applying changes from beta

dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java

@@ -51,6 +51,7 @@ public class Constants {
 	public static final String RETRY_DELAY = "retryDelay";
 	public static final String CONNECT_TIMEOUT = "connectTimeOut";
 	public static final String READ_TIMEOUT = "readTimeOut";
+	public static final String REQUEST_METHOD = "requestMethod";
 	public static final String FROM_DATE_OVERRIDE = "fromDateOverride";
 	public static final String UNTIL_DATE_OVERRIDE = "untilDateOverride";
 

dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpClientParams.java

@@ -1,6 +1,9 @@
 
 package eu.dnetlib.dhp.common.collection;
 
+import java.util.HashMap;
+import java.util.Map;
+
 /**
  * Bundles the http connection parameters driving the client behaviour.
  */
@@ -13,6 +16,8 @@ public class HttpClientParams {
 	public static int _connectTimeOut = 10; // seconds
 	public static int _readTimeOut = 30; // seconds
 
+	public static String _requestMethod = "GET";
+
 	/**
 	 * Maximum number of allowed retires before failing
 	 */
@@ -38,17 +43,30 @@ public class HttpClientParams {
 	 */
 	private int readTimeOut;
 
+	/**
+	 * Custom http headers
+	 */
+	private Map<String, String> headers;
+
+	/**
+	 * Request method (i.e., GET, POST etc)
+	 */
+	private String requestMethod;
+
 	public HttpClientParams() {
-		this(_maxNumberOfRetry, _requestDelay, _retryDelay, _connectTimeOut, _readTimeOut);
+		this(_maxNumberOfRetry, _requestDelay, _retryDelay, _connectTimeOut, _readTimeOut, new HashMap<>(),
+			_requestMethod);
 	}
 
 	public HttpClientParams(int maxNumberOfRetry, int requestDelay, int retryDelay, int connectTimeOut,
-		int readTimeOut) {
+		int readTimeOut, Map<String, String> headers, String requestMethod) {
 		this.maxNumberOfRetry = maxNumberOfRetry;
 		this.requestDelay = requestDelay;
 		this.retryDelay = retryDelay;
 		this.connectTimeOut = connectTimeOut;
 		this.readTimeOut = readTimeOut;
+		this.headers = headers;
+		this.requestMethod = requestMethod;
 	}
 
 	public int getMaxNumberOfRetry() {
@@ -91,4 +109,19 @@ public class HttpClientParams {
 		this.readTimeOut = readTimeOut;
 	}
 
+	public Map<String, String> getHeaders() {
+		return headers;
+	}
+
+	public void setHeaders(Map<String, String> headers) {
+		this.headers = headers;
+	}
+
+	public String getRequestMethod() {
+		return requestMethod;
+	}
+
+	public void setRequestMethod(String requestMethod) {
+		this.requestMethod = requestMethod;
+	}
 }

dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java

@@ -107,7 +107,14 @@ public class HttpConnector2 {
 			urlConn.setReadTimeout(getClientParams().getReadTimeOut() * 1000);
 			urlConn.setConnectTimeout(getClientParams().getConnectTimeOut() * 1000);
 			urlConn.addRequestProperty(HttpHeaders.USER_AGENT, userAgent);
+			urlConn.setRequestMethod(getClientParams().getRequestMethod());
 
+			// if provided, add custom headers
+			if (!getClientParams().getHeaders().isEmpty()) {
+				for (Map.Entry<String, String> headerEntry : getClientParams().getHeaders().entrySet()) {
+					urlConn.addRequestProperty(headerEntry.getKey(), headerEntry.getValue());
+				}
+			}
 			if (log.isDebugEnabled()) {
 				logHeaderFields(urlConn);
 			}

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());
@@ -77,127 +71,96 @@ public class GroupEntitiesSparkJob {
 			conf,
 			isSparkSessionManaged,
 			spark -> {
-				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
+				HdfsSupport.remove(checkpointPath, 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) {
 
-		final TypedColumn<OafEntity, OafEntity> aggregator = new GroupingAggregator().toColumn();
+		Dataset<OafEntity> allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC);
-		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
-		spark
+		for (Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
-			.read()
+			String entity = e.getKey().name();
-			.textFile(toSeq(listEntityPaths(inputPath, sc)))
+			Class<? extends OafEntity> entityClass = e.getValue();
-			.map((MapFunction<String, OafEntity>) GroupEntitiesSparkJob::parseOaf, Encoders.kryo(OafEntity.class))
+			String entityInputPath = inputPath + "/" + entity;
-			.filter((FilterFunction<OafEntity>) e -> StringUtils.isNotBlank(ModelSupport.idFn().apply(e)))
+
-			.groupByKey((MapFunction<OafEntity, String>) oaf -> ModelSupport.idFn().apply(oaf), Encoders.STRING())
+			if (!HdfsSupport.exists(entityInputPath, spark.sparkContext().hadoopConfiguration())) {
-			.agg(aggregator)
+				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>, String>) t -> t._2().getClass().getName() +
+				(MapFunction<Tuple2<String, OafEntity>, Tuple2<String, OafEntity>>) t -> new Tuple2(
-					"|" + OBJECT_MAPPER.writeValueAsString(t._2()),
+					t._2().getClass().getName(), t._2()),
-				Encoders.STRING())
+				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()
-			.option("compression", "gzip")
 			.mode(SaveMode.Overwrite)
-			.text(outputPath);
+			.option("compression", "gzip")
-	}
+			.save(checkpointPath);
 
