String, String, MapDocument>) s -> {
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MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConfig, s);
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return new Tuple2<>(d.getIdentifier(), d);
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});
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// create blocks for deduplication
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JavaPairRDD<String, Block> blocks = Deduper.createSortedBlocks(mapDocuments, dedupConfig);
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// create relations by comparing only elements in the same group
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JavaRDD<Relation> relations = Deduper.computeRelations(sc, blocks, dedupConfig, useTree);
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// save the simrel in the workingdir
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spark
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.createDataset(relations.rdd(), Encoders.bean(Relation.class))
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.write()
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.mode(SaveMode.Overwrite)
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.save(workingPath + "/simrels");
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}
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}
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