Merge branch 'beta' into importpoci

dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/DispatchEntitiesSparkJob.java

@@ -1,97 +0,0 @@
-
-package eu.dnetlib.dhp.oa.merge;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.util.Objects;
-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.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-
-public class DispatchEntitiesSparkJob {
-
-	private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesSparkJob.class);
-
-	public static void main(String[] args) throws Exception {
-
-		String jsonConfiguration = IOUtils
-			.toString(
-				Objects
-					.requireNonNull(
-						DispatchEntitiesSparkJob.class
-							.getResourceAsStream(
-								"/eu/dnetlib/dhp/oa/merge/dispatch_entities_parameters.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 inputPath = parser.get("inputPath");
-		log.info("inputPath: {}", inputPath);
-
-		String outputPath = parser.get("outputPath");
-		log.info("outputPath: {}", outputPath);
-
-		boolean filterInvisible = Boolean.parseBoolean(parser.get("filterInvisible"));
-		log.info("filterInvisible: {}", filterInvisible);
-
-		SparkConf conf = new SparkConf();
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> dispatchEntities(spark, inputPath, outputPath, filterInvisible));
-	}
-
-	private static void dispatchEntities(
-		SparkSession spark,
-		String inputPath,
-		String outputPath,
-		boolean filterInvisible) {
-
-		Dataset<String> df = spark.read().textFile(inputPath);
-
-		ModelSupport.oafTypes.entrySet().parallelStream().forEach(entry -> {
-			String entityType = entry.getKey();
-			Class<?> clazz = entry.getValue();
-
-			final String entityPath = outputPath + "/" + entityType;
-			if (!entityType.equalsIgnoreCase("relation")) {
-				HdfsSupport.remove(entityPath, spark.sparkContext().hadoopConfiguration());
-				Dataset<Row> entityDF = spark
-					.read()
-					.schema(Encoders.bean(clazz).schema())
-					.json(
-						df
-							.filter((FilterFunction<String>) s -> s.startsWith(clazz.getName()))
-							.map(
-								(MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"),
-								Encoders.STRING()));
-
-				if (filterInvisible) {
-					entityDF = entityDF.filter("dataInfo.invisible != true");
-				}
-
-				entityDF
-					.write()
-					.mode(SaveMode.Overwrite)
-					.option("compression", "gzip")
-					.json(entityPath);
-			}
-		});
-	}
-}

dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java

@@ -2,36 +2,28 @@
 package eu.dnetlib.dhp.oa.merge;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import static eu.dnetlib.dhp.utils.DHPUtils.toSeq;
+import static org.apache.spark.sql.functions.col;
+import static org.apache.spark.sql.functions.when;
 
-import java.io.IOException;
+import java.util.Map;
-import java.util.List;
-import java.util.Objects;
 import java.util.Optional;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ForkJoinPool;
 import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
 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.api.java.function.ReduceFunction;
 import org.apache.spark.sql.*;
-import org.apache.spark.sql.expressions.Aggregator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.jayway.jsonpath.Configuration;
-import com.jayway.jsonpath.DocumentContext;
-import com.jayway.jsonpath.JsonPath;
-import com.jayway.jsonpath.Option;
-
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import scala.Tuple2;
 
@@ -39,13 +31,9 @@ import scala.Tuple2;
  * Groups the graph content by entity identifier to ensure ID uniqueness
  */
 public class GroupEntitiesSparkJob {
-
 	private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class);
 
-	private static final String ID_JPATH = "$.id";
+	private static final Encoder<OafEntity> OAFENTITY_KRYO_ENC =  Encoders.kryo(OafEntity.class);
-
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
-		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
 
 	public static void main(String[] args) throws Exception {
 
@@ -66,9 +54,15 @@ public class GroupEntitiesSparkJob {
 		String graphInputPath = parser.get("graphInputPath");
 		log.info("graphInputPath: {}", graphInputPath);
 
+		String checkpointPath = parser.get("checkpointPath");
+		log.info("checkpointPath: {}", checkpointPath);
+
 		String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
+		boolean filterInvisible = Boolean.valueOf(parser.get("filterInvisible"));
+		log.info("filterInvisible: {}", filterInvisible);
+
 		SparkConf conf = new SparkConf();
 		conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
 		conf.registerKryoClasses(ModelSupport.getOafModelClasses());
@@ -78,126 +72,95 @@ public class GroupEntitiesSparkJob {
 			isSparkSessionManaged,
 			spark -> {
 				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
-				groupEntities(spark, graphInputPath, outputPath);
+				groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible);
 			});
 	}
 
 	private static void groupEntities(
 		SparkSession spark,
 		String inputPath,
-		String outputPath) {
+		String checkpointPath,
+		String outputPath,
+		boolean filterInvisible) {
+
+		Dataset<OafEntity> allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC);
+
+		for (Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
+			String entity = e.getKey().name();
+			Class<? extends OafEntity> entityClass = e.getValue();
+			String entityInputPath = inputPath + "/" + entity;
+
+			if (!HdfsSupport.exists(entityInputPath, spark.sparkContext().hadoopConfiguration())) {
+				continue;
+			}
+
+			allEntities = allEntities
+				.union(
+					((Dataset<OafEntity>) spark
+						.read()
+						.schema(Encoders.bean(entityClass).schema())
+						.json(entityInputPath)
+						.filter("length(id) > 0")
+						.as(Encoders.bean(entityClass)))
+							.map((MapFunction<OafEntity, OafEntity>) r -> r, OAFENTITY_KRYO_ENC));
+		}
+
+		Dataset<?> groupedEntities = allEntities
+			.groupByKey((MapFunction<OafEntity, String>) OafEntity::getId, Encoders.STRING())
+			.reduceGroups((ReduceFunction<OafEntity>) (b, a) -> OafMapperUtils.mergeEntities(b, a))
+			.map(
+				(MapFunction<Tuple2<String, OafEntity>, Tuple2<String, OafEntity>>) t -> new Tuple2(
+					t._2().getClass().getName(), t._2()),
+				Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC));
+
+		// pivot on "_1" (classname of the entity)
+		// created columns  containing only entities of the same class
+		for (Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
+			String entity = e.getKey().name();
+			Class<? extends OafEntity> entityClass = e.getValue();
+
+			groupedEntities = groupedEntities
+				.withColumn(
+					entity,
+					when(col("_1").equalTo(entityClass.getName()), col("_2")));
+		}
+
+		groupedEntities
+			.drop("_1", "_2")
+			.write()
+			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
+			.save(checkpointPath);
+
+		ForkJoinPool parPool = new ForkJoinPool(ModelSupport.entityTypes.size());
+
+		ModelSupport.entityTypes
+			.entrySet()
+			.stream()
+			.map(e -> parPool.submit(() -> {
+				String entity = e.getKey().name();
+				Class<? extends OafEntity> entityClass = e.getValue();
 