-	public static class GroupingAggregator extends Aggregator<OafEntity, OafEntity, OafEntity> {
+		ForkJoinPool parPool = new ForkJoinPool(ModelSupport.entityTypes.size());
 
-		@Override
+		ModelSupport.entityTypes
-		public OafEntity zero() {
+			.entrySet()
-			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 IllegalArgumentException(e);
-		}
-	}
-
-	private static List<String> listEntityPaths(String inputPath, JavaSparkContext sc) {
-		return HdfsSupport
-			.listFiles(inputPath, sc.hadoopConfiguration())
 			.stream()
-			.filter(f -> !f.toLowerCase().contains("relation"))
+			.map(e -> parPool.submit(() -> {
-			.collect(Collectors.toList());
+				String entity = e.getKey().name();
-	}
+				Class<? extends OafEntity> entityClass = e.getValue();
 
+				spark
+					.read()
+					.load(checkpointPath)
+					.select(col(entity).as("value"))
+					.filter("value IS NOT NULL")
+					.as(OAFENTITY_KRYO_ENC)
+					.map((MapFunction<OafEntity, OafEntity>) r -> r, (Encoder<OafEntity>) Encoders.bean(entityClass))
+					.filter(filterInvisible ? "dataInfo.invisible != TRUE" : "TRUE")
+					.write()
+					.mode(SaveMode.Overwrite)
+					.option("compression", "gzip")
+					.json(outputPath + "/" + entity);
+			}))
+			.collect(Collectors.toList())
+			.forEach(t -> {
+				try {
+					t.get();
+				} catch (InterruptedException | ExecutionException e) {
+					throw new RuntimeException(e);
+				}
+			});
+	}
 }

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

@@ -36,6 +36,19 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 
 	public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5;
 	private static final String NAME_CLEANING_REGEX = "[\\r\\n\\t\\s]+";
+	private static final HashSet<String> PEER_REVIEWED_TYPES = new HashSet<>();
+
+	static {
+		PEER_REVIEWED_TYPES.add("Article");
+		PEER_REVIEWED_TYPES.add("Part of book or chapter of book");
+		PEER_REVIEWED_TYPES.add("Book");
+		PEER_REVIEWED_TYPES.add("Doctoral thesis");
+		PEER_REVIEWED_TYPES.add("Master thesis");
+		PEER_REVIEWED_TYPES.add("Data Paper");
+		PEER_REVIEWED_TYPES.add("Thesis");
+		PEER_REVIEWED_TYPES.add("Bachelor thesis");
+		PEER_REVIEWED_TYPES.add("Conference object");
+	}
 
 	public static <T extends Oaf> T cleanContext(T value, String contextId, String verifyParam) {
 		if (ModelSupport.isSubClass(value, Result.class)) {
@@ -273,6 +286,12 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 
 	public static <T extends Oaf> T cleanup(T value, VocabularyGroup vocs) {
 
+		if (Objects.isNull(value.getDataInfo())) {
+			final DataInfo d = new DataInfo();
+			d.setDeletedbyinference(false);
+			value.setDataInfo(d);
+		}
+
 		if (value instanceof OafEntity) {
 
 			OafEntity e = (OafEntity) value;
@@ -292,6 +311,10 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 			} else if (value instanceof Result) {
 				Result r = (Result) value;
 
