dnet-hadoop/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java

package eu.dnetlib.dhp.oa.provision;

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

import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.provision.model.EntityRelEntity;
import eu.dnetlib.dhp.oa.provision.model.TypedRow;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import java.util.List;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
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 scala.Tuple2;
import scala.collection.JavaConverters;
import scala.collection.Seq;

/**
 * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects. The
 * operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization, and
 * all the possible relationships (similarity links produced by the Dedup process are excluded).
 * <p>
 * The operation is implemented by sequentially joining one entity type at time (E) with the relationships (R), and
 * again by E, finally grouped by E.id;
 * <p>
 * The workflow is organized in different parts aimed to to reduce the complexity of the operation 1)
 * PrepareRelationsJob: only consider relationships that are not virtually deleted ($.dataInfo.deletedbyinference ==
 * false), each entity can be linked at most to 100 other objects
 * <p>
 * 2) JoinRelationEntityByTargetJob: (phase 1): prepare tuples [relation - target entity] (R - T): for each entity type
 * E_i map E_i as RelatedEntity T_i to simplify the model and extracting only the necessary information join (R.target =
 * T_i.id) save the tuples (R_i, T_i) (phase 2): create the union of all the entity types E, hash by id read the tuples
 * (R, T), hash by R.source join E.id = (R, T).source, where E becomes the Source Entity S save the tuples (S, R, T)
 * <p>
 * 3) AdjacencyListBuilderJob: given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mapping the
 * result as JoinedEntity
 * <p>
 * 4) XmlConverterJob: convert the JoinedEntities as XML records
 */
public class CreateRelatedEntitiesJob_phase2 {

	private static final Logger log = LoggerFactory.getLogger(CreateRelatedEntitiesJob_phase2.class);

	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();

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

		String jsonConfiguration = IOUtils
			.toString(
				PrepareRelationsJob.class
					.getResourceAsStream(
						"/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase2.json"));
		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
		parser.parseArgument(args);

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

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

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

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

		int numPartitions = Integer.parseInt(parser.get("numPartitions"));
		log.info("numPartitions: {}", numPartitions);

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

		runWithSparkSession(
			conf,
			isSparkSessionManaged,
			spark -> {
				removeOutputDir(spark, outputPath);
				joinAllEntities(
					spark, inputRelatedEntitiesPath, inputGraphRootPath, outputPath, numPartitions);
			});
	}

	private static void joinAllEntities(
		SparkSession spark,
		String inputRelatedEntitiesPath,
		String inputGraphRootPath,
		String outputPath,
		int numPartitions) {

		Dataset<Tuple2<String, TypedRow>> entities = readAllEntities(spark, inputGraphRootPath, numPartitions);
		Dataset<Tuple2<String, EntityRelEntity>> relsBySource = readRelatedEntities(spark, inputRelatedEntitiesPath);

		entities
			.joinWith(relsBySource, entities.col("_1").equalTo(relsBySource.col("_1")), "left_outer")
			.map(
				(MapFunction<Tuple2<Tuple2<String, TypedRow>, Tuple2<String, EntityRelEntity>>, EntityRelEntity>) value -> {
					EntityRelEntity re = new EntityRelEntity();
					re.setEntity(value._1()._2());
					Optional<EntityRelEntity> related = Optional.ofNullable(value._2()).map(Tuple2::_2);
					if (related.isPresent()) {
						re.setRelation(related.get().getRelation());
						re.setTarget(related.get().getTarget());
					}
					return re;
				},
				Encoders.bean(EntityRelEntity.class))
			.repartition(numPartitions)
			.filter(
				(FilterFunction<EntityRelEntity>) value -> value.getEntity() != null
					&& StringUtils.isNotBlank(value.getEntity().getId()))
			.write()
			.mode(SaveMode.Overwrite)
			.parquet(outputPath);
	}

	private static Dataset<Tuple2<String, TypedRow>> readAllEntities(
		SparkSession spark, String inputGraphPath, int numPartitions) {
		Dataset<TypedRow> publication = readPathEntity(spark, inputGraphPath + "/publication", Publication.class);
		Dataset<TypedRow> dataset = readPathEntity(
			spark, inputGraphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class);
		Dataset<TypedRow> other = readPathEntity(
			spark, inputGraphPath + "/otherresearchproduct", OtherResearchProduct.class);
		Dataset<TypedRow> software = readPathEntity(spark, inputGraphPath + "/software", Software.class);
		Dataset<TypedRow> datasource = readPathEntity(spark, inputGraphPath + "/datasource", Datasource.class);
		Dataset<TypedRow> organization = readPathEntity(spark, inputGraphPath + "/organization", Organization.class);
		Dataset<TypedRow> project = readPathEntity(spark, inputGraphPath + "/project", Project.class);

		return publication
			.union(dataset)
			.union(other)
			.union(software)
			.union(datasource)
			.union(organization)
			.union(project)
			.map(
				(MapFunction<TypedRow, Tuple2<String, TypedRow>>) value -> new Tuple2<>(value.getId(), value),
				Encoders.tuple(Encoders.STRING(), Encoders.kryo(TypedRow.class)))
			.repartition(numPartitions);
	}

	private static Dataset<Tuple2<String, EntityRelEntity>> readRelatedEntities(
		SparkSession spark, String inputRelatedEntitiesPath) {

		log.info("Reading related entities from: {}", inputRelatedEntitiesPath);

		final List<String> paths = HdfsSupport
			.listFiles(inputRelatedEntitiesPath, spark.sparkContext().hadoopConfiguration());

		log.info("Found paths: {}", String.join(",", paths));

		return spark
			.read()
			.load(toSeq(paths))
			.as(Encoders.bean(EntityRelEntity.class))
			.map(
				(MapFunction<EntityRelEntity, Tuple2<String, EntityRelEntity>>) value -> new Tuple2<>(
					value.getRelation().getSource(), value),
				Encoders.tuple(Encoders.STRING(), Encoders.kryo(EntityRelEntity.class)));
	}

	private static <E extends OafEntity> Dataset<TypedRow> readPathEntity(
		SparkSession spark, String inputEntityPath, Class<E> entityClazz) {

		log.info("Reading Graph table from: {}", inputEntityPath);
		return spark
			.read()
			.textFile(inputEntityPath)
			.map(
				(MapFunction<String, E>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
				Encoders.bean(entityClazz))
			.filter("dataInfo.invisible == false")
			.map(
				(MapFunction<E, TypedRow>) value -> getTypedRow(
					StringUtils.substringAfterLast(inputEntityPath, "/"), value),
				Encoders.bean(TypedRow.class));
	}

	private static TypedRow getTypedRow(String type, OafEntity entity)
		throws JsonProcessingException {
		TypedRow t = new TypedRow();
		t.setType(type);
		t.setDeleted(entity.getDataInfo().getDeletedbyinference());
		t.setId(entity.getId());
		t.setOaf(OBJECT_MAPPER.writeValueAsString(entity));
		return t;
	}

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

	private static Seq<String> toSeq(List<String> list) {
		return JavaConverters.asScalaIteratorConverter(list.iterator()).asScala().toSeq();
	}
}