-		final TypedColumn<OafEntity, OafEntity> aggregator = new GroupingAggregator().toColumn();
-		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 				spark
 					.read()
-			.textFile(toSeq(listEntityPaths(inputPath, sc)))
+					.load(checkpointPath)
-			.map((MapFunction<String, OafEntity>) GroupEntitiesSparkJob::parseOaf, Encoders.kryo(OafEntity.class))
+					.select(col(entity).as("value"))
-			.filter((FilterFunction<OafEntity>) e -> StringUtils.isNotBlank(ModelSupport.idFn().apply(e)))
+					.filter("value IS NOT NULL")
-			.groupByKey((MapFunction<OafEntity, String>) oaf -> ModelSupport.idFn().apply(oaf), Encoders.STRING())
+					.as(OAFENTITY_KRYO_ENC)
-			.agg(aggregator)
+					.map((MapFunction<OafEntity, OafEntity>) r -> r, (Encoder<OafEntity>) Encoders.bean(entityClass))
-			.map(
+					.filter(filterInvisible ? "dataInfo.invisible != TRUE" : "TRUE")
-				(MapFunction<Tuple2<String, OafEntity>, String>) t -> t._2().getClass().getName() +
-					"|" + OBJECT_MAPPER.writeValueAsString(t._2()),
-				Encoders.STRING())
 					.write()
-			.option("compression", "gzip")
 					.mode(SaveMode.Overwrite)
-			.text(outputPath);
+					.option("compression", "gzip")
-	}
+					.json(outputPath + "/" + entity);
-
+			}))
-	public static class GroupingAggregator extends Aggregator<OafEntity, OafEntity, OafEntity> {
+			.collect(Collectors.toList())
-
+			.forEach(t -> {
-		@Override
-		public OafEntity zero() {
-			return null;
-		}
-
-		@Override
-		public OafEntity reduce(OafEntity b, OafEntity a) {
-			return mergeAndGet(b, a);
-		}
-
-		private OafEntity mergeAndGet(OafEntity b, OafEntity a) {
-			if (Objects.nonNull(a) && Objects.nonNull(b)) {
-				return OafMapperUtils.mergeEntities(b, a);
-			}
-			return Objects.isNull(a) ? b : a;
-		}
-
-		@Override
-		public OafEntity merge(OafEntity b, OafEntity a) {
-			return mergeAndGet(b, a);
-		}
-
-		@Override
-		public OafEntity finish(OafEntity j) {
-			return j;
-		}
-
-		@Override
-		public Encoder<OafEntity> bufferEncoder() {
-			return Encoders.kryo(OafEntity.class);
-		}
-
-		@Override
-		public Encoder<OafEntity> outputEncoder() {
-			return Encoders.kryo(OafEntity.class);
-		}
-
-	}
-
-	private static OafEntity parseOaf(String s) {
-
-		DocumentContext dc = JsonPath
-			.parse(s, Configuration.defaultConfiguration().addOptions(Option.SUPPRESS_EXCEPTIONS));
-		final String id = dc.read(ID_JPATH);
-		if (StringUtils.isNotBlank(id)) {
-
-			String prefix = StringUtils.substringBefore(id, "|");
-			switch (prefix) {
-				case "10":
-					return parse(s, Datasource.class);
-				case "20":
-					return parse(s, Organization.class);
-				case "40":
-					return parse(s, Project.class);
-				case "50":
-					String resultType = dc.read("$.resulttype.classid");
-					switch (resultType) {
-						case "publication":
-							return parse(s, Publication.class);
-						case "dataset":
-							return parse(s, eu.dnetlib.dhp.schema.oaf.Dataset.class);
-						case "software":
-							return parse(s, Software.class);
-						case "other":
-							return parse(s, OtherResearchProduct.class);
-						default:
-							throw new IllegalArgumentException(String.format("invalid resultType: '%s'", resultType));
-					}
-				default:
-					throw new IllegalArgumentException(String.format("invalid id prefix: '%s'", prefix));
-			}
-		} else {
-			throw new IllegalArgumentException(String.format("invalid oaf: '%s'", s));
-		}
-	}
-
-	private static <T extends OafEntity> OafEntity parse(String s, Class<T> clazz) {
 				try {
-			return OBJECT_MAPPER.readValue(s, clazz);
+					t.get();
-		} catch (IOException e) {
+				} catch (InterruptedException | ExecutionException e) {
-			throw new IllegalArgumentException(e);
+					throw new RuntimeException(e);
 				}
+			});
 	}
-
-	private static List<String> listEntityPaths(String inputPath, JavaSparkContext sc) {
-		return HdfsSupport
-			.listFiles(inputPath, sc.hadoopConfiguration())
-			.stream()
-			.filter(f -> !f.toLowerCase().contains("relation"))
-			.collect(Collectors.toList());
-	}
-
 }

dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/dispatch_entities_parameters.json

