Consistency graph workflow merges all the entities by ID

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/OafMapperUtils.java

@@ -19,24 +19,24 @@ public class OafMapperUtils {
 
 	public static Oaf merge(final Oaf o1, final Oaf o2) {
 		if (ModelSupport.isSubClass(o1, OafEntity.class)) {
-			if (ModelSupport.isSubClass(o1, Result.class)) {
+			return mergeEntities((OafEntity) o1, (OafEntity) o2);
-
-				return mergeResults((Result) o1, (Result) o2);
-			} else if (ModelSupport.isSubClass(o1, Datasource.class)) {
-				((Datasource) o1).mergeFrom((Datasource) o2);
-			} else if (ModelSupport.isSubClass(o1, Organization.class)) {
-				((Organization) o1).mergeFrom((Organization) o2);
-			} else if (ModelSupport.isSubClass(o1, Project.class)) {
-				((Project) o1).mergeFrom((Project) o2);
-			} else {
-				throw new RuntimeException("invalid OafEntity subtype:" + o1.getClass().getCanonicalName());
-			}
 		} else if (ModelSupport.isSubClass(o1, Relation.class)) {
 			((Relation) o1).mergeFrom((Relation) o2);
-		} else {
+		}
 		throw new RuntimeException("invalid Oaf type:" + o1.getClass().getCanonicalName());
 	}
-		return o1;
+
+	public static OafEntity mergeEntities(OafEntity e1, OafEntity e2) {
+		if (ModelSupport.isSubClass(e1, Result.class)) {
+			return mergeResults((Result) e1, (Result) e2);
+		} else if (ModelSupport.isSubClass(e1, Datasource.class)) {
+			((Datasource) e1).mergeFrom((Datasource) e2);
+		} else if (ModelSupport.isSubClass(e1, Organization.class)) {
+			((Organization) e1).mergeFrom((Organization) e2);
+		} else if (ModelSupport.isSubClass(e1, Project.class)) {
+			((Project) e1).mergeFrom((Project) e2);
+		}
+		throw new RuntimeException("invalid OafEntity subtype:" + e1.getClass().getCanonicalName());
 	}
 
 	public static Result mergeResults(Result r1, Result r2) {

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

@@ -0,0 +1,93 @@
+
+package eu.dnetlib.dhp.oa.dedup;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+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.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.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+
+public class DispatchEntitiesSparkJob {
+
+	private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesSparkJob.class);
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static void main(String[] args) throws Exception {
+
+		String jsonConfiguration = IOUtils
+			.toString(
+				DispatchEntitiesSparkJob.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/oa/dedup/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);
+
+		String graphTableClassName = parser.get("graphTableClassName");
+		log.info("graphTableClassName: {}", graphTableClassName);
+
+		Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
+
+		SparkConf conf = new SparkConf();
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
+				dispatchEntities(spark, inputPath, entityClazz, outputPath);
+			});
+	}
+
+	private static <T extends Oaf> void dispatchEntities(
+		SparkSession spark,
+		String inputPath,
+		Class<T> clazz,
+		String outputPath) {
+
+		spark
+			.read()
+			.textFile(inputPath)
+			.filter((FilterFunction<String>) s -> isEntityType(s, clazz))
+			.map((MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"), Encoders.STRING())
+			.map(
+				(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz),
+				Encoders.bean(clazz))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
+			.json(outputPath);
+	}
+
+	private static <T extends Oaf> boolean isEntityType(final String s, final Class<T> clazz) {
+		return StringUtils.substringBefore(s, "|").equals(clazz.getName());
+	}
+
+}

