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

package eu.dnetlib.dhp.oa.dedup;

import java.io.IOException;

import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;

public class SparkUpdateEntity extends AbstractSparkAction {

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

	private static final String IDJSONPATH = "$.id";

	public SparkUpdateEntity(ArgumentApplicationParser parser, SparkSession spark) {
		super(parser, spark);
	}

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

		SparkConf conf = new SparkConf();
		conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
		conf.registerKryoClasses(ModelSupport.getOafModelClasses());

		new SparkUpdateEntity(parser, getSparkSession(conf))
			.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
	}

	public void run(ISLookUpService isLookUpService) throws IOException {

		final String graphBasePath = parser.get("graphBasePath");
		final String workingPath = parser.get("workingPath");
		final String dedupGraphPath = parser.get("dedupGraphPath");

		log.info("graphBasePath:  '{}'", graphBasePath);
		log.info("workingPath:    '{}'", workingPath);
		log.info("dedupGraphPath: '{}'", dedupGraphPath);

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

		// for each entity
		ModelSupport.entityTypes
			.forEach(
				(type, clazz) -> {
					final String outputPath = dedupGraphPath + "/" + type;
					removeOutputDir(spark, outputPath);

					JavaRDD<String> sourceEntity = sc
						.textFile(DedupUtility.createEntityPath(graphBasePath, type.toString()));

					if (mergeRelExists(workingPath, type.toString())) {

						final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, "*", type.toString());
						final String dedupRecordPath = DedupUtility
							.createDedupRecordPath(workingPath, "*", type.toString());

						final Dataset<Relation> rel = spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class));

						final JavaPairRDD<String, String> mergedIds = rel
							.where("relClass == 'merges'")
							.where("source != target")
							.select(rel.col("target"))
							.distinct()
							.toJavaRDD()
							.mapToPair(
								(PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "d"));

						JavaPairRDD<String, String> entitiesWithId = sourceEntity
							.mapToPair(
								(PairFunction<String, String, String>) s -> new Tuple2<>(
									MapDocumentUtil.getJPathString(IDJSONPATH, s), s));
						JavaRDD<String> map = entitiesWithId
							.leftOuterJoin(mergedIds)
							.map(
								k -> k._2()._2().isPresent()
									? updateDeletedByInference(k._2()._1(), clazz)
									: k._2()._1());

						sourceEntity = map.union(sc.textFile(dedupRecordPath));
					}

					sourceEntity.saveAsTextFile(outputPath, GzipCodec.class);
				});
	}

	public boolean mergeRelExists(String basePath, String entity) {

		boolean result = false;
		try {
			FileSystem fileSystem = FileSystem.get(new Configuration());

			FileStatus[] fileStatuses = fileSystem.listStatus(new Path(basePath));

			for (FileStatus fs : fileStatuses) {
				if (fs.isDirectory())
					if (fileSystem
						.exists(
							new Path(DedupUtility.createMergeRelPath(basePath, fs.getPath().getName(), entity))))
						result = true;
			}

			return result;
		} catch (IOException e) {
			throw new RuntimeException(e);
		}
	}

	private static <T extends OafEntity> String updateDeletedByInference(
		final String json, final Class<T> clazz) {
		try {
			Oaf entity = OBJECT_MAPPER.readValue(json, clazz);
			if (entity.getDataInfo() == null)
				entity.setDataInfo(new DataInfo());
			entity.getDataInfo().setDeletedbyinference(true);
			return OBJECT_MAPPER.writeValueAsString(entity);
		} catch (IOException e) {
			throw new RuntimeException("Unable to convert json", e);
		}
	}
}