@@ -1,26 +0,0 @@
-[
-  {
-    "paramName": "issm",
-    "paramLongName": "isSparkSessionManaged",
-    "paramDescription": "when true will stop SparkSession after job execution",
-    "paramRequired": false
-  },
-  {
-    "paramName": "i",
-    "paramLongName": "inputPath",
-    "paramDescription": "the source path",
-    "paramRequired": true
-  },
-  {
-    "paramName": "o",
-    "paramLongName": "outputPath",
-    "paramDescription": "path of the output graph",
-    "paramRequired": true
-  },
-  {
-    "paramName": "fi",
-    "paramLongName": "filterInvisible",
-    "paramDescription": "if true filters out invisible entities",
-    "paramRequired": true
-  }
-]

dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json

@@ -8,13 +8,25 @@
   {
     "paramName": "gin",
     "paramLongName": "graphInputPath",
-    "paramDescription": "the graph root path",
+    "paramDescription": "the input graph root path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "cp",
+    "paramLongName": "checkpointPath",
+    "paramDescription": "checkpoint directory",
     "paramRequired": true
   },
   {
     "paramName": "out",
     "paramLongName": "outputPath",
-    "paramDescription": "the output merged graph root path",
+    "paramDescription": "the output graph root path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "fi",
+    "paramLongName": "filterInvisible",
+    "paramDescription": "if true filters out invisible entities",
     "paramRequired": true
   }
 ]

dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala

@@ -81,7 +81,7 @@ case class SparkModel(conf: DedupConfig) {
               MapDocumentUtil.truncateList(
                 MapDocumentUtil.getJPathList(fdef.getPath, documentContext, fdef.getType),
                 fdef.getSize
-              ).toArray
+              ).asScala
 
             case Type.StringConcat =>
               val jpaths = CONCAT_REGEX.split(fdef.getPath)

dhp-pace-core/src/main/java/eu/dnetlib/pace/util/MapDocumentUtil.java

@@ -117,6 +117,11 @@ public class MapDocumentUtil {
 			return result;
 		}
 
+		if (type == Type.List && jresult instanceof List) {
+			((List<?>) jresult).forEach(x -> result.add(x.toString()));
+			return result;
+		}
+
 		if (jresult instanceof JSONArray) {
 			((JSONArray) jresult).forEach(it -> {
 				try {

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/TrustUtils.java

@@ -2,7 +2,9 @@
 package eu.dnetlib.dhp.broker.oa.util;
 
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 
+import org.apache.commons.io.IOUtils;
 import org.apache.spark.sql.Row;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -27,10 +29,14 @@ public class TrustUtils {
 	static {
 		mapper = new ObjectMapper();
 		try {
-			dedupConfig = mapper
+			dedupConfig = DedupConfig
-				.readValue(
+				.load(
-					DedupConfig.class.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/dedupConfig/dedupConfig.json"),
+					IOUtils
-					DedupConfig.class);
+						.toString(
+							DedupConfig.class
+								.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/dedupConfig/dedupConfig.json"),
+							StandardCharsets.UTF_8));
+
 			deduper = new SparkDeduper(dedupConfig);
 		} catch (final IOException e) {
 			log.error("Error loading dedupConfig, e");
@@ -57,7 +63,7 @@ public class TrustUtils {
 			return TrustUtils.rescale(score, threshold);
 		} catch (final Exception e) {
 			log.error("Error computing score between results", e);
-			return BrokerConstants.MIN_TRUST;
+			throw new RuntimeException(e);
 		}
 	}
 

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/RelationAggregator.java

@@ -1,57 +0,0 @@
-
-package eu.dnetlib.dhp.oa.dedup;
-
-import java.util.Objects;
-
-import org.apache.spark.sql.Encoder;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.expressions.Aggregator;
-
-import eu.dnetlib.dhp.schema.oaf.Relation;
-
-public class RelationAggregator extends Aggregator<Relation, Relation, Relation> {
-
-	private static final Relation ZERO = new Relation();
-
-	@Override
-	public Relation zero() {
-		return ZERO;
-	}
-
-	@Override
-	public Relation reduce(Relation b, Relation a) {
-		return mergeRel(b, a);
-	}
-
-	@Override
-	public Relation merge(Relation b, Relation a) {
-		return mergeRel(b, a);
-	}
-
-	@Override
-	public Relation finish(Relation r) {
-		return r;
-	}
-
-	private Relation mergeRel(Relation b, Relation a) {
-		if (Objects.equals(b, ZERO)) {
-			return a;
-		}
-		if (Objects.equals(a, ZERO)) {
-			return b;
-		}
-
-		b.mergeFrom(a);
-		return b;
-	}
-
-	@Override
-	public Encoder<Relation> bufferEncoder() {
-		return Encoders.kryo(Relation.class);
-	}
-
-	@Override
-	public Encoder<Relation> outputEncoder() {
-		return Encoders.kryo(Relation.class);
-	}
-}

