dnet-hadoop/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCollectSimRels.java

package eu.dnetlib.dhp.oa.dedup;

import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import java.util.stream.StreamSupport;

import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.sql.*;
import org.dom4j.DocumentException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.config.DedupConfig;
import scala.Tuple2;

public class SparkCollectSimRels extends AbstractSparkAction {

	private static final Logger log = LoggerFactory.getLogger(SparkCollectSimRels.class);

	Dataset<Row> simGroupsDS;
	Dataset<Row> groupsDS;

	public SparkCollectSimRels(ArgumentApplicationParser parser, SparkSession spark, Dataset<Row> simGroupsDS,
		Dataset<Row> groupsDS) {
		super(parser, spark);
		this.simGroupsDS = simGroupsDS;
		this.groupsDS = groupsDS;
	}

	public static void main(String[] args) throws Exception {
		ArgumentApplicationParser parser = new ArgumentApplicationParser(
			IOUtils
				.toString(
					SparkBlockStats.class
						.getResourceAsStream(
							"/eu/dnetlib/dhp/oa/dedup/collectSimRels_parameters.json")));
		parser.parseArgument(args);

		SparkConf conf = new SparkConf();

		final String dbUrl = parser.get("postgresUrl");
		final String dbUser = parser.get("postgresUser");
		final String dbPassword = parser.get("postgresPassword");

		SparkSession spark = getSparkSession(conf);

		DataFrameReader readOptions = spark
			.read()
			.format("jdbc")
			.option("url", dbUrl)
			.option("user", dbUser)
			.option("password", dbPassword);

		new SparkCollectSimRels(
			parser,
			spark,
			readOptions.option("dbtable", "similarity_groups").load(),
			readOptions.option("dbtable", "groups").load())
				.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
	}

	@Override
	void run(ISLookUpService isLookUpService) throws DocumentException, ISLookUpException, IOException {

		// read oozie parameters
		final String isLookUpUrl = parser.get("isLookUpUrl");
		final String actionSetId = parser.get("actionSetId");
		final String workingPath = parser.get("workingPath");
		final int numPartitions = Optional
			.ofNullable(parser.get("numPartitions"))
			.map(Integer::valueOf)
			.orElse(NUM_PARTITIONS);
		final String dbUrl = parser.get("postgresUrl");
		final String dbUser = parser.get("postgresUser");

		log.info("numPartitions: '{}'", numPartitions);
		log.info("isLookUpUrl:   '{}'", isLookUpUrl);
		log.info("actionSetId:   '{}'", actionSetId);
		log.info("workingPath:   '{}'", workingPath);
		log.info("postgresUser: {}", dbUser);
		log.info("postgresUrl: {}", dbUrl);
		log.info("postgresPassword: xxx");

		JavaPairRDD<String, List<String>> similarityGroup = simGroupsDS
			.toJavaRDD()
			.mapToPair(r -> new Tuple2<>(r.getString(0), r.getString(1)))
			.groupByKey()
			.mapToPair(
				i -> new Tuple2<>(i._1(), StreamSupport
					.stream(i._2().spliterator(), false)
					.collect(Collectors.toList())));

		JavaPairRDD<String, String> groupIds = groupsDS
			.toJavaRDD()
			.mapToPair(r -> new Tuple2<>(r.getString(0), r.getString(1)));

		JavaRDD<Tuple2<Tuple2<String, String>, List<String>>> groups = similarityGroup
			.leftOuterJoin(groupIds)
			.filter(g -> g._2()._2().isPresent())
			.map(g -> new Tuple2<>(new Tuple2<>(g._1(), g._2()._2().get()), g._2()._1()));

		JavaRDD<Relation> relations = groups.flatMap(g -> {
			String firstId = g._2().get(0);
			List<Relation> rels = new ArrayList<>();

			for (String id : g._2()) {
				if (!firstId.equals(id))
					rels.add(createSimRel(firstId, id, g._1()._2()));
			}

			return rels.iterator();
		});

		Dataset<Relation> resultRelations = spark
			.createDataset(
				relations.filter(r -> r.getRelType().equals("resultResult")).rdd(),
				Encoders.bean(Relation.class))
			.repartition(numPartitions);

		Dataset<Relation> organizationRelations = spark
			.createDataset(
				relations.filter(r -> r.getRelType().equals("organizationOrganization")).rdd(),
				Encoders.bean(Relation.class))
			.repartition(numPartitions);

		for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) {
			switch (dedupConf.getWf().getSubEntityValue()) {
				case "organization":
					savePostgresRelation(organizationRelations, workingPath, actionSetId, "organization");
					break;
				default:
					savePostgresRelation(
						resultRelations, workingPath, actionSetId, dedupConf.getWf().getSubEntityValue());
					break;
			}
		}

	}

	private Relation createSimRel(String source, String target, String entity) {
		final Relation r = new Relation();
		r.setSubRelType("dedupSimilarity");
		r.setRelClass("isSimilarTo");
		r.setDataInfo(new DataInfo());

		switch (entity) {
			case "result":
				r.setSource("50|" + source);
				r.setTarget("50|" + target);
				r.setRelType("resultResult");
				break;
			case "organization":
				r.setSource("20|" + source);
				r.setTarget("20|" + target);
				r.setRelType("organizationOrganization");
				break;
			default:
				throw new IllegalArgumentException("unmanaged entity type: " + entity);
		}
		return r;
	}

	private void savePostgresRelation(Dataset<Relation> newRelations, String workingPath, String actionSetId,
		String entityType) {
		newRelations
			.write()
			.mode(SaveMode.Append)
			.parquet(DedupUtility.createSimRelPath(workingPath, actionSetId, entityType));
	}

}