Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop

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

@@ -32,15 +32,15 @@ public class CheckDuplictedIdsJob {
 			IOUtils
 				.toString(
 					CheckDuplictedIdsJob.class
-						.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json")));
+						.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/check_duplicates.json")));
 		parser.parseArgument(args);
 
 		final SparkConf conf = new SparkConf();
 
-		final String eventsPath = parser.get("workingPath") + "/events";
+		final String eventsPath = parser.get("outputDir") + "/events";
 		log.info("eventsPath: {}", eventsPath);
 
-		final String countPath = parser.get("workingPath") + "/counts";
+		final String countPath = parser.get("outputDir") + "/counts";
 		log.info("countPath: {}", countPath);
 
 		final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
@@ -59,6 +59,7 @@ public class CheckDuplictedIdsJob {
 			.map(o -> ClusterUtils.incrementAccumulator(o, total), Encoders.tuple(Encoders.STRING(), Encoders.LONG()))
 			.write()
 			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
 			.json(countPath);
 		;
 

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

@@ -44,10 +44,10 @@ public class GenerateEventsJob {
 			.orElse(Boolean.TRUE);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingDir = parser.get("workingDir");
-		log.info("workingPath: {}", workingPath);
+		log.info("workingDir: {}", workingDir);
 
-		final String eventsPath = workingPath + "/events";
+		final String eventsPath = parser.get("outputDir") + "/events";
 		log.info("eventsPath: {}", eventsPath);
 
 		final Set<String> dsIdWhitelist = ClusterUtils.parseParamAsList(parser, "datasourceIdWhitelist");
@@ -59,6 +59,9 @@ public class GenerateEventsJob {
 		final Set<String> dsIdBlacklist = ClusterUtils.parseParamAsList(parser, "datasourceIdBlacklist");
 		log.info("datasourceIdBlacklist: {}", StringUtils.join(dsIdBlacklist, ","));
 
+		final Set<String> topicWhitelist = ClusterUtils.parseParamAsList(parser, "topicWhitelist");
+		log.info("topicWhitelist: {}", StringUtils.join(topicWhitelist, ","));
+
 		final SparkConf conf = new SparkConf();
 
 		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
@@ -70,12 +73,12 @@ public class GenerateEventsJob {
 			final LongAccumulator total = spark.sparkContext().longAccumulator("total_events");
 
 			final Dataset<ResultGroup> groups = ClusterUtils
-				.readPath(spark, workingPath + "/duplicates", ResultGroup.class);
+				.readPath(spark, workingDir + "/duplicates", ResultGroup.class);
 
 			final Dataset<Event> dataset = groups
 				.map(
 					g -> EventFinder
-						.generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators),
+						.generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, topicWhitelist, accumulators),
 					Encoders
 						.bean(EventGroup.class))
 				.flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class));

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

@@ -46,7 +46,7 @@ public class GenerateStatsJob {
 
 		final SparkConf conf = new SparkConf();
 
-		final String eventsPath = parser.get("workingPath") + "/events";
+		final String eventsPath = parser.get("outputDir") + "/events";
 		log.info("eventsPath: {}", eventsPath);
 
 		final String dbUrl = parser.get("dbUrl");

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

@@ -46,7 +46,7 @@ public class IndexEventSubsetJob {
 
 		final SparkConf conf = new SparkConf();
 
-		final String eventsPath = parser.get("workingPath") + "/events";
+		final String eventsPath = parser.get("outputDir") + "/events";
 		log.info("eventsPath: {}", eventsPath);
 
 		final String index = parser.get("index");
@@ -55,6 +55,18 @@ public class IndexEventSubsetJob {
 		final String indexHost = parser.get("esHost");
 		log.info("indexHost: {}", indexHost);
 
+		final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount");
+		log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount);
+
+		final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait");
+		log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait);
+
+		final String esBatchSizeEntries = parser.get("esBatchSizeEntries");
+		log.info("esBatchSizeEntries: {}", esBatchSizeEntries);
+
+		final String esNodesWanOnly = parser.get("esNodesWanOnly");
+		log.info("esNodesWanOnly: {}", esNodesWanOnly);
+
 		final int maxEventsForTopic = NumberUtils.toInt(parser.get("maxEventsForTopic"));
 		log.info("maxEventsForTopic: {}", maxEventsForTopic);
 
@@ -86,10 +98,10 @@ public class IndexEventSubsetJob {
 		esCfg.put("es.index.auto.create", "false");
 		esCfg.put("es.nodes", indexHost);
 		esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY
-		esCfg.put("es.batch.write.retry.count", "8");
+		esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
-		esCfg.put("es.batch.write.retry.wait", "60s");
+		esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
-		esCfg.put("es.batch.size.entries", "200");
+		esCfg.put("es.batch.size.entries", esBatchSizeEntries);
-		esCfg.put("es.nodes.wan.only", "true");
+		esCfg.put("es.nodes.wan.only", esNodesWanOnly);
 
 		log.info("*** Start indexing");
 		JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);

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

@@ -54,7 +54,7 @@ public class IndexNotificationsJob {
 
 		final SparkConf conf = new SparkConf();
 
-		final String eventsPath = parser.get("workingPath") + "/events";
+		final String eventsPath = parser.get("outputDir") + "/events";
 		log.info("eventsPath: {}", eventsPath);
 
 		final String index = parser.get("index");
@@ -63,6 +63,18 @@ public class IndexNotificationsJob {
 		final String indexHost = parser.get("esHost");
 		log.info("indexHost: {}", indexHost);
 
+		final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount");
+		log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount);
+
+		final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait");
+		log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait);
+
+		final String esBatchSizeEntries = parser.get("esBatchSizeEntries");
+		log.info("esBatchSizeEntries: {}", esBatchSizeEntries);
+
+		final String esNodesWanOnly = parser.get("esNodesWanOnly");
+		log.info("esNodesWanOnly: {}", esNodesWanOnly);
+
 		final String brokerApiBaseUrl = parser.get("brokerApiBaseUrl");
 		log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl);
 