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCleanRelation.scala

@@ -1,78 +0,0 @@
-package eu.dnetlib.dhp.oa.dedup
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetlib.dhp.common.HdfsSupport
-import eu.dnetlib.dhp.schema.oaf.Relation
-import eu.dnetlib.dhp.utils.ISLookupClientFactory
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService
-import org.apache.commons.io.IOUtils
-import org.apache.spark.SparkConf
-import org.apache.spark.sql._
-import org.apache.spark.sql.functions.col
-import org.apache.spark.sql.types.{DataTypes, StructField, StructType}
-import org.slf4j.LoggerFactory
-
-object SparkCleanRelation {
-  private val log = LoggerFactory.getLogger(classOf[SparkCleanRelation])
-
-  @throws[Exception]
-  def main(args: Array[String]): Unit = {
-    val parser = new ArgumentApplicationParser(
-      IOUtils.toString(
-        classOf[SparkCleanRelation].getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json")
-      )
-    )
-    parser.parseArgument(args)
-    val conf = new SparkConf
-
-    new SparkCleanRelation(parser, AbstractSparkAction.getSparkSession(conf))
-      .run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")))
-  }
-}
-
-class SparkCleanRelation(parser: ArgumentApplicationParser, spark: SparkSession)
-    extends AbstractSparkAction(parser, spark) {
-  override def run(isLookUpService: ISLookUpService): Unit = {
-    val graphBasePath = parser.get("graphBasePath")
-    val inputPath = parser.get("inputPath")
-    val outputPath = parser.get("outputPath")
-
-    SparkCleanRelation.log.info("graphBasePath: '{}'", graphBasePath)
-    SparkCleanRelation.log.info("inputPath: '{}'", inputPath)
-    SparkCleanRelation.log.info("outputPath: '{}'", outputPath)
-
-    AbstractSparkAction.removeOutputDir(spark, outputPath)
-
-    val entities =
-      Seq("datasource", "project", "organization", "publication", "dataset", "software", "otherresearchproduct")
-
-    val idsSchema = StructType.fromDDL("`id` STRING, `dataInfo` STRUCT<`deletedbyinference`:BOOLEAN,`invisible`:BOOLEAN>")
-
-    val emptyIds = spark.createDataFrame(spark.sparkContext.emptyRDD[Row].setName("empty"),
-      idsSchema)
-
-    val ids = entities
-      .foldLeft(emptyIds)((ds, entity) => {
-        val entityPath = graphBasePath + '/' + entity
-        if (HdfsSupport.exists(entityPath, spark.sparkContext.hadoopConfiguration)) {
-          ds.union(spark.read.schema(idsSchema).json(entityPath))
-        } else {
-          ds
-        }
-      })
-      .filter("dataInfo.deletedbyinference != true AND dataInfo.invisible != true")
-      .select("id")
-      .distinct()
-
-    val relations = spark.read.schema(Encoders.bean(classOf[Relation]).schema).json(inputPath)
-      .filter("dataInfo.deletedbyinference != true AND dataInfo.invisible != true")
-
-    AbstractSparkAction.save(
-      relations
-        .join(ids, col("source") === ids("id"), "leftsemi")
-        .join(ids, col("target") === ids("id"), "leftsemi"),
-      outputPath,
-      SaveMode.Overwrite
-    )
-  }
-}

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java

@@ -3,23 +3,19 @@ package eu.dnetlib.dhp.oa.dedup;
 
 import static org.apache.spark.sql.functions.col;
 
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.Objects;
-
-import org.apache.commons.beanutils.BeanUtils;
 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.api.java.function.ReduceFunction;
 import org.apache.spark.sql.*;
+import org.apache.spark.sql.catalyst.encoders.RowEncoder;
+import org.apache.spark.sql.types.StructType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.DataInfo;
@@ -70,73 +66,63 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 		log.info("workingPath: '{}'", workingPath);
 		log.info("graphOutputPath: '{}'", graphOutputPath);
 
-		final String outputRelationPath = DedupUtility.createEntityPath(graphOutputPath, "relation");
-		removeOutputDir(spark, outputRelationPath);
-
 		Dataset<Relation> mergeRels = spark
 				.read()
 				.load(DedupUtility.createMergeRelPath(workingPath, "*", "*"))
 				.as(REL_BEAN_ENC);
 
 		// <mergedObjectID, dedupID>
-		Dataset<Row> mergedIds = mergeRels
+		Dataset<Row> idsToMerge = mergeRels
 				.where(col("relClass").equalTo(ModelConstants.MERGES))
 				.select(col("source").as("dedupID"), col("target").as("mergedObjectID"))
-			.distinct()
+				.distinct();
-			.cache();
 
 		Dataset<Row> allRels = spark
 				.read()
 				.schema(REL_BEAN_ENC.schema())
-			.json(DedupUtility.createEntityPath(graphBasePath, "relation"));
+				.json(graphBasePath + "/relation");
 
 		Dataset<Relation> dedupedRels = allRels
-			.joinWith(mergedIds, allRels.col("source").equalTo(mergedIds.col("mergedObjectID")), "left_outer")
+				.joinWith(idsToMerge, allRels.col("source").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
-			.joinWith(mergedIds, col("_1.target").equalTo(mergedIds.col("mergedObjectID")), "left_outer")
+				.joinWith(idsToMerge, col("_1.target").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
 				.select("_1._1", "_1._2.dedupID", "_2.dedupID")
 				.as(Encoders.tuple(REL_BEAN_ENC, Encoders.STRING(), Encoders.STRING()))
-			.flatMap(SparkPropagateRelation::addInferredRelations, REL_KRYO_ENC);
+				.map((MapFunction<Tuple3<Relation, String, String>, Relation>) t -> {
-
+					Relation rel = t._1();
-		Dataset<Relation> processedRelations = distinctRelations(
-			dedupedRels.union(mergeRels.map((MapFunction<Relation, Relation>) r -> r, REL_KRYO_ENC)))
-				.filter((FilterFunction<Relation>) r -> !Objects.equals(r.getSource(), r.getTarget()));
-
-		save(processedRelations, outputRelationPath, SaveMode.Overwrite);
-	}
-
-	private static Iterator<Relation> addInferredRelations(Tuple3<Relation, String, String> t) throws Exception {
-		Relation existingRel = t._1();
 					String newSource = t._2();
 					String newTarget = t._3();
 
-		if (newSource == null && newTarget == null) {
+					if (rel.getDataInfo() == null) {
-			return Collections.singleton(t._1()).iterator();
+						rel.setDataInfo(new DataInfo());
 					}
 
-		// update existing relation
+					if (newSource != null || newTarget != null) {
-		if (existingRel.getDataInfo() == null) {
+						rel.getDataInfo().setDeletedbyinference(false);
-			existingRel.setDataInfo(new DataInfo());
-		}
-		existingRel.getDataInfo().setDeletedbyinference(true);
-
-		// Create new relation inferred by dedupIDs
-		Relation inferredRel = (Relation) BeanUtils.cloneBean(existingRel);
-
-		inferredRel.setDataInfo((DataInfo) BeanUtils.cloneBean(existingRel.getDataInfo()));
-		inferredRel.getDataInfo().setDeletedbyinference(false);
 
 						if (newSource != null)
-			inferredRel.setSource(newSource);
+							rel.setSource(newSource);
 
 						if (newTarget != null)
-			inferredRel.setTarget(newTarget);
+							rel.setTarget(newTarget);
-
-		return Arrays.asList(existingRel, inferredRel).iterator();
 					}
 
