dnet-hadoop/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateScholix.java

package eu.dnetlib.dhp.provision;

import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.provision.scholix.*;
import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary;
import eu.dnetlib.dhp.schema.oaf.Relation;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import scala.Tuple2;

public class SparkGenerateScholix {


    public static void main(String[] args) throws Exception {
        final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkGenerateScholix.class.getResourceAsStream("/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json")));
        parser.parseArgument(args);
        SparkConf conf = new SparkConf();
        conf.set("spark.sql.shuffle.partitions","4000");
        conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
        final SparkSession spark = SparkSession
                .builder()
                .config(conf)
                .appName(SparkExtractRelationCount.class.getSimpleName())
                .master(parser.get("master"))
                .getOrCreate();

        conf.registerKryoClasses(new Class[]{
                Scholix.class,
                ScholixCollectedFrom.class,
                ScholixEntityId.class,
                ScholixIdentifier.class,
                ScholixRelationship.class,
                ScholixResource.class
        });



        final String graphPath = parser.get("graphPath");
        final String workingDirPath = parser.get("workingDirPath");

        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());

        final Dataset<ScholixSummary> scholixSummary = spark.read().load(workingDirPath + "/summary").as(Encoders.bean(ScholixSummary.class));
        final Dataset<Relation>  rels = spark.read().load(graphPath + "/relation").as(Encoders.bean(Relation.class));


        Dataset<Scholix> firstJoin = scholixSummary.joinWith(rels, scholixSummary.col("id").equalTo(rels.col("source")))
                .map((MapFunction<Tuple2<ScholixSummary, Relation>, Scholix>) f -> Scholix.generateScholixWithSource(f._1(), f._2()), Encoders.bean(Scholix.class));

        firstJoin.write().mode(SaveMode.Overwrite).save(workingDirPath+"/scholix_1");

        Dataset<Scholix> scholix_final = spark.read().load(workingDirPath+"/scholix_1").as(Encoders.bean(Scholix.class));

        scholixSummary
                .map((MapFunction<ScholixSummary, ScholixResource>) ScholixResource::fromSummary, Encoders.bean(ScholixResource.class))
                .repartition(1000)
                .write()
                .mode(SaveMode.Overwrite)
                .save(workingDirPath+"/scholix_target");

        Dataset<ScholixResource> target = spark.read().load(workingDirPath+"/scholix_target").as(Encoders.bean(ScholixResource.class));

        scholix_final.joinWith(target, scholix_final.col("identifier").equalTo(target.col("dnetIdentifier")), "inner")
                .map((MapFunction<Tuple2<Scholix, ScholixResource>, Scholix>) f -> {
                    final Scholix scholix = f._1();
                    final ScholixResource scholixTarget = f._2();
                    scholix.setTarget(scholixTarget);
                    scholix.generateIdentifier();
                    scholix.generatelinkPublisher();
                    return scholix;
                }, Encoders.kryo(Scholix.class)).javaRDD().map(s-> {
            ObjectMapper mapper = new ObjectMapper();
            return mapper.writeValueAsString(s);
        }).saveAsTextFile(workingDirPath+"/scholix_json", GzipCodec.class);
    }
}