@@ -92,10 +104,10 @@ public class IndexNotificationsJob {
 			esCfg.put("es.index.auto.create", "false");
 			esCfg.put("es.nodes", indexHost);
 			esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY
-			esCfg.put("es.batch.write.retry.count", "8");
+			esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
-			esCfg.put("es.batch.write.retry.wait", "60s");
+			esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
-			esCfg.put("es.batch.size.entries", "200");
+			esCfg.put("es.batch.size.entries", esBatchSizeEntries);
-			esCfg.put("es.nodes.wan.only", "true");
+			esCfg.put("es.nodes.wan.only", esNodesWanOnly);
 
 			log.info("*** Start indexing");
 			JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);

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

@@ -36,7 +36,7 @@ public class IndexOnESJob {
 
 		final SparkConf conf = new SparkConf();
 
-		final String eventsPath = parser.get("workingPath") + "/events";
+		final String eventsPath = parser.get("outputDir") + "/events";
 		log.info("eventsPath: {}", eventsPath);
 
 		final String index = parser.get("index");
@@ -45,6 +45,18 @@ public class IndexOnESJob {
 		final String indexHost = parser.get("esHost");
 		log.info("indexHost: {}", indexHost);
 
+		final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount");
+		log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount);
+
+		final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait");
+		log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait);
+
+		final String esBatchSizeEntries = parser.get("esBatchSizeEntries");
+		log.info("esBatchSizeEntries: {}", esBatchSizeEntries);
+
+		final String esNodesWanOnly = parser.get("esNodesWanOnly");
+		log.info("esNodesWanOnly: {}", esNodesWanOnly);
+
 		final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
 
 		final JavaRDD<String> inputRdd = ClusterUtils
@@ -53,15 +65,13 @@ public class IndexOnESJob {
 			.javaRDD();
 
 		final Map<String, String> esCfg = new HashMap<>();
-		// esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54");
-
 		esCfg.put("es.index.auto.create", "false");
 		esCfg.put("es.nodes", indexHost);
 		esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY
-		esCfg.put("es.batch.write.retry.count", "8");
+		esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
-		esCfg.put("es.batch.write.retry.wait", "60s");
+		esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
-		esCfg.put("es.batch.size.entries", "200");
+		esCfg.put("es.batch.size.entries", esBatchSizeEntries);
-		esCfg.put("es.nodes.wan.only", "true");
+		esCfg.put("es.nodes.wan.only", esNodesWanOnly);
 
 		JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);
 	}

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java

@@ -42,10 +42,10 @@ public class JoinStep0Job {
 		final String graphPath = parser.get("graphPath");
 		log.info("graphPath: {}", graphPath);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingDir = parser.get("workingDir");
-		log.info("workingPath: {}", workingPath);
+		log.info("workingDir: {}", workingDir);
 
-		final String joinedEntitiesPath = workingPath + "/joinedEntities_step0";
+		final String joinedEntitiesPath = workingDir + "/joinedEntities_step0";
 		log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
 
 		final SparkConf conf = new SparkConf();
@@ -57,10 +57,10 @@ public class JoinStep0Job {
 			final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
 
 			final Dataset<OaBrokerMainEntity> sources = ClusterUtils
-				.readPath(spark, workingPath + "/simpleEntities", OaBrokerMainEntity.class);
+				.readPath(spark, workingDir + "/simpleEntities", OaBrokerMainEntity.class);
 
 			final Dataset<RelatedDatasource> typedRels = ClusterUtils
-				.readPath(spark, workingPath + "/relatedDatasources", RelatedDatasource.class);
+				.readPath(spark, workingDir + "/relatedDatasources", RelatedDatasource.class);
 
 			final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedDatasource>, OaBrokerMainEntity> aggr = new RelatedDatasourceAggregator()
 				.toColumn();

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java

@@ -40,10 +40,10 @@ public class JoinStep1Job {
 			.orElse(Boolean.TRUE);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingDir = parser.get("workingDir");
-		log.info("workingPath: {}", workingPath);
+		log.info("workingDir: {}", workingDir);
 
-		final String joinedEntitiesPath = workingPath + "/joinedEntities_step1";
+		final String joinedEntitiesPath = workingDir + "/joinedEntities_step1";
 		log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
 
 		final SparkConf conf = new SparkConf();
@@ -55,10 +55,10 @@ public class JoinStep1Job {
 			final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
 
 			final Dataset<OaBrokerMainEntity> sources = ClusterUtils
-				.readPath(spark, workingPath + "/joinedEntities_step0", OaBrokerMainEntity.class);
+				.readPath(spark, workingDir + "/joinedEntities_step0", OaBrokerMainEntity.class);
 
 			final Dataset<RelatedProject> typedRels = ClusterUtils
-				.readPath(spark, workingPath + "/relatedProjects", RelatedProject.class);
+				.readPath(spark, workingDir + "/relatedProjects", RelatedProject.class);
 
 			final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedProject>, OaBrokerMainEntity> aggr = new RelatedProjectAggregator()
 				.toColumn();

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java

@@ -39,10 +39,10 @@ public class JoinStep2Job {
 			.orElse(Boolean.TRUE);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingDir = parser.get("workingDir");
-		log.info("workingPath: {}", workingPath);
+		log.info("workingDir: {}", workingDir);
 
-		final String joinedEntitiesPath = workingPath + "/joinedEntities_step2";
+		final String joinedEntitiesPath = workingDir + "/joinedEntities_step2";
 		log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
 
 		final SparkConf conf = new SparkConf();
@@ -54,10 +54,10 @@ public class JoinStep2Job {
 			final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
 
 			final Dataset<OaBrokerMainEntity> sources = ClusterUtils
-				.readPath(spark, workingPath + "/joinedEntities_step1", OaBrokerMainEntity.class);
+				.readPath(spark, workingDir + "/joinedEntities_step1", OaBrokerMainEntity.class);
 
 			final Dataset<RelatedSoftware> typedRels = ClusterUtils
-				.readPath(spark, workingPath + "/relatedSoftwares", RelatedSoftware.class);
+				.readPath(spark, workingDir + "/relatedSoftwares", RelatedSoftware.class);
 
 			final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedSoftware>, OaBrokerMainEntity> aggr = new RelatedSoftwareAggregator()
 				.toColumn();