-	private Dataset<Relation> distinctRelations(Dataset<Relation> rels) {
+					return rel;
-		return rels
+				}, REL_BEAN_ENC);
-			.filter(getRelationFilterFunction())
+
+		// ids of records that are both not deletedbyinference and not invisible
+		Dataset<Row> ids = validIds(spark, graphBasePath);
+
+		// filter relations that point to valid records, can force them to be visible
+		Dataset<Relation> cleanedRels = dedupedRels
+				.join(ids, col("source").equalTo(ids.col("id")), "leftsemi")
+				.join(ids, col("target").equalTo(ids.col("id")), "leftsemi")
+				.as(REL_BEAN_ENC)
+				.map((MapFunction<Relation, Relation>) r -> {
+					r.getDataInfo().setInvisible(false);
+					return r;
+				}, REL_KRYO_ENC);
+
+		Dataset<Relation> distinctRels = cleanedRels
 			.groupByKey(
 				(MapFunction<Relation, String>) r -> String
 					.join(" ", r.getSource(), r.getTarget(), r.getRelType(), r.getSubRelType(), r.getRelClass()),
@@ -146,13 +132,33 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 				return b;
 			})
 			.map((MapFunction<Tuple2<String, Relation>, Relation>) Tuple2::_2, REL_BEAN_ENC);
+
+		final String outputRelationPath = graphOutputPath + "/relation";
+		removeOutputDir(spark, outputRelationPath);
+		save(
+			distinctRels
+				.union(mergeRels)
+				.filter("source != target AND dataInfo.deletedbyinference != true AND dataInfo.invisible != true"),
+			outputRelationPath,
+			SaveMode.Overwrite);
 	}
 
-	private FilterFunction<Relation> getRelationFilterFunction() {
+	static Dataset<Row> validIds(SparkSession spark, String graphBasePath) {
-		return r -> StringUtils.isNotBlank(r.getSource()) ||
+		StructType idsSchema = StructType
-			StringUtils.isNotBlank(r.getTarget()) ||
+			.fromDDL("`id` STRING, `dataInfo` STRUCT<`deletedbyinference`:BOOLEAN,`invisible`:BOOLEAN>");
-			StringUtils.isNotBlank(r.getRelType()) ||
+
-			StringUtils.isNotBlank(r.getSubRelType()) ||
+		Dataset<Row> allIds = spark.emptyDataset(RowEncoder.apply(idsSchema));
-			StringUtils.isNotBlank(r.getRelClass());
+
+		for (EntityType entityType : ModelSupport.entityTypes.keySet()) {
+			String entityPath = graphBasePath + '/' + entityType.name();
+			if (HdfsSupport.exists(entityPath, spark.sparkContext().hadoopConfiguration())) {
+				allIds = allIds.union(spark.read().schema(idsSchema).json(entityPath));
+			}
+		}
+
+		return allIds
+			.filter("dataInfo.deletedbyinference != true AND dataInfo.invisible != true")
+			.select("id")
+			.distinct();
 	}
 }

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json

@@ -1,20 +0,0 @@
-[
-  {
-    "paramName": "i",
-    "paramLongName": "graphBasePath",
-    "paramDescription": "the base path of raw graph",
-    "paramRequired": true
-  },
-  {
-    "paramName": "w",
-    "paramLongName": "inputPath",
-    "paramDescription": "the path to the input relation to cleanup",
-    "paramRequired": true
-  },
-  {
-    "paramName": "o",
-    "paramLongName": "outputPath",
-    "paramDescription": "the path of the output relation cleaned",
-    "paramRequired": true
-  }
-]

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml

@@ -100,35 +100,9 @@
                 --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--graphOutputPath</arg><arg>${workingPath}/propagaterelation/</arg>
+            <arg>--graphOutputPath</arg><arg>${graphOutputPath}</arg>
             <arg>--workingPath</arg><arg>${workingPath}</arg>
         </spark>
-        <ok to="CleanRelation"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="CleanRelation">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean Relations</name>
-            <class>eu.dnetlib.dhp.oa.dedup.SparkCleanRelation</class>
-            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemoryOverhead}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=15000
-            </spark-opts>
-            <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--inputPath</arg><arg>${workingPath}/propagaterelation/relation</arg>
-            <arg>--outputPath</arg><arg>${graphOutputPath}/relation</arg>
-        </spark>
         <ok to="group_entities"/>
         <error to="Kill"/>
     </action>
@@ -152,31 +126,7 @@
                 --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
-            <arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>
+            <arg>--checkpointPath</arg><arg>${workingPath}/grouped_entities</arg>
-        </spark>
-        <ok to="dispatch_entities"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="dispatch_entities">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Dispatch grouped entitities</name>
-            <class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
-            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemoryOverhead}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
             <arg>--outputPath</arg><arg>${graphOutputPath}</arg>
             <arg>--filterInvisible</arg><arg>${filterInvisible}</arg>
         </spark>

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java

@@ -3,7 +3,6 @@ package eu.dnetlib.dhp.oa.dedup;
 
 import static java.nio.file.Files.createTempDirectory;
 
-import static org.apache.spark.sql.functions.col;
 import static org.apache.spark.sql.functions.count;
 import static org.junit.jupiter.api.Assertions.*;
 import static org.mockito.Mockito.lenient;
@@ -23,14 +22,13 @@ import java.util.stream.Collectors;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 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.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.api.java.function.PairFunction;
-import org.apache.spark.sql.*;
 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.junit.jupiter.api.*;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.mockito.Mock;
@@ -46,8 +44,6 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
-import eu.dnetlib.pace.util.MapDocumentUtil;
-import scala.Tuple2;
 
