dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/SparkGraphImporterJob.java

package eu.dnetlib.dhp.graph;

import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;

public class SparkGraphImporterJob {

    public static void main(String[] args) throws Exception {

        final ArgumentApplicationParser parser = new ArgumentApplicationParser(
                IOUtils.toString(SparkGraphImporterJob.class.getResourceAsStream(
                        "/eu/dnetlib/dhp/graph/input_graph_parameters.json")));
        parser.parseArgument(args);

        new SparkGraphImporterJob().run(parser);
    }

    private void run(ArgumentApplicationParser parser) {
        try(SparkSession spark = getSparkSession(parser)) {

            final String inputPath = parser.get("sourcePath");
            final String hiveDbName = parser.get("hive_db_name");

            runWith(spark, inputPath, hiveDbName);
        }
    }

    // public for testing
    public void runWith(SparkSession spark, String inputPath, String hiveDbName) {

        spark.sql(String.format("DROP DATABASE IF EXISTS %s CASCADE", hiveDbName));
        spark.sql(String.format("CREATE DATABASE IF NOT EXISTS %s", hiveDbName));

        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
        // Read the input file and convert it into RDD of serializable object
        GraphMappingUtils.types.forEach((name, clazz) -> spark.createDataset(sc.textFile(inputPath + "/" + name)
                .map(s -> new ObjectMapper().readValue(s, clazz))
                .rdd(), Encoders.bean(clazz))
                .write()
                .mode(SaveMode.Overwrite)
                .saveAsTable(hiveDbName + "." + name));
    }

    private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
        SparkConf conf = new SparkConf();
        conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
        return SparkSession
                .builder()
                .appName(SparkGraphImporterJob.class.getSimpleName())
                .master(parser.get("master"))
                .config(conf)
                .enableHiveSupport()
                .getOrCreate();
    }
}