dnet-hadoop/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java

package eu.dnetlib.dhp.oa.graph.raw;

import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;

import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.stream.Collectors;
import java.util.stream.Stream;

import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FilterFunction;
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 org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.fasterxml.jackson.databind.ObjectMapper;

import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;

public class MergeClaimsApplication {

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

	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();

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

		Boolean isSparkSessionManaged = Optional
			.ofNullable(parser.get("isSparkSessionManaged"))
			.map(Boolean::valueOf)
			.orElse(Boolean.TRUE);
		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);

		final String rawGraphPath = parser.get("rawGraphPath");
		log.info("rawGraphPath: {}", rawGraphPath);

		final String claimsGraphPath = parser.get("claimsGraphPath");
		log.info("claimsGraphPath: {}", claimsGraphPath);

		final String outputRawGaphPath = parser.get("outputRawGaphPath");
		log.info("outputRawGaphPath: {}", outputRawGaphPath);

		String graphTableClassName = parser.get("graphTableClassName");
		log.info("graphTableClassName: {}", graphTableClassName);

		Class<? extends Oaf> clazz = (Class<? extends Oaf>) Class.forName(graphTableClassName);

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

		runWithSparkSession(
			conf,
			isSparkSessionManaged,
			spark -> {
				String type = clazz.getSimpleName().toLowerCase();

				String rawPath = rawGraphPath + "/" + type;
				String claimPath = claimsGraphPath + "/" + type;
				String outPath = outputRawGaphPath + "/" + type;

				removeOutputDir(spark, outPath);
				mergeByType(spark, rawPath, claimPath, outPath, clazz);
			});
	}

	private static <T extends Oaf> void mergeByType(
		SparkSession spark, String rawPath, String claimPath, String outPath, Class<T> clazz) {
		Dataset<Tuple2<String, T>> raw = readFromPath(spark, rawPath, clazz)
			.map(
				(MapFunction<T, Tuple2<String, T>>) value -> new Tuple2<>(ModelSupport.idFn().apply(value), value),
				Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));

		final JavaSparkContext jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
		Dataset<Tuple2<String, T>> claim = jsc
			.broadcast(readFromPath(spark, claimPath, clazz))
			.getValue()
			.map(
				(MapFunction<T, Tuple2<String, T>>) value -> new Tuple2<>(ModelSupport.idFn().apply(value), value),
				Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));

		raw
			.joinWith(claim, raw.col("_1").equalTo(claim.col("_1")), "full_outer")
			.map(
				(MapFunction<Tuple2<Tuple2<String, T>, Tuple2<String, T>>, T>) value -> processClaims(
					Optional.ofNullable(value._1()),
					Optional.ofNullable(value._2())),
				Encoders.bean(clazz))
			.filter(Objects::nonNull)
			.map(
				(MapFunction<T, String>) value -> OBJECT_MAPPER.writeValueAsString(value),
				Encoders.STRING())
			.write()
			.mode(SaveMode.Overwrite)
			.option("compression", "gzip")
			.text(outPath);
	}

	private static <T extends Oaf> T processClaims(Optional<Tuple2<String, T>> opRaw,
		Optional<Tuple2<String, T>> opClaim) {

		// when both are present
		if (opClaim.isPresent() && opRaw.isPresent()) {
			T oafClaim = opClaim.get()._2();
			if (oafClaim instanceof Result) {
				T oafRaw = opRaw.get()._2();

				// merge the context lists from both oaf objects ...
				final List<Context> context = mergeContexts((Result) oafClaim, (Result) oafRaw);

				// ... and set it on the result from the aggregator
				((Result) oafRaw).setContext(context);
				return oafRaw;
			}
		}

		// otherwise prefer the result from the aggregator
		return opRaw.isPresent()
			? opRaw.get()._2()
			: opClaim.map(Tuple2::_2).orElse(null);
	}

	private static List<Context> mergeContexts(Result oafClaim, Result oafRaw) {
		return new ArrayList<>(
			Stream
				.concat(
					Optional
						.ofNullable(oafClaim.getContext())
						.map(List::stream)
						.orElse(Stream.empty()),
					Optional
						.ofNullable(oafRaw.getContext())
						.map(List::stream)
						.orElse(Stream.empty()))
				.collect(
					Collectors
						.toMap(
							Context::getId,
							c -> c,
							(c1, c2) -> {
								Context c = new Context();
								c.setId(c1.getId());
								c
									.setDataInfo(
										new ArrayList<>(
											Stream
												.concat(
													Optional
														.ofNullable(c1.getDataInfo())
														.map(List::stream)
														.orElse(Stream.empty()),
													Optional
														.ofNullable(c2.getDataInfo())
														.map(List::stream)
														.orElse(Stream.empty()))
												.collect(
													Collectors
														.toMap(
															d -> Optional
																.ofNullable(d.getProvenanceaction())
																.map(Qualifier::getClassid)
																.orElse(""),
															d -> d,
															(d1, d2) -> d1))
												.values()));
								return c;
							}))
				.values());
	}

	private static <T extends Oaf> Dataset<T> readFromPath(
		SparkSession spark, String path, Class<T> clazz) {
		return spark
			.read()
			.textFile(path)
			.map(
				(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz),
				Encoders.bean(clazz))
			.filter((FilterFunction<T>) value -> Objects.nonNull(ModelSupport.idFn().apply(value)));
	}

	private static void removeOutputDir(SparkSession spark, String path) {
		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
	}
}