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

@@ -0,0 +1,202 @@
+
+package eu.dnetlib.dhp.oa.dedup;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static eu.dnetlib.dhp.utils.DHPUtils.toSeq;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+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.sql.*;
+import org.apache.spark.sql.expressions.Aggregator;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+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.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.*;
+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 final static String ID_JPATH = "$.id";
+
+	private final static String SOURCE_JPATH = "$.source";
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static void main(String[] args) throws Exception {
+
+		String jsonConfiguration = IOUtils
+			.toString(
+				GroupEntitiesSparkJob.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/oa/dedup/group_graph_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 graphInputPath = parser.get("graphInputPath");
+		log.info("graphInputPath: {}", graphInputPath);
+
+		String outputPath = parser.get("outputPath");
+		log.info("outputPath: {}", outputPath);
+
+		SparkConf conf = new SparkConf();
+		conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
+		conf.registerKryoClasses(ModelSupport.getOafModelClasses());
+
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
+				groupEntities(spark, graphInputPath, outputPath);
+			});
+	}
+
+	private static void groupEntities(
+		SparkSession spark,
+		String inputPath,
+		String outputPath) {
+
+		final TypedColumn<OafEntity, OafEntity> aggregator = new GroupingAggregator().toColumn();
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+		spark
+			.read()
+			.textFile(toSeq(listPaths(inputPath, sc)))
+			.map((MapFunction<String, OafEntity>) s -> parseOaf(s), Encoders.kryo(OafEntity.class))
+			.filter((FilterFunction<OafEntity>) e -> StringUtils.isNotBlank(ModelSupport.idFn().apply(e)))
+			.groupByKey((MapFunction<OafEntity, String>) oaf -> ModelSupport.idFn().apply(oaf), Encoders.STRING())
+			.agg(aggregator)
+			.map(
+				(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);
+	}
+
+	public static class GroupingAggregator extends Aggregator<OafEntity, OafEntity, OafEntity> {
+
+		@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);
+		} catch (IOException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	private static List<String> listPaths(String inputPath, JavaSparkContext sc) {
+		return HdfsSupport
+			.listFiles(inputPath, sc.hadoopConfiguration())
+			.stream()
+			.filter(f -> !f.equals("relation"))
+			.collect(Collectors.toList());
+	}
+
+}

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

@@ -3,6 +3,8 @@ package eu.dnetlib.dhp.oa.dedup;
 
 import static org.apache.spark.sql.functions.col;
 
+import java.util.Objects;
+
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.spark.SparkConf;
@@ -28,7 +30,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 		SOURCE, TARGET
 	}
 
-	public SparkPropagateRelation(ArgumentApplicationParser parser, SparkSession spark) throws Exception {
+	public SparkPropagateRelation(ArgumentApplicationParser parser, SparkSession spark) {
 		super(parser, spark);
 	}
 
@@ -55,13 +57,13 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 
 		final String graphBasePath = parser.get("graphBasePath");
 		final String workingPath = parser.get("workingPath");
-		final String dedupGraphPath = parser.get("dedupGraphPath");
+		final String graphOutputPath = parser.get("graphOutputPath");
 
 		log.info("graphBasePath: '{}'", graphBasePath);
 		log.info("workingPath: '{}'", workingPath);
-		log.info("dedupGraphPath: '{}'", dedupGraphPath);
+		log.info("graphOutputPath: '{}'", graphOutputPath);
 
-		final String outputRelationPath = DedupUtility.createEntityPath(dedupGraphPath, "relation");
+		final String outputRelationPath = DedupUtility.createEntityPath(graphOutputPath, "relation");
 		removeOutputDir(spark, outputRelationPath);
 
 		Dataset<Relation> mergeRels = spark
@@ -101,7 +103,8 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 				newRels
 					.union(updated)
 					.union(mergeRels)
-					.map((MapFunction<Relation, Relation>) r -> r, Encoders.kryo(Relation.class))),
+					.map((MapFunction<Relation, Relation>) r -> r, Encoders.kryo(Relation.class)))
+						.filter((FilterFunction<Relation>) r -> !Objects.equals(r.getSource(), r.getTarget())),
 			outputRelationPath, SaveMode.Overwrite);
 	}
 

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

@@ -2,15 +2,15 @@
     <parameters>
         <property>
             <name>graphBasePath</name>
-            <description>the raw graph base path</description>
+            <description>the input graph base path</description>
         </property>
         <property>
             <name>workingPath</name>
             <description>path of the working directory</description>
         </property>
         <property>
-            <name>dedupGraphPath</name>
+            <name>graphOutputPath</name>
-            <description>path of the dedup graph</description>
+            <description>path of the output graph</description>
         </property>
         <property>
             <name>sparkDriverMemory</name>
@@ -91,116 +91,224 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=7680
             </spark-opts>
-            <arg>--i</arg><arg>${graphBasePath}</arg>
+            <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--o</arg><arg>${dedupGraphPath}</arg>
+            <arg>--o</arg><arg>${graphOutputPath}</arg>
-            <arg>--w</arg><arg>${workingPath}</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
         </spark>
-        <ok to="fork_copy_entities"/>
+        <ok to="group_entities"/>
         <error to="Kill"/>
     </action>
 
