From 8047d16dd9f56787ad469746839f86d70facdadc Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 27 May 2020 12:38:12 +0200
Subject: [PATCH] added RDD based adjacency list creation procedure

---
 .../oa/provision/AdjacencyListBuilderJob.java | 40 ++++++++++++++++++-
 1 file changed, 39 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java
index 99247b7562..9f221ae45c 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java
@@ -9,14 +9,20 @@ import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.function.Function2;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.api.java.function.MapGroupsFunction;
+import org.apache.spark.api.java.function.PairFunction;
+import org.apache.spark.rdd.RDD;
 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.google.common.collect.Lists;
+
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.oa.provision.model.EntityRelEntity;
@@ -83,7 +89,7 @@ public class AdjacencyListBuilderJob {
 			isSparkSessionManaged,
 			spark -> {
 				removeOutputDir(spark, outputPath);
-				createAdjacencyLists(spark, inputPath, outputPath);
+				createAdjacencyListsRDD(spark, inputPath, outputPath);
 			});
 	}
 
@@ -118,6 +124,38 @@ public class AdjacencyListBuilderJob {
 			.parquet(outputPath);
 	}
 
+	private static void createAdjacencyListsRDD(
+		SparkSession spark, String inputPath, String outputPath) {
+
+		log.info("Reading joined entities from: {}", inputPath);
+		RDD<JoinedEntity> joinedEntities = spark
+			.read()
+			.load(inputPath)
+			.as(Encoders.bean(EntityRelEntity.class))
+			.javaRDD()
+			.mapToPair(re -> {
+				JoinedEntity je = new JoinedEntity();
+				je.setEntity(re.getEntity());
+				je.setLinks(Lists.newArrayList());
+				if (re.getRelation() != null && re.getTarget() != null) {
+					je.getLinks().add(new Tuple2(re.getRelation(), re.getTarget()));
+				}
+				return new scala.Tuple2<>(re.getEntity().getId(), je);
+			})
+			.reduceByKey((je1, je2) -> {
+				je1.getLinks().addAll(je2.getLinks());
+				return je1;
+			})
+			.map(t -> t._2())
+			.rdd();
+
+		spark
+			.createDataset(joinedEntities, Encoders.bean(JoinedEntity.class))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.parquet(outputPath);
+	}
+
 	private static void removeOutputDir(SparkSession spark, String path) {
 		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
 	}