 @ExtendWith(MockitoExtension.class)
 @TestMethodOrder(MethodOrderer.OrderAnnotation.class)
@@ -62,6 +58,8 @@ public class SparkDedupTest implements Serializable {
 	private static String testGraphBasePath;
 	private static String testOutputBasePath;
 	private static String testDedupGraphBasePath;
+	private static String testConsistencyGraphBasePath;
+
 	private static final String testActionSetId = "test-orchestrator";
 	private static String whitelistPath;
 	private static List<String> whiteList;
@@ -75,6 +73,7 @@ public class SparkDedupTest implements Serializable {
 			.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI())
 			.toFile()
 			.getAbsolutePath();
+
 		testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
 			.toAbsolutePath()
 			.toString();
@@ -83,6 +82,10 @@ public class SparkDedupTest implements Serializable {
 			.toAbsolutePath()
 			.toString();
 
+		testConsistencyGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
+			.toAbsolutePath()
+			.toString();
+
 		whitelistPath = Paths
 			.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/whitelist.simrels.txt").toURI())
 			.toFile()
@@ -674,22 +677,45 @@ public class SparkDedupTest implements Serializable {
 		assertEquals(mergedOrp, deletedOrp);
 	}
 
+	@Test
+	@Order(6)
+	void copyRelationsNoOpenorgsTest() throws Exception {
+
+		ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					SparkCopyRelationsNoOpenorgs.class
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
+		parser
+			.parseArgument(
+				new String[] {
+					"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
+				});
+
+		new SparkCopyRelationsNoOpenorgs(parser, spark).run(isLookUpService);
+
+		final Dataset<Row> outputRels = spark.read().text(testDedupGraphBasePath + "/relation");
+
+		System.out.println(outputRels.count());
+		// assertEquals(2382, outputRels.count());
+	}
+
 	@Test
 	@Order(7)
 	void propagateRelationTest() throws Exception {
 
 		ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"));
-		String outputRelPath = testDedupGraphBasePath + "/propagaterelation";
 		parser
 			.parseArgument(
 				new String[] {
-					"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", outputRelPath
+					"-i", testDedupGraphBasePath, "-w", testOutputBasePath, "-o", testConsistencyGraphBasePath
 				});
 
 		new SparkPropagateRelation(parser, spark).run(isLookUpService);
 
-		long relations = jsc.textFile(outputRelPath + "/relation").count();
+		long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
 
 //		assertEquals(4860, relations);
 		System.out.println("relations = " + relations);
@@ -699,95 +725,52 @@ public class SparkDedupTest implements Serializable {
 			.read()
 			.load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*"))
 			.as(Encoders.bean(Relation.class));
-		final JavaPairRDD<String, String> mergedIds = mergeRels
-			.where("relClass == 'merges'")
-			.select(mergeRels.col("target"))
-			.distinct()
-			.toJavaRDD()
-			.mapToPair(
-				(PairFunction<Row, String, String>) r -> new Tuple2<String, String>(r.getString(0), "d"));
 
-		JavaRDD<String> toCheck = jsc
+		Dataset<Row> inputRels = spark
-			.textFile(outputRelPath + "/relation")
+			.read()
-			.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json))
+			.json(testDedupGraphBasePath + "/relation");
-			.join(mergedIds)
-			.map(t -> t._2()._1())
-			.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json))
-			.join(mergedIds)
-			.map(t -> t._2()._1());
 
-		long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
+		Dataset<Row> outputRels = spark
-		long updated = toCheck.count();
+			.read()
+			.json(testConsistencyGraphBasePath + "/relation");
 
-		assertEquals(updated, deletedbyinference);
+		assertEquals(
+			0, outputRels
+				.filter("dataInfo.deletedbyinference == true OR dataInfo.invisible == true")
+				.count());
+
+		assertEquals(
+			5, outputRels
+				.filter("relClass NOT IN ('merges', 'isMergedIn')")
+				.count());
+
+		assertEquals(5 + mergeRels.count(), outputRels.count());
 	}
 
 	@Test
 	@Order(8)
-	void testCleanBaseRelations() throws Exception {
+	void testCleanedPropagatedRelations() throws Exception {
-		ArgumentApplicationParser parser = new ArgumentApplicationParser(
-			classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json"));
-
-		// append dangling relations to be cleaned up
 		Dataset<Row> df_before = spark
 			.read()
 			.schema(Encoders.bean(Relation.class).schema())
-			.json(testGraphBasePath + "/relation");
+			.json(testDedupGraphBasePath + "/relation");
-		Dataset<Row> df_input = df_before
-			.unionByName(df_before.drop("source").withColumn("source", functions.lit("n/a")))
-			.unionByName(df_before.drop("target").withColumn("target", functions.lit("n/a")));
-		df_input.write().mode(SaveMode.Overwrite).json(testOutputBasePath + "_tmp");
-
-		parser
-			.parseArgument(
-				new String[] {
-					"--graphBasePath", testGraphBasePath,
-					"--inputPath", testGraphBasePath + "/relation",
-					"--outputPath", testDedupGraphBasePath + "/relation"
-				});
-
-		new SparkCleanRelation(parser, spark).run(isLookUpService);
 
 		Dataset<Row> df_after = spark
 			.read()
 			.schema(Encoders.bean(Relation.class).schema())
-			.json(testDedupGraphBasePath + "/relation");
+			.json(testConsistencyGraphBasePath + "/relation");
-
-		assertNotEquals(df_before.count(), df_input.count());
-		assertNotEquals(df_input.count(), df_after.count());
-		assertEquals(5, df_after.count());
-	}
-
-	@Test
-	@Order(9)
-	void testCleanDedupedRelations() throws Exception {
-		ArgumentApplicationParser parser = new ArgumentApplicationParser(
-			classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json"));
-
-		String inputRelPath = testDedupGraphBasePath + "/propagaterelation/relation";
-
-		// append dangling relations to be cleaned up
-		Dataset<Row> df_before = spark.read().schema(Encoders.bean(Relation.class).schema()).json(inputRelPath);
-
-		df_before.filter(col("dataInfo.deletedbyinference").notEqual(true)).show(50, false);
-
-		parser
-			.parseArgument(
-				new String[] {
-					"--graphBasePath", testGraphBasePath,
-					"--inputPath", inputRelPath,
-					"--outputPath", testDedupGraphBasePath + "/relation"
-				});
-
-		new SparkCleanRelation(parser, spark).run(isLookUpService);
-
-		Dataset<Row> df_after = spark
-			.read()
-			.schema(Encoders.bean(Relation.class).schema())
-			.json(testDedupGraphBasePath + "/relation");
 
 		assertNotEquals(df_before.count(), df_after.count());
-		assertEquals(0, df_after.count());
+
+		assertEquals(
+			0, df_after
+				.filter("dataInfo.deletedbyinference == true OR dataInfo.invisible == true")
+				.count());
+
+		assertEquals(
+			5, df_after
+				.filter("relClass NOT IN ('merges', 'isMergedIn')")
+				.count());
 	}
 