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java

@@ -40,10 +40,10 @@ public class JoinStep3Job {
 			.orElse(Boolean.TRUE);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingDir = parser.get("workingDir");
-		log.info("workingPath: {}", workingPath);
+		log.info("workingDir: {}", workingDir);
 
-		final String joinedEntitiesPath = workingPath + "/joinedEntities_step3";
+		final String joinedEntitiesPath = workingDir + "/joinedEntities_step3";
 		log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
 
 		final SparkConf conf = new SparkConf();
@@ -55,10 +55,10 @@ public class JoinStep3Job {
 			final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
 
 			final Dataset<OaBrokerMainEntity> sources = ClusterUtils
-				.readPath(spark, workingPath + "/joinedEntities_step2", OaBrokerMainEntity.class);
+				.readPath(spark, workingDir + "/joinedEntities_step2", OaBrokerMainEntity.class);
 
 			final Dataset<RelatedDataset> typedRels = ClusterUtils
-				.readPath(spark, workingPath + "/relatedDatasets", RelatedDataset.class);
+				.readPath(spark, workingDir + "/relatedDatasets", RelatedDataset.class);
 
 			final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedDataset>, OaBrokerMainEntity> aggr = new RelatedDatasetAggregator()
 				.toColumn();

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java

@@ -40,10 +40,10 @@ public class JoinStep4Job {
 			.orElse(Boolean.TRUE);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingDir = parser.get("workingDir");
-		log.info("workingPath: {}", workingPath);
+		log.info("workingDir: {}", workingDir);
 
-		final String joinedEntitiesPath = workingPath + "/joinedEntities_step4";
+		final String joinedEntitiesPath = workingDir + "/joinedEntities_step4";
 		log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
 
 		final SparkConf conf = new SparkConf();
@@ -55,10 +55,10 @@ public class JoinStep4Job {
 			final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
 
 			final Dataset<OaBrokerMainEntity> sources = ClusterUtils
-				.readPath(spark, workingPath + "/joinedEntities_step3", OaBrokerMainEntity.class);
+				.readPath(spark, workingDir + "/joinedEntities_step3", OaBrokerMainEntity.class);
 
 			final Dataset<RelatedPublication> typedRels = ClusterUtils
-				.readPath(spark, workingPath + "/relatedPublications", RelatedPublication.class);
+				.readPath(spark, workingDir + "/relatedPublications", RelatedPublication.class);
 
 			final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedPublication>, OaBrokerMainEntity> aggr = new RelatedPublicationAggregator()
 				.toColumn();

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

@@ -55,10 +55,10 @@ public class PartitionEventsByDsIdJob {
 
 		final SparkConf conf = new SparkConf();
 
-		final String eventsPath = parser.get("workingPath") + "/events";
+		final String eventsPath = parser.get("outputDir") + "/events";
 		log.info("eventsPath: {}", eventsPath);
 
-		final String partitionPath = parser.get("workingPath") + "/eventsByOpendoarId";
+		final String partitionPath = parser.get("outputDir") + "/eventsByOpendoarId";
 		log.info("partitionPath: {}", partitionPath);
 
 		final String opendoarIds = parser.get("opendoarIds");
@@ -91,6 +91,7 @@ public class PartitionEventsByDsIdJob {
 				.write()
 				.partitionBy("group")
 				.mode(SaveMode.Overwrite)
+				.option("compression", "gzip")
 				.json(partitionPath);
 
 		});

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

@@ -45,10 +45,10 @@ public class PrepareGroupsJob {
 		final String graphPath = parser.get("graphPath");
 		log.info("graphPath: {}", graphPath);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingDir = parser.get("workingDir");
-		log.info("workingPath: {}", workingPath);
+		log.info("workingDir: {}", workingDir);
 
-		final String groupsPath = workingPath + "/duplicates";
+		final String groupsPath = workingDir + "/duplicates";
 		log.info("groupsPath: {}", groupsPath);
 
 		final SparkConf conf = new SparkConf();
@@ -60,10 +60,10 @@ public class PrepareGroupsJob {
 			final LongAccumulator total = spark.sparkContext().longAccumulator("total_groups");
 
 			final Dataset<OaBrokerMainEntity> results = ClusterUtils
-				.readPath(spark, workingPath + "/joinedEntities_step4", OaBrokerMainEntity.class);
+				.readPath(spark, workingDir + "/joinedEntities_step4", OaBrokerMainEntity.class);
 
 			final Dataset<Relation> mergedRels = ClusterUtils
-				.readPath(spark, graphPath + "/relation", Relation.class)
+				.loadRelations(graphPath, spark)
 				.filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));
 
 			final TypedColumn<Tuple2<OaBrokerMainEntity, Relation>, ResultGroup> aggr = new ResultAggregator()

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

@@ -42,10 +42,10 @@ public class PrepareRelatedDatasetsJob {
 		final String graphPath = parser.get("graphPath");
 		log.info("graphPath: {}", graphPath);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingDir = parser.get("workingDir");
-		log.info("workingPath: {}", workingPath);
+		log.info("workingDir: {}", workingDir);
 
-		final String relsPath = workingPath + "/relatedDatasets";
+		final String relsPath = workingDir + "/relatedDatasets";
 		log.info("relsPath: {}", relsPath);
 
 		final SparkConf conf = new SparkConf();
@@ -62,7 +62,7 @@ public class PrepareRelatedDatasetsJob {
 				.map(ConversionUtils::oafDatasetToBrokerDataset, Encoders.bean(OaBrokerRelatedDataset.class));
 
 			final Dataset<Relation> rels = ClusterUtils
-				.readPath(spark, graphPath + "/relation", Relation.class)
+				.loadRelations(graphPath, spark)
 				.filter(r -> r.getDataInfo().getDeletedbyinference())
 				.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
 				.filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass()))
@@ -72,7 +72,8 @@ public class PrepareRelatedDatasetsJob {
 			final Dataset<RelatedDataset> dataset = rels
 				.joinWith(datasets, datasets.col("openaireId").equalTo(rels.col("target")), "inner")
 				.map(t -> {
-					final RelatedDataset rel = new RelatedDataset(t._1.getSource(), t._2);
+					final RelatedDataset rel = new RelatedDataset(t._1.getSource(),
+						t._2);
 					rel.getRelDataset().setRelType(t._1.getRelClass());
 					return rel;
 				}, Encoders.bean(RelatedDataset.class));

