no need to filter relations in CreateRelatedEntitiesJob_phase1; replaced 'left outer' join with 'left' join in CreateRelatedEntitiesJob_phase2; cleanup;

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java

@@ -1,91 +0,0 @@
-
-package eu.dnetlib.dhp.oa.provision;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Optional;
-import java.util.stream.Collectors;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.api.java.function.MapGroupsFunction;
-import org.apache.spark.sql.*;
-import org.apache.spark.sql.expressions.Aggregator;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.oa.provision.model.*;
-import scala.Tuple2;
-import scala.collection.JavaConverters;
-import scala.collection.Seq;
-
-/**
- * AdjacencyListBuilderJob: given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mapping the
- * result as JoinedEntity
- */
-public class AdjacencyListBuilderJob {
-
-	private static final Logger log = LoggerFactory.getLogger(AdjacencyListBuilderJob.class);
-
-	public static final int MAX_LINKS = 100;
-
-	public static void main(String[] args) throws Exception {
-
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
-			IOUtils
-				.toString(
-					AdjacencyListBuilderJob.class
-						.getResourceAsStream(
-							"/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json")));
-		parser.parseArgument(args);
-
-		Boolean isSparkSessionManaged = Optional
-			.ofNullable(parser.get("isSparkSessionManaged"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
-
-		String inputPath = parser.get("inputPath");
-		log.info("inputPath: {}", inputPath);
-
-		String outputPath = parser.get("outputPath");
-		log.info("outputPath: {}", outputPath);
-
-		SparkConf conf = new SparkConf();
-		conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
-		conf.registerKryoClasses(ProvisionModelSupport.getModelClasses());
-
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-				removeOutputDir(spark, outputPath);
-				createAdjacencyListsKryo(spark, inputPath, outputPath);
-			});
-	}
-
-	private static void createAdjacencyListsKryo(
-		SparkSession spark, String inputPath, String outputPath) {
-
-		log.info("Reading joined entities from: {}", inputPath);
-
-		final List<String> paths = HdfsSupport
-			.listFiles(inputPath, spark.sparkContext().hadoopConfiguration());
-
-		log.info("Found paths: {}", String.join(",", paths));
-
-	}
-
-	private static Seq<String> toSeq(List<String> list) {
-		return JavaConverters.asScalaIteratorConverter(list.iterator()).asScala().toSeq();
-	}
-
-	private static void removeOutputDir(SparkSession spark, String path) {
-		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
-	}
-}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java

@@ -92,7 +92,6 @@ public class CreateRelatedEntitiesJob_phase1 {
 		String outputPath) {
 
 		Dataset<Tuple2<String, Relation>> relsByTarget = readPathRelation(spark, inputRelationsPath)
-			.filter("dataInfo.deletedbyinference == false")
 			.map(
 				(MapFunction<Relation, Tuple2<String, Relation>>) r -> new Tuple2<>(r.getTarget(),
 					r),

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

@@ -105,7 +105,7 @@ public class CreateRelatedEntitiesJob_phase2 {
 		TypedColumn<JoinedEntity, JoinedEntity> aggregator = new AdjacencyListAggregator().toColumn();
 
 		entities
-			.joinWith(relatedEntities, entities.col("_1").equalTo(relatedEntities.col("_1")), "left_outer")
+			.joinWith(relatedEntities, entities.col("_1").equalTo(relatedEntities.col("_1")), "left")
 			.map((MapFunction<Tuple2<Tuple2<String, E>, Tuple2<String, RelatedEntityWrapper>>, JoinedEntity>) value -> {
 				JoinedEntity je = new JoinedEntity(value._1()._2());
 				Optional
@@ -114,7 +114,6 @@ public class CreateRelatedEntitiesJob_phase2 {
 					.ifPresent(r -> je.getLinks().add(r));
 				return je;
 			}, Encoders.kryo(JoinedEntity.class))
-			.filter(filterEmptyEntityFn())
 			.groupByKey(
 				(MapFunction<JoinedEntity, String>) value -> value.getEntity().getId(),
 				Encoders.STRING())
@@ -122,7 +121,6 @@ public class CreateRelatedEntitiesJob_phase2 {
 			.map(
 				(MapFunction<Tuple2<String, JoinedEntity>, JoinedEntity>) value -> value._2(),
 				Encoders.kryo(JoinedEntity.class))
-			.filter(filterEmptyEntityFn())
 			.write()
 			.mode(SaveMode.Overwrite)
 			.parquet(outputPath);

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java

@@ -3,8 +3,10 @@ package eu.dnetlib.dhp.oa.provision;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
-import java.util.*;
+import java.util.HashSet;
-import java.util.function.Supplier;
+import java.util.Optional;
+import java.util.PriorityQueue;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
@@ -15,8 +17,10 @@ import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.api.java.function.Function;
 import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.rdd.RDD;
+import org.apache.spark.sql.Encoder;
-import org.apache.spark.sql.*;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
 import org.apache.spark.sql.expressions.Aggregator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -24,7 +28,6 @@ import org.slf4j.LoggerFactory;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.base.Splitter;
 import com.google.common.collect.Iterables;
-import com.google.common.collect.Maps;
 import com.google.common.collect.Sets;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;