 	@Test
@@ -813,6 +796,7 @@ public class SparkDedupTest implements Serializable {
 	public static void finalCleanUp() throws IOException {
 		FileUtils.deleteDirectory(new File(testOutputBasePath));
 		FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
+		FileUtils.deleteDirectory(new File(testConsistencyGraphBasePath));
 	}
 
 	public boolean isDeletedByInference(String s) {

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsProvisionTest.java

@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.dedup;
 
 import static java.nio.file.Files.createTempDirectory;
 
+import static org.apache.spark.sql.functions.col;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.Mockito.lenient;
 
@@ -15,10 +16,6 @@ import java.nio.file.Paths;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 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.PairFunction;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.Row;
@@ -33,8 +30,6 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
-import eu.dnetlib.pace.util.MapDocumentUtil;
-import scala.Tuple2;
 
 @ExtendWith(MockitoExtension.class)
 @TestMethodOrder(MethodOrderer.OrderAnnotation.class)
@@ -44,11 +39,11 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 	ISLookUpService isLookUpService;
 
 	private static SparkSession spark;
-	private static JavaSparkContext jsc;
 
 	private static String testGraphBasePath;
 	private static String testOutputBasePath;
 	private static String testDedupGraphBasePath;
+	private static String testConsistencyGraphBasePath;
 	private static final String testActionSetId = "test-orchestrator";
 
 	@BeforeAll
@@ -64,6 +59,9 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 		testDedupGraphBasePath = createTempDirectory(SparkOpenorgsProvisionTest.class.getSimpleName() + "-")
 			.toAbsolutePath()
 			.toString();
+		testConsistencyGraphBasePath = createTempDirectory(SparkOpenorgsProvisionTest.class.getSimpleName() + "-")
+			.toAbsolutePath()
+			.toString();
 
 		FileUtils.deleteDirectory(new File(testOutputBasePath));
 		FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
@@ -76,8 +74,13 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 			.master("local[*]")
 			.config(conf)
 			.getOrCreate();
+	}
 
-		jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+	@AfterAll
+	public static void finalCleanUp() throws IOException {
+		FileUtils.deleteDirectory(new File(testOutputBasePath));
+		FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
+		FileUtils.deleteDirectory(new File(testConsistencyGraphBasePath));
 	}
 
 	@BeforeEach
@@ -186,26 +189,21 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 
 		new SparkUpdateEntity(parser, spark).run(isLookUpService);
 
-		long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
+		Dataset<Row> organizations = spark.read().json(testDedupGraphBasePath + "/organization");
 
-		long mergedOrgs = spark
+		Dataset<Row> mergedOrgs = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
-			.as(Encoders.bean(Relation.class))
 			.where("relClass=='merges'")
-			.javaRDD()
+			.select("target")
-			.map(Relation::getTarget)
+			.distinct();
-			.distinct()
-			.count();
 
-		assertEquals(80, organizations);
+		assertEquals(80, organizations.count());
 
-		long deletedOrgs = jsc
+		Dataset<Row> deletedOrgs = organizations
-			.textFile(testDedupGraphBasePath + "/organization")
+			.filter("dataInfo.deletedbyinference = TRUE");
-			.filter(this::isDeletedByInference)
-			.count();
 
-		assertEquals(mergedOrgs, deletedOrgs);
+		assertEquals(mergedOrgs.count(), deletedOrgs.count());
 	}
 
 	@Test
@@ -226,10 +224,9 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 
 		new SparkCopyRelationsNoOpenorgs(parser, spark).run(isLookUpService);
 
-		final JavaRDD<String> rels = jsc.textFile(testDedupGraphBasePath + "/relation");
+		final Dataset<Row> outputRels = spark.read().text(testDedupGraphBasePath + "/relation");
-
-		assertEquals(2382, rels.count());
 
+		assertEquals(2382, outputRels.count());
 	}
 
 	@Test
@@ -244,51 +241,41 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 		parser
 			.parseArgument(
 				new String[] {
-					"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
+					"-i", testDedupGraphBasePath, "-w", testOutputBasePath, "-o", testConsistencyGraphBasePath
 				});
 
 		new SparkPropagateRelation(parser, spark).run(isLookUpService);
 
-		long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
-
-		assertEquals(4896, relations);
-
-		// check deletedbyinference
 		final Dataset<Relation> mergeRels = spark
 			.read()
 			.load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*"))
 			.as(Encoders.bean(Relation.class));
-		final JavaPairRDD<String, String> mergedIds = mergeRels
+
+		Dataset<Row> inputRels = spark
+			.read()
+			.json(testDedupGraphBasePath + "/relation");
+
+		Dataset<Row> outputRels = spark
+			.read()
+			.json(testConsistencyGraphBasePath + "/relation");
+
+		final Dataset<Row> mergedIds = mergeRels
 			.where("relClass == 'merges'")
-			.select(mergeRels.col("target"))
+			.select(col("target").as("id"))
-			.distinct()
+			.distinct();
-			.toJavaRDD()
-			.mapToPair(
-				(PairFunction<Row, String, String>) r -> new Tuple2<String, String>(r.getString(0), "d"));
 