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

@@ -48,10 +48,10 @@ public class PrepareRelatedDatasourcesJob {
 		final String graphPath = parser.get("graphPath");
 		log.info("graphPath: {}", graphPath);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingDir = parser.get("workingDir");
-		log.info("workingPath: {}", workingPath);
+		log.info("workingDir: {}", workingDir);
 
-		final String relsPath = workingPath + "/relatedDatasources";
+		final String relsPath = workingDir + "/relatedDatasources";
 		log.info("relsPath: {}", relsPath);
 
 		final SparkConf conf = new SparkConf();

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

@@ -44,10 +44,10 @@ public class PrepareRelatedProjectsJob {
 		final String graphPath = parser.get("graphPath");
 		log.info("graphPath: {}", graphPath);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingDir = parser.get("workingDir");
-		log.info("workingPath: {}", workingPath);
+		log.info("workingDir: {}", workingDir);
 
-		final String relsPath = workingPath + "/relatedProjects";
+		final String relsPath = workingDir + "/relatedProjects";
 		log.info("relsPath: {}", relsPath);
 
 		final SparkConf conf = new SparkConf();
@@ -64,7 +64,7 @@ public class PrepareRelatedProjectsJob {
 				.map(ConversionUtils::oafProjectToBrokerProject, Encoders.bean(OaBrokerProject.class));
 
 			final Dataset<Relation> rels = ClusterUtils
-				.readPath(spark, graphPath + "/relation", Relation.class)
+				.loadRelations(graphPath, spark)
 				.filter(r -> r.getDataInfo().getDeletedbyinference())
 				.filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT))
 				.filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS))

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

@@ -43,10 +43,10 @@ public class PrepareRelatedPublicationsJob {
 		final String graphPath = parser.get("graphPath");
 		log.info("graphPath: {}", graphPath);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingDir = parser.get("workingDir");
-		log.info("workingPath: {}", workingPath);
+		log.info("workingDir: {}", workingDir);
 
-		final String relsPath = workingPath + "/relatedPublications";
+		final String relsPath = workingDir + "/relatedPublications";
 		log.info("relsPath: {}", relsPath);
 
 		final SparkConf conf = new SparkConf();
@@ -65,7 +65,7 @@ public class PrepareRelatedPublicationsJob {
 					Encoders.bean(OaBrokerRelatedPublication.class));
 
 			final Dataset<Relation> rels = ClusterUtils
-				.readPath(spark, graphPath + "/relation", Relation.class)
+				.loadRelations(graphPath, spark)
 				.filter(r -> r.getDataInfo().getDeletedbyinference())
 				.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
 				.filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass()))
@@ -75,7 +75,8 @@ public class PrepareRelatedPublicationsJob {
 			final Dataset<RelatedPublication> dataset = rels
 				.joinWith(pubs, pubs.col("openaireId").equalTo(rels.col("target")), "inner")
 				.map(t -> {
-					final RelatedPublication rel = new RelatedPublication(t._1.getSource(), t._2);
+					final RelatedPublication rel = new RelatedPublication(
+						t._1.getSource(), t._2);
 					rel.getRelPublication().setRelType(t._1.getRelClass());
 					return rel;
 				}, Encoders.bean(RelatedPublication.class));

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

@@ -44,10 +44,10 @@ public class PrepareRelatedSoftwaresJob {
 		final String graphPath = parser.get("graphPath");
 		log.info("graphPath: {}", graphPath);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingDir = parser.get("workingDir");
-		log.info("workingPath: {}", workingPath);
+		log.info("workingDir: {}", workingDir);
 
-		final String relsPath = workingPath + "/relatedSoftwares";
+		final String relsPath = workingDir + "/relatedSoftwares";
 		log.info("relsPath: {}", relsPath);
 
 		final SparkConf conf = new SparkConf();
@@ -64,7 +64,7 @@ public class PrepareRelatedSoftwaresJob {
 				.map(ConversionUtils::oafSoftwareToBrokerSoftware, Encoders.bean(OaBrokerRelatedSoftware.class));
 
 			final Dataset<Relation> rels = ClusterUtils
-				.readPath(spark, graphPath + "/relation", Relation.class)
+				.loadRelations(graphPath, spark)
 				.filter(r -> r.getDataInfo().getDeletedbyinference())
 				.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
 				.filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS))

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

@@ -44,10 +44,10 @@ public class PrepareSimpleEntititiesJob {
 		final String graphPath = parser.get("graphPath");
 		log.info("graphPath: {}", graphPath);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingDir = parser.get("workingDir");
-		log.info("workingPath: {}", workingPath);
+		log.info("workingDir: {}", workingDir);
 
-		final String simpleEntitiesPath = workingPath + "/simpleEntities";
+		final String simpleEntitiesPath = workingDir + "/simpleEntities";
 		log.info("simpleEntitiesPath: {}", simpleEntitiesPath);
 
 		final SparkConf conf = new SparkConf();

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

@@ -17,6 +17,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.oaf.Relation;
 
 public class ClusterUtils {
 
@@ -30,6 +31,16 @@ public class ClusterUtils {
 		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
 	}
 
+	public static Dataset<Relation> loadRelations(final String graphPath, final SparkSession spark) {
+		return ClusterUtils
+			.readPath(spark, graphPath + "/relation", Relation.class)
+			.map(r -> {
+				r.setSource(ConversionUtils.cleanOpenaireId(r.getSource()));
+				r.setTarget(ConversionUtils.cleanOpenaireId(r.getTarget()));
+				return r;
+			}, Encoders.bean(Relation.class));
+	}
+
 	public static <R> Dataset<R> readPath(
 		final SparkSession spark,
 		final String inputPath,
@@ -67,6 +78,7 @@ public class ClusterUtils {
 			.map(o -> ClusterUtils.incrementAccumulator(o, acc), Encoders.bean(clazz))
 			.write()
 			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
 			.json(path);
 	}
 