-    <fork name="fork_copy_entities">
+    <action name="group_entities">
-        <path start="copy_datasource"/>
+        <spark xmlns="uri:oozie:spark-action:0.2">
-        <path start="copy_project"/>
+            <master>yarn</master>
-        <path start="copy_organization"/>
+            <mode>cluster</mode>
-        <path start="copy_publication"/>
+            <name>group graph entities</name>
-        <path start="copy_dataset"/>
+            <class>eu.dnetlib.dhp.oa.dedup.GroupEntitiesSparkJob</class>
-        <path start="copy_software"/>
+            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
-        <path start="copy_otherresearchproduct"/>
+            <spark-opts>
+                --executor-cores=${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}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+            </spark-opts>
+            <arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
+            <arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>
+        </spark>
+        <ok to="fork_dispatch_entities"/>
+        <error to="Kill"/>
+    </action>
+
+    <fork name="fork_dispatch_entities">
+        <path start="dispatch_datasource"/>
+        <path start="dispatch_project"/>
+        <path start="dispatch_organization"/>
+        <path start="dispatch_publication"/>
+        <path start="dispatch_dataset"/>
+        <path start="dispatch_software"/>
+        <path start="dispatch_otherresearchproduct"/>
     </fork>
 
-    <action name="copy_datasource">
+    <action name="dispatch_datasource">
-        <distcp xmlns="uri:oozie:distcp-action:0.2">
+        <spark xmlns="uri:oozie:spark-action:0.2">
-            <prepare>
+            <master>yarn</master>
-                <delete path="${dedupGraphPath}/datasource"/>
+            <mode>cluster</mode>
-            </prepare>
+            <name>Dispatch publications</name>
-            <arg>-pb</arg>
+            <class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
-            <arg>${graphBasePath}/datasource</arg>
+            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
-            <arg>${dedupGraphPath}/datasource</arg>
+            <spark-opts>
-        </distcp>
+                --executor-cores=${sparkExecutorCores}
-        <ok to="wait_copy"/>
+                --executor-memory=${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}/datasource</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
+        </spark>
+        <ok to="wait_dispatch"/>
         <error to="Kill"/>
     </action>
 
-    <action name="copy_project">
+    <action name="dispatch_project">
-        <distcp xmlns="uri:oozie:distcp-action:0.2">
+        <spark xmlns="uri:oozie:spark-action:0.2">
-            <prepare>
+            <master>yarn</master>
-                <delete path="${dedupGraphPath}/project"/>
+            <mode>cluster</mode>
-            </prepare>
+            <name>Dispatch project</name>
-            <arg>-pb</arg>
+            <class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
-            <arg>${graphBasePath}/project</arg>
+            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
-            <arg>${dedupGraphPath}/project</arg>
+            <spark-opts>
-        </distcp>
+                --executor-cores=${sparkExecutorCores}
-        <ok to="wait_copy"/>
+                --executor-memory=${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}/project</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
+        </spark>
+        <ok to="wait_dispatch"/>
         <error to="Kill"/>
     </action>
 
-    <action name="copy_organization">
+    <action name="dispatch_organization">
-        <distcp xmlns="uri:oozie:distcp-action:0.2">
+        <spark xmlns="uri:oozie:spark-action:0.2">
-            <prepare>
+            <master>yarn</master>
-                <delete path="${dedupGraphPath}/organization"/>
+            <mode>cluster</mode>
-            </prepare>
+            <name>Dispatch organization</name>
-            <arg>-pb</arg>
+            <class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
-            <arg>${graphBasePath}/organization</arg>
+            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
-            <arg>${dedupGraphPath}/organization</arg>
+            <spark-opts>
-        </distcp>
+                --executor-cores=${sparkExecutorCores}
-        <ok to="wait_copy"/>
+                --executor-memory=${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}/organization</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
+        </spark>
+        <ok to="wait_dispatch"/>
         <error to="Kill"/>
     </action>
 