-		JavaRDD<String> toCheck = jsc
+		Dataset<Row> toUpdateRels = inputRels
-			.textFile(testDedupGraphBasePath + "/relation")
+			.as("rel")
-			.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json))
+			.join(mergedIds.as("s"), col("rel.source").equalTo(col("s.id")), "left_outer")
-			.join(mergedIds)
+			.join(mergedIds.as("t"), col("rel.target").equalTo(col("t.id")), "left_outer")
-			.map(t -> t._2()._1())
+			.filter("s.id IS NOT NULL OR t.id IS NOT NULL")
-			.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json))
+			.distinct();
-			.join(mergedIds)
-			.map(t -> t._2()._1());
 
-		long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
+		Dataset<Row> updatedRels = inputRels
-		long updated = toCheck.count();
+			.select("source", "target", "relClass")
+			.except(outputRels.select("source", "target", "relClass"));
 
-		assertEquals(updated, deletedbyinference);
+		assertEquals(toUpdateRels.count(), updatedRels.count());
+		assertEquals(140, outputRels.count());
 	}
-
-	@AfterAll
-	public static void finalCleanUp() throws IOException {
-		FileUtils.deleteDirectory(new File(testOutputBasePath));
-		FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
-	}
-
-	public boolean isDeletedByInference(String s) {
-		return s.contains("\"deletedbyinference\":true");
-	}
-
 }

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml

@@ -96,30 +96,7 @@
                 --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
-            <arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>
+            <arg>--checkpointPath</arg><arg>${workingPath}/grouped_entities</arg>
-        </spark>
-        <ok to="dispatch_entities"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="dispatch_entities">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Dispatch grouped entities</name>
-            <class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
             <arg>--outputPath</arg><arg>${graphOutputPath}</arg>
             <arg>--filterInvisible</arg><arg>${filterInvisible}</arg>
         </spark>

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java

@@ -1,16 +1,15 @@
 
 package eu.dnetlib.dhp.oa.graph.group;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import com.fasterxml.jackson.databind.DeserializationFeature;
-
+import com.fasterxml.jackson.databind.ObjectMapper;
-import java.io.IOException;
+import eu.dnetlib.dhp.common.HdfsSupport;
-import java.net.URISyntaxException;
+import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
-import java.nio.file.Files;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
-import java.nio.file.Path;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
-import java.nio.file.Paths;
+import eu.dnetlib.dhp.schema.oaf.Result;
-
+import eu.dnetlib.dhp.utils.DHPUtils;
 import org.apache.commons.io.FileUtils;
-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;
@@ -19,15 +18,13 @@ import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
 import org.junit.jupiter.api.*;
 
-import com.fasterxml.jackson.databind.DeserializationFeature;
+import java.io.IOException;
-import com.fasterxml.jackson.databind.ObjectMapper;
+import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 
-import eu.dnetlib.dhp.common.HdfsSupport;
+import static org.junit.jupiter.api.Assertions.assertEquals;
-import eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob;
-import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.Result;
-import eu.dnetlib.dhp.utils.DHPUtils;
 
 @TestMethodOrder(MethodOrderer.OrderAnnotation.class)
 public class GroupEntitiesSparkJobTest {
@@ -40,8 +37,9 @@ public class GroupEntitiesSparkJobTest {
     private static Path workingDir;
     private Path dataInputPath;
 
-	private Path groupEntityPath;
+    private Path checkpointPath;
-	private Path dispatchEntityPath;
+
+    private Path outputPath;
 
     @BeforeAll
     public static void beforeAll() throws IOException {
@@ -58,8 +56,8 @@ public class GroupEntitiesSparkJobTest {
     @BeforeEach
     public void beforeEach() throws IOException, URISyntaxException {
         dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI());
-		groupEntityPath = workingDir.resolve("grouped_entity");
+        checkpointPath = workingDir.resolve("grouped_entity");
-		dispatchEntityPath = workingDir.resolve("dispatched_entity");
+        outputPath = workingDir.resolve("dispatched_entity");
     }
 
     @AfterAll
@@ -71,44 +69,35 @@ public class GroupEntitiesSparkJobTest {
     @Test
     @Order(1)
     void testGroupEntities() throws Exception {
-		GroupEntitiesSparkJob.main(new String[] {
+        GroupEntitiesSparkJob.main(new String[]{
                 "-isSparkSessionManaged",
                 Boolean.FALSE.toString(),
                 "-graphInputPath",
                 dataInputPath.toString(),
+                "-checkpointPath",
+                checkpointPath.toString(),
                 "-outputPath",
-			groupEntityPath.toString()
+                outputPath.toString(),
+                "-filterInvisible",
+                Boolean.FALSE.toString()
         });
 
-		Dataset<Result> output = spark
+        Dataset<OafEntity> checkpointTable = spark
                 .read()
-			.textFile(groupEntityPath.toString())
+                .load(checkpointPath.toString())
-			.map((MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"), Encoders.STRING())
+                .selectExpr("COALESCE(*)")
-			.map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
+                .as(Encoders.kryo(OafEntity.class));
+
 
         assertEquals(
                 1,
-			output
+                checkpointTable
                         .filter(
-					(FilterFunction<Result>) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9"
+                                (FilterFunction<OafEntity>) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9"
                                         .equals(r.getId()) &&
                                         r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")))
                         .count());
-	}
 
-	@Test
-	@Order(2)
-	void testDispatchEntities() throws Exception {
-		DispatchEntitiesSparkJob.main(new String[] {
-			"-isSparkSessionManaged",
-			Boolean.FALSE.toString(),
-			"-inputPath",
-			groupEntityPath.toString(),
-			"-outputPath",
-			dispatchEntityPath.resolve(".").toString(),
-			"-filterInvisible",
-			Boolean.TRUE.toString()
-		});
 
         Dataset<Result> output = spark
                 .read()
@@ -116,7 +105,7 @@ public class GroupEntitiesSparkJobTest {
                         DHPUtils
                                 .toSeq(
                                         HdfsSupport
-							.listFiles(dispatchEntityPath.toString(), spark.sparkContext().hadoopConfiguration())))
+                                                .listFiles(outputPath.toString(), spark.sparkContext().hadoopConfiguration())))
                 .map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
 
         assertEquals(3, output.count());