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

@@ -74,7 +74,7 @@ public class ConversionUtils {
 		}
 
 		final OaBrokerRelatedDataset res = new OaBrokerRelatedDataset();
-		res.setOpenaireId(d.getId());
+		res.setOpenaireId(cleanOpenaireId(d.getId()));
 		res.setOriginalId(first(d.getOriginalId()));
 		res.setTitle(structPropValue(d.getTitle()));
 		res.setPids(mappedList(d.getPid(), ConversionUtils::oafPidToBrokerPid));
@@ -89,7 +89,7 @@ public class ConversionUtils {
 		}
 
 		final OaBrokerRelatedPublication res = new OaBrokerRelatedPublication();
-		res.setOpenaireId(p.getId());
+		res.setOpenaireId(cleanOpenaireId(p.getId()));
 		res.setOriginalId(first(p.getOriginalId()));
 		res.setTitle(structPropValue(p.getTitle()));
 		res.setPids(mappedList(p.getPid(), ConversionUtils::oafPidToBrokerPid));
@@ -106,7 +106,7 @@ public class ConversionUtils {
 
 		final OaBrokerMainEntity res = new OaBrokerMainEntity();
 
-		res.setOpenaireId(result.getId());
+		res.setOpenaireId(cleanOpenaireId(result.getId()));
 		res.setOriginalId(first(result.getOriginalId()));
 		res.setTypology(classId(result.getResulttype()));
 		res.setTitles(structPropList(result.getTitle()));
@@ -129,6 +129,10 @@ public class ConversionUtils {
 		return res;
 	}
 
+	public static String cleanOpenaireId(final String id) {
+		return id.contains("|") ? StringUtils.substringAfter(id, "|") : id;
+	}
+
 	private static OaBrokerAuthor oafAuthorToBrokerAuthor(final Author author) {
 		if (author == null) {
 			return null;
@@ -188,7 +192,7 @@ public class ConversionUtils {
 		}
 
 		final OaBrokerProject res = new OaBrokerProject();
-		res.setOpenaireId(p.getId());
+		res.setOpenaireId(cleanOpenaireId(p.getId()));
 		res.setTitle(fieldValue(p.getTitle()));
 		res.setAcronym(fieldValue(p.getAcronym()));
 		res.setCode(fieldValue(p.getCode()));
@@ -214,7 +218,7 @@ public class ConversionUtils {
 		}
 
 		final OaBrokerRelatedSoftware res = new OaBrokerRelatedSoftware();
-		res.setOpenaireId(sw.getId());
+		res.setOpenaireId(cleanOpenaireId(sw.getId()));
 		res.setName(structPropValue(sw.getTitle()));
 		res.setDescription(fieldValue(sw.getDescription()));
 		res.setRepository(fieldValue(sw.getCodeRepositoryUrl()));
@@ -230,7 +234,7 @@ public class ConversionUtils {
 
 		final OaBrokerRelatedDatasource res = new OaBrokerRelatedDatasource();
 		res.setName(StringUtils.defaultIfBlank(fieldValue(ds.getOfficialname()), fieldValue(ds.getEnglishname())));
-		res.setOpenaireId(ds.getId());
+		res.setOpenaireId(cleanOpenaireId(ds.getId()));
 		res.setType(classId(ds.getDatasourcetype()));
 		return res;
 	}

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

@@ -59,9 +59,18 @@ public class DatasourceRelationsAccumulator implements Serializable {
 		final DatasourceRelationsAccumulator res = new DatasourceRelationsAccumulator();
 		collectedFromSet
 			.stream()
-			.map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.COLLECTED_FROM_REL))
+			.map(
+				s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s),
+					BrokerConstants.COLLECTED_FROM_REL))
 			.forEach(res::addTuple);
-		hostedBySet.stream().map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.HOSTED_BY_REL)).forEach(res::addTuple);
+
+		hostedBySet
+			.stream()
+			.map(
+				s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s),
+					BrokerConstants.HOSTED_BY_REL))
+			.forEach(res::addTuple);
+
 		return res;
 	}
 

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

@@ -76,6 +76,7 @@ public class EventFinder {
 		final Set<String> dsIdWhitelist,
 		final Set<String> dsIdBlacklist,
 		final Set<String> dsTypeWhitelist,
+		final Set<String> topicWhitelist,
 		final Map<String, LongAccumulator> accumulators) {
 
 		final List<UpdateInfo<?>> list = new ArrayList<>();
@@ -84,7 +85,13 @@ public class EventFinder {
 			for (final OaBrokerRelatedDatasource targetDs : target.getDatasources()) {
 				if (verifyTarget(targetDs, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) {
 					for (final UpdateMatcher<?> matcher : matchers) {
-						list.addAll(matcher.searchUpdatesForRecord(target, targetDs, results.getData(), accumulators));
+						for (final UpdateInfo<?> info : matcher
+							.searchUpdatesForRecord(target, targetDs, results.getData(), accumulators)) {
+							if (topicWhitelist == null || topicWhitelist.isEmpty()
+								|| topicWhitelist.contains(info.getTopic().getPath())) {
+								list.add(info);
+							}
+						}
 					}
 				}
 			}

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json

@@ -0,0 +1,9 @@
+[
+
+	{
+		"paramName": "o",
+		"paramLongName": "outputDir",
+		"paramDescription": "the path where the data are stored",
+		"paramRequired": true
+	}
+]

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json

@@ -7,7 +7,7 @@
 	},
 	{
 		"paramName": "o",
-		"paramLongName": "workingPath",
+		"paramLongName": "workingDir",
 		"paramDescription": "the path where the temporary data will be stored",
 		"paramRequired": true
 	}