-    <action name="copy_publication">
+    <action name="dispatch_publication">
-        <distcp xmlns="uri:oozie:distcp-action:0.2">
+        <spark xmlns="uri:oozie:spark-action:0.2">
-            <prepare>
+            <master>yarn</master>
-                <delete path="${dedupGraphPath}/publication"/>
+            <mode>cluster</mode>
-            </prepare>
+            <name>Dispatch publication</name>
-            <arg>-pb</arg>
+            <class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
-            <arg>${graphBasePath}/publication</arg>
+            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
-            <arg>${dedupGraphPath}/publication</arg>
+            <spark-opts>
-        </distcp>
+                --executor-cores=${sparkExecutorCores}
-        <ok to="wait_copy"/>
+                --executor-memory=${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}/publication</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
+        </spark>
+        <ok to="wait_dispatch"/>
         <error to="Kill"/>
     </action>
 
-    <action name="copy_dataset">
+    <action name="dispatch_dataset">
-        <distcp xmlns="uri:oozie:distcp-action:0.2">
+        <spark xmlns="uri:oozie:spark-action:0.2">
-            <prepare>
+            <master>yarn</master>
-                <delete path="${dedupGraphPath}/dataset"/>
+            <mode>cluster</mode>
-            </prepare>
+            <name>Dispatch dataset</name>
-            <arg>-pb</arg>
+            <class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
-            <arg>${graphBasePath}/dataset</arg>
+            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
-            <arg>${dedupGraphPath}/dataset</arg>
+            <spark-opts>
-        </distcp>
+                --executor-cores=${sparkExecutorCores}
-        <ok to="wait_copy"/>
+                --executor-memory=${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}/dataset</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
+        </spark>
+        <ok to="wait_dispatch"/>
         <error to="Kill"/>
     </action>
 
-    <action name="copy_software">
+    <action name="dispatch_software">
-        <distcp xmlns="uri:oozie:distcp-action:0.2">
+        <spark xmlns="uri:oozie:spark-action:0.2">
-            <prepare>
+            <master>yarn</master>
-                <delete path="${dedupGraphPath}/software"/>
+            <mode>cluster</mode>
-            </prepare>
+            <name>Dispatch software</name>
-            <arg>-pb</arg>
+            <class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
-            <arg>${graphBasePath}/software</arg>
+            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
-            <arg>${dedupGraphPath}/software</arg>
+            <spark-opts>
-        </distcp>
+                --executor-cores=${sparkExecutorCores}
-        <ok to="wait_copy"/>
+                --executor-memory=${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}/software</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
+        </spark>
+        <ok to="wait_dispatch"/>
         <error to="Kill"/>
     </action>
 
-    <action name="copy_otherresearchproduct">
+    <action name="dispatch_otherresearchproduct">
-        <distcp xmlns="uri:oozie:distcp-action:0.2">
+        <spark xmlns="uri:oozie:spark-action:0.2">
-            <prepare>
+            <master>yarn</master>
-                <delete path="${dedupGraphPath}/otherresearchproduct"/>
+            <mode>cluster</mode>
-            </prepare>
+            <name>Dispatch otherresearchproduct</name>
-            <arg>-pb</arg>
+            <class>eu.dnetlib.dhp.oa.dedup.DispatchEntitiesSparkJob</class>
-            <arg>${graphBasePath}/otherresearchproduct</arg>
+            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
-            <arg>${dedupGraphPath}/otherresearchproduct</arg>
+            <spark-opts>
-        </distcp>
+                --executor-cores=${sparkExecutorCores}
-        <ok to="wait_copy"/>
+                --executor-memory=${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}/otherresearchproduct</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
+        </spark>
+        <ok to="wait_dispatch"/>
         <error to="Kill"/>
     </action>
 
-    <join name="wait_copy" to="End"/>
+    <join name="wait_dispatch" to="End"/>
 
     <end name="End"/>
 </workflow-app>

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

@@ -0,0 +1,26 @@
+[
+  {
+    "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": "c",
+    "paramLongName": "graphTableClassName",
+    "paramDescription": "the graph entity class name",
+    "paramRequired": true
+  }
+]

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

@@ -13,7 +13,7 @@
   },
   {
     "paramName": "o",
-    "paramLongName": "dedupGraphPath",
+    "paramLongName": "graphOutputPath",
     "paramDescription": "the path of the dedup graph",
     "paramRequired": true
   }