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml

@@ -6,7 +6,7 @@
             <description>the path where the graph is stored</description>
         </property>
         <property>
-            <name>workingPath</name>
+            <name>outputDir</name>
             <description>the path where the the generated data will be stored</description>
         </property>
 		<property>
@@ -24,6 +24,11 @@
             <value>-</value>
             <description>a black list (comma separeted, - for empty list) of datasource ids</description>
         </property>
+        <property>
+            <name>topicWhitelist</name>
+            <value>*</value>
+            <description>a white list (comma separeted, * for all) of topics</description>
+        </property>
         <property>
             <name>esEventIndexName</name>
             <description>the elasticsearch index name for events</description>
@@ -36,6 +41,26 @@
             <name>esIndexHost</name>
             <description>the elasticsearch host</description>
         </property>
+        <property>
+            <name>esBatchWriteRetryCount</name>
+            <value>8</value>
+            <description>an ES configuration property</description>
+        </property>
+		<property>
+            <name>esBatchWriteRetryWait</name>
+            <value>60s</value>
+            <description>an ES configuration property</description>
+        </property>
+		<property>
+            <name>esBatchSizeEntries</name>
+            <value>200</value>
+            <description>an ES configuration property</description>
+        </property>
+		<property>
+            <name>esNodesWanOnly</name>
+            <value>true</value>
+            <description>an ES configuration property</description>
+        </property>
         <property>
         	<name>maxIndexedEventsForDsAndTopic</name>
         	<description>the max number of events for each couple (ds/topic)</description>
@@ -111,15 +136,15 @@
         </configuration>
     </global>
 
-    <start to="ensure_working_path"/>
+    <start to="ensure_output_dir"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
     
-    <action name="ensure_working_path">
+    <action name="ensure_output_dir">
         <fs>
-            <mkdir path='${workingPath}'/>
+            <mkdir path='${outputDir}'/>
         </fs>
         <ok to="start_entities_and_rels"/>
         <error to="Kill"/>
@@ -152,7 +177,7 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
         </spark>
         <ok to="wait_entities_and_rels"/>
         <error to="Kill"/>
@@ -176,7 +201,7 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
         </spark>
         <ok to="wait_entities_and_rels"/>
         <error to="Kill"/>
@@ -201,7 +226,7 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
         </spark>
         <ok to="wait_entities_and_rels"/>
         <error to="Kill"/>
@@ -225,7 +250,7 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
         </spark>
         <ok to="wait_entities_and_rels"/>
         <error to="Kill"/>
@@ -249,7 +274,7 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
         </spark>
         <ok to="wait_entities_and_rels"/>
         <error to="Kill"/>
@@ -273,7 +298,7 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
         </spark>
         <ok to="wait_entities_and_rels"/>
         <error to="Kill"/>
@@ -299,7 +324,7 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
         </spark>
         <ok to="join_entities_step1"/>
         <error to="Kill"/>
@@ -323,7 +348,7 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
         </spark>
         <ok to="join_entities_step2"/>
         <error to="Kill"/>
@@ -347,7 +372,7 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
         </spark>
         <ok to="join_entities_step3"/>
         <error to="Kill"/>
@@ -371,7 +396,7 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
         </spark>
         <ok to="join_entities_step4"/>
         <error to="Kill"/>
@@ -395,7 +420,7 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
         </spark>
         <ok to="prepare_groups"/>
         <error to="Kill"/>
@@ -419,7 +444,7 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
         </spark>
         <ok to="generate_events"/>
         <error to="Kill"/>
@@ -442,10 +467,12 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
+            <arg>--outputDir</arg><arg>${outputDir}</arg>
 			<arg>--datasourceIdWhitelist</arg><arg>${datasourceIdWhitelist}</arg>
 			<arg>--datasourceTypeWhitelist</arg><arg>${datasourceTypeWhitelist}</arg>
 			<arg>--datasourceIdBlacklist</arg><arg>${datasourceIdBlacklist}</arg>
+			<arg>--topicWhitelist</arg><arg>${topicWhitelist}</arg>
         </spark>
         <ok to="index_event_subset"/>
         <error to="Kill"/>
@@ -468,9 +495,13 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--outputDir</arg><arg>${outputDir}</arg>
             <arg>--index</arg><arg>${esEventIndexName}</arg>
             <arg>--esHost</arg><arg>${esIndexHost}</arg>
+            <arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
+            <arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
+            <arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
+            <arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
             <arg>--maxEventsForTopic</arg><arg>${maxIndexedEventsForDsAndTopic}</arg>
             <arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
         </spark>
@@ -495,9 +526,13 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--outputDir</arg><arg>${outputDir}</arg>
             <arg>--index</arg><arg>${esNotificationsIndexName}</arg>
             <arg>--esHost</arg><arg>${esIndexHost}</arg>
+            <arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
+            <arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
+            <arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
+            <arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
             <arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
         </spark>
         <ok to="stats"/>
@@ -521,7 +556,7 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--outputDir</arg><arg>${outputDir}</arg>
             <arg>--dbUrl</arg><arg>${brokerDbUrl}</arg>
             <arg>--dbUser</arg><arg>${brokerDbUser}</arg>
             <arg>--dbPassword</arg><arg>${brokerDbPassword}</arg>

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json

@@ -1,7 +1,13 @@
 [
+	{
+		"paramName": "wp",
+		"paramLongName": "workingDir",
+		"paramDescription": "the path where the temporary data are stored",
+		"paramRequired": true
+	},
 	{
 		"paramName": "o",
-		"paramLongName": "workingPath",
+		"paramLongName": "outputDir",
 		"paramDescription": "the path where the generated events will be stored",
 		"paramRequired": true
 	},
@@ -22,5 +28,11 @@
 		"paramLongName": "datasourceIdBlacklist",
 		"paramDescription": "a black list (comma separeted, - for empty list) of datasource ids",
 		"paramRequired": true
+	},
+	{
+		"paramName": "topicWhitelist",
+		"paramLongName": "topicWhitelist",
+		"paramDescription": "a white list (comma separeted, * for all) of topics",
+		"paramRequired": true
 	}
 ]

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json

@@ -1,8 +1,8 @@
 [
 	{
 		"paramName": "o",
-		"paramLongName": "workingPath",
+		"paramLongName": "outputDir",
-		"paramDescription": "the workinh path",
+		"paramDescription": "the data path",
 		"paramRequired": true
 	},
 	{
@@ -16,5 +16,29 @@
 		"paramLongName": "esHost",
 		"paramDescription": "the ES host",
 		"paramRequired": true
+	},
+	{
+		"paramName": "esBatchWriteRetryCount",
+		"paramLongName": "esBatchWriteRetryCount",
+		"paramDescription": "an ES configuration property",
+		"paramRequired": true
+	},
+	{
+		"paramName": "esBatchWriteRetryWait",
+		"paramLongName": "esBatchWriteRetryWait",
+		"paramDescription": "an ES configuration property",
+		"paramRequired": true
+	},
+	{
+		"paramName": "esBatchSizeEntries",
+		"paramLongName": "esBatchSizeEntries",
+		"paramDescription": "an ES configuration property",
+		"paramRequired": true
+	},
+	{
+		"paramName": "esNodesWanOnly",
+		"paramLongName": "esNodesWanOnly",
+		"paramDescription": "an ES configuration property",
+		"paramRequired": true
 	}
 ]

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json

@@ -1,8 +1,8 @@
 [
 	{
 		"paramName": "o",
-		"paramLongName": "workingPath",
+		"paramLongName": "outputDir",
-		"paramDescription": "the workinh path",
+		"paramDescription": "the path where the generated data are stored",
 		"paramRequired": true
 	},
 	{
@@ -17,6 +17,30 @@
 		"paramDescription": "the ES host",
 		"paramRequired": true
 	},	
+	{
+		"paramName": "esBatchWriteRetryCount",
+		"paramLongName": "esBatchWriteRetryCount",
+		"paramDescription": "an ES configuration property",
+		"paramRequired": true
+	},
+	{
+		"paramName": "esBatchWriteRetryWait",
+		"paramLongName": "esBatchWriteRetryWait",
+		"paramDescription": "an ES configuration property",
+		"paramRequired": true
+	},
+	{
+		"paramName": "esBatchSizeEntries",
+		"paramLongName": "esBatchSizeEntries",
+		"paramDescription": "an ES configuration property",
+		"paramRequired": true
+	},
+	{
+		"paramName": "esNodesWanOnly",
+		"paramLongName": "esNodesWanOnly",
+		"paramDescription": "an ES configuration property",
+		"paramRequired": true
+	},	
 	{
 		"paramName": "n",
 		"paramLongName": "maxEventsForTopic",

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json

@@ -1,8 +1,8 @@
 [
 	{
 		"paramName": "o",
-		"paramLongName": "workingPath",
+		"paramLongName": "outputDir",
-		"paramDescription": "the workinh path",
+		"paramDescription": "the dir that contains the events folder",
 		"paramRequired": true
 	},
 	{
@@ -17,6 +17,30 @@
 		"paramDescription": "the ES host",
 		"paramRequired": true
 	},
+	{
+		"paramName": "esBatchWriteRetryCount",
+		"paramLongName": "esBatchWriteRetryCount",
+		"paramDescription": "an ES configuration property",
+		"paramRequired": true
+	},
+	{
+		"paramName": "esBatchWriteRetryWait",
+		"paramLongName": "esBatchWriteRetryWait",
+		"paramDescription": "an ES configuration property",
+		"paramRequired": true
+	},
+	{
+		"paramName": "esBatchSizeEntries",
+		"paramLongName": "esBatchSizeEntries",
+		"paramDescription": "an ES configuration property",
+		"paramRequired": true
+	},
+	{
+		"paramName": "esNodesWanOnly",
+		"paramLongName": "esNodesWanOnly",
+		"paramDescription": "an ES configuration property",
+		"paramRequired": true
+	},
 	{
 		"paramName": "broker",
 		"paramLongName": "brokerApiBaseUrl",

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml

@@ -6,8 +6,8 @@
             <description>the path where the graph is stored</description>
         </property>
         <property>
-            <name>workingPath</name>
+            <name>outputDir</name>
-            <description>the path where the the generated data will be stored</description>
+            <description>the path where the the generated data are stored</description>
         </property>
 		<property>
             <name>datasourceIdWhitelist</name>
@@ -36,6 +36,26 @@
             <name>esIndexHost</name>
             <description>the elasticsearch host</description>
         </property>
+        <property>
+            <name>esBatchWriteRetryCount</name>
+            <value>8</value>
+            <description>an ES configuration property</description>
+        </property>
+		<property>
+            <name>esBatchWriteRetryWait</name>
+            <value>60s</value>
+            <description>an ES configuration property</description>
+        </property>
+		<property>
+            <name>esBatchSizeEntries</name>
+            <value>200</value>
+            <description>an ES configuration property</description>
+        </property>
+		<property>
+            <name>esNodesWanOnly</name>
+            <value>true</value>
+            <description>an ES configuration property</description>
+        </property>
         <property>
         	<name>maxIndexedEventsForDsAndTopic</name>
         	<description>the max number of events for each couple (ds/topic)</description>
@@ -122,9 +142,13 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--outputDir</arg><arg>${outputDir}</arg>
             <arg>--index</arg><arg>${esNotificationsIndexName}</arg>
             <arg>--esHost</arg><arg>${esIndexHost}</arg>
+            <arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
+            <arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
+            <arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
+            <arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
             <arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json

@@ -1,8 +1,8 @@
 [
 	{
 		"paramName": "o",
-		"paramLongName": "workingPath",
+		"paramLongName": "outputDir",
-		"paramDescription": "the path where the temporary data will be stored",
+		"paramDescription": "the path where the data will be stored",
 		"paramRequired": true
 	},
 	{

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml

@@ -6,7 +6,7 @@
             <description>the opendoar IDs whitelist (comma separated)</description>
         </property>
         <property>
-            <name>workingPath</name>
+            <name>outputDir</name>
             <description>the path where the the generated data will be stored</description>
         </property>
         <property>
@@ -87,7 +87,7 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
             <arg>--opendoarIds</arg><arg>${opendoarIds}</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/config-default.xml

@@ -0,0 +1,18 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+</configuration>

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml

@@ -0,0 +1,140 @@
+<workflow-app name="reindex_events" xmlns="uri:oozie:workflow:0.5">
+
+    <parameters>
+        <property>
+            <name>outputDir</name>
+            <description>the path where the the generated data will be stored</description>
+        </property>
+        <property>
+            <name>esEventIndexName</name>
+            <description>the elasticsearch index name for events</description>
+        </property>
+        <property>
+            <name>esIndexHost</name>
+            <description>the elasticsearch host</description>
+        </property>
+        <property>
+            <name>esBatchWriteRetryCount</name>
+            <value>8</value>
+            <description>an ES configuration property</description>
+        </property>
+		<property>
+            <name>esBatchWriteRetryWait</name>
+            <value>60s</value>
+            <description>an ES configuration property</description>
+        </property>
+		<property>
+            <name>esBatchSizeEntries</name>
+            <value>200</value>
+            <description>an ES configuration property</description>
+        </property>
+		<property>
+            <name>esNodesWanOnly</name>
+            <value>true</value>
+            <description>an ES configuration property</description>
+        </property>
+        <property>
+        	<name>maxIndexedEventsForDsAndTopic</name>
+        	<description>the max number of events for each couple (ds/topic)</description>
+        </property>
+        <property>
+        	<name>brokerApiBaseUrl</name>
+        	<description>the url of the broker service api</description>
+        </property>
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
+        <property>
+            <name>spark2YarnHistoryServerAddress</name>
+            <description>spark 2.* yarn history server address</description>
+        </property>
+        <property>
+            <name>spark2EventLogDir</name>
+            <description>spark 2.* event log dir location</description>
+        </property>
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+        </configuration>
+    </global>
+
+    <start to="index_event_subset"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+        
+     <action name="index_event_subset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>IndexEventSubsetOnESJob</name>
+            <class>eu.dnetlib.dhp.broker.oa.IndexEventSubsetJob</class>
+            <jar>dhp-broker-events-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.dynamicAllocation.maxExecutors="8" 
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=3840
+            </spark-opts>
+            <arg>--outputDir</arg><arg>${outputDir}</arg>
+            <arg>--index</arg><arg>${esEventIndexName}</arg>
+            <arg>--esHost</arg><arg>${esIndexHost}</arg>
+            <arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
+            <arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
+            <arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
+            <arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
+            <arg>--maxEventsForTopic</arg><arg>${maxIndexedEventsForDsAndTopic}</arg>
+            <arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+    
+   
+
+    <end name="End"/>
+
+</workflow-app>

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json

@@ -1,8 +1,8 @@
 [
 	{
-		"paramName": "wp",
+		"paramName": "o",
-		"paramLongName": "workingPath",
+		"paramLongName": "outputDir",
-		"paramDescription": "the working path",
+		"paramDescription": "the path where generated data are stored",
 		"paramRequired": true
 	},
 	{

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java

@@ -23,7 +23,15 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT;
 import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
 import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE;
 import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM;
-import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.*;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.asString;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.createOpenaireId;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.dataInfo;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.journal;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listFields;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listKeyValues;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.qualifier;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty;
 
 import java.io.Closeable;
 import java.io.IOException;
@@ -462,44 +470,48 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
 
 				return Arrays.asList(r);
 			} else {
+				final String validationDate = rs.getString("curation_date");
+
 				final String sourceId = createOpenaireId(rs.getString(SOURCE_TYPE), rs.getString("source_id"), false);
 				final String targetId = createOpenaireId(rs.getString(TARGET_TYPE), rs.getString("target_id"), false);
 
 				final Relation r1 = new Relation();
 				final Relation r2 = new Relation();
 
-				if (rs.getString(SOURCE_TYPE).equals("project")) {
+				r1.setValidated(true);
-					r1.setCollectedfrom(collectedFrom);
+				r1.setValidationDate(validationDate);
-					r1.setRelType(RESULT_PROJECT);
+				r1.setCollectedfrom(collectedFrom);
-					r1.setSubRelType(OUTCOME);
-					r1.setRelClass(PRODUCES);
-
-					r2.setCollectedfrom(collectedFrom);
-					r2.setRelType(RESULT_PROJECT);
-					r2.setSubRelType(OUTCOME);
-					r2.setRelClass(IS_PRODUCED_BY);
-				} else {
-					r1.setCollectedfrom(collectedFrom);
-					r1.setRelType(RESULT_RESULT);
-					r1.setSubRelType(RELATIONSHIP);
-					r1.setRelClass(IS_RELATED_TO);
-
-					r2.setCollectedfrom(collectedFrom);
-					r2.setRelType(RESULT_RESULT);
-					r2.setSubRelType(RELATIONSHIP);
-					r2.setRelClass(IS_RELATED_TO);
-				}
-
 				r1.setSource(sourceId);
 				r1.setTarget(targetId);
 				r1.setDataInfo(info);
 				r1.setLastupdatetimestamp(lastUpdateTimestamp);
 
+				r2.setValidationDate(validationDate);
+				r2.setValidated(true);
+				r2.setCollectedfrom(collectedFrom);
 				r2.setSource(targetId);
 				r2.setTarget(sourceId);
 				r2.setDataInfo(info);
 				r2.setLastupdatetimestamp(lastUpdateTimestamp);
 
+				if (rs.getString(SOURCE_TYPE).equals("project")) {
+					r1.setRelType(RESULT_PROJECT);
+					r1.setSubRelType(OUTCOME);
+					r1.setRelClass(PRODUCES);
+
+					r2.setRelType(RESULT_PROJECT);
+					r2.setSubRelType(OUTCOME);
+					r2.setRelClass(IS_PRODUCED_BY);
+				} else {
+					r1.setRelType(RESULT_RESULT);
+					r1.setSubRelType(RELATIONSHIP);
+					r1.setRelClass(IS_RELATED_TO);
+
+					r2.setRelType(RESULT_RESULT);
+					r2.setSubRelType(RELATIONSHIP);
+					r2.setRelClass(IS_RELATED_TO);
+				}
+
 				return Arrays.asList(r1, r2);
 			}
 

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryClaims.sql

@@ -1 +1 @@
-SELECT source_type, source_id, target_type, target_id, semantics FROM claim WHERE approved=TRUE;
+SELECT source_type, source_id, target_type, target_id, semantics, curation_date::text FROM claim WHERE approved=TRUE;