+				if (Objects.isNull(r.getContext())) {
+					r.setContext(new ArrayList<>());
+				}
+
 				if (Objects.nonNull(r.getFulltext())
 					&& (ModelConstants.SOFTWARE_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()) ||
 						ModelConstants.DATASET_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()))) {
@@ -493,6 +516,35 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 						if (Objects.isNull(i.getRefereed()) || StringUtils.isBlank(i.getRefereed().getClassid())) {
 							i.setRefereed(qualifier("0000", "Unknown", ModelConstants.DNET_REVIEW_LEVELS));
 						}
+
+						// from the script from Dimitris
+						if ("0000".equals(i.getRefereed().getClassid())) {
+							final boolean isFromCrossref = Optional
+								.ofNullable(i.getCollectedfrom())
+								.map(KeyValue::getKey)
+								.map(id -> id.equals(ModelConstants.CROSSREF_ID))
+								.orElse(false);
+							final boolean hasDoi = Optional
+								.ofNullable(i.getPid())
+								.map(
+									pid -> pid
+										.stream()
+										.anyMatch(
+											p -> PidType.doi.toString().equals(p.getQualifier().getClassid())))
+								.orElse(false);
+							final boolean isPeerReviewedType = PEER_REVIEWED_TYPES
+								.contains(i.getInstancetype().getClassname());
+							final boolean noOtherLitType = r
+								.getInstance()
+								.stream()
+								.noneMatch(ii -> "Other literature type".equals(ii.getInstancetype().getClassname()));
+							if (isFromCrossref && hasDoi && isPeerReviewedType && noOtherLitType) {
+								i.setRefereed(qualifier("0001", "peerReviewed", ModelConstants.DNET_REVIEW_LEVELS));
+							} else {
+								i.setRefereed(qualifier("0002", "nonPeerReviewed", ModelConstants.DNET_REVIEW_LEVELS));
+							}
+						}
+
 						if (Objects.nonNull(i.getDateofacceptance())) {
 							Optional<String> date = cleanDateField(i.getDateofacceptance());
 							if (date.isPresent()) {

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/util/DiffPatchMatch.java

@@ -1,24 +1,6 @@
 
 package eu.dnetlib.pace.util;
 
-/*
- * Diff Match and Patch
- * Copyright 2018 The diff-match-patch Authors.
- * https://github.com/google/diff-match-patch
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
 /*
  * Diff Match and Patch
  * Copyright 2018 The diff-match-patch Authors.

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java

@@ -40,6 +40,7 @@ public class Constants {
 	public static final String SDG_CLASS_NAME = "Sustainable Development Goals";
 
 	public static final String NULL = "NULL";
+	public static final String NA = "N/A";
 
 	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
@@ -61,10 +62,16 @@ public class Constants {
 			.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
 	}
 
-	public static Subject getSubject(String sbj, String classid, String classname,
+	public static Subject getSubject(String sbj, String classid, String classname, String diqualifierclassid,
-		String diqualifierclassid) {
+		Boolean split) {
-		if (sbj == null || sbj.equals(NULL))
+		if (sbj == null || sbj.equals(NULL) || sbj.startsWith(NA))
 			return null;
+		String trust = "";
+		String subject = sbj;
+		if (split) {
+			sbj = subject.split("@@")[0];
+			trust = subject.split("@@")[1];
+		}
 		Subject s = new Subject();
 		s.setValue(sbj);
 		s
@@ -89,9 +96,14 @@ public class Constants {
 								UPDATE_CLASS_NAME,
 								ModelConstants.DNET_PROVENANCE_ACTIONS,
 								ModelConstants.DNET_PROVENANCE_ACTIONS),
-						""));
+						trust));
 
 		return s;
+	}
+
+	public static Subject getSubject(String sbj, String classid, String classname,
+		String diqualifierclassid) {
+		return getSubject(sbj, classid, classname, diqualifierclassid, false);
 
 	}
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSSparkJob.java

@@ -75,9 +75,12 @@ public class GetFOSSparkJob implements Serializable {
 		fosData.map((MapFunction<Row, FOSDataModel>) r -> {
 			FOSDataModel fosDataModel = new FOSDataModel();
 			fosDataModel.setDoi(r.getString(0).toLowerCase());
-			fosDataModel.setLevel1(r.getString(1));
+			fosDataModel.setLevel1(r.getString(2));
-			fosDataModel.setLevel2(r.getString(2));
+			fosDataModel.setLevel2(r.getString(3));
-			fosDataModel.setLevel3(r.getString(3));
+			fosDataModel.setLevel3(r.getString(4));
+			fosDataModel.setLevel4(r.getString(5));
+			fosDataModel.setScoreL3(String.valueOf(r.getDouble(6)));
+			fosDataModel.setScoreL4(String.valueOf(r.getDouble(7)));
 			return fosDataModel;
 		}, Encoders.bean(FOSDataModel.class))
 			.write()

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java

@@ -1,178 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
-
-import static eu.dnetlib.dhp.actionmanager.Constants.*;
-import static eu.dnetlib.dhp.actionmanager.Constants.UPDATE_CLASS_NAME;
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.io.Serializable;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Optional;
-import java.util.stream.Collectors;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.JavaRDD;
-import org.apache.spark.api.java.JavaSparkContext;
-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.actionmanager.bipmodel.BipScore;
-import eu.dnetlib.dhp.actionmanager.bipmodel.score.deserializers.BipResultModel;
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Instance;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
-import eu.dnetlib.dhp.schema.oaf.Measure;
-import eu.dnetlib.dhp.schema.oaf.Result;
-import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
-import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
-import eu.dnetlib.dhp.utils.DHPUtils;
-
-public class PrepareBipFinder implements Serializable {
-
-	private static final Logger log = LoggerFactory.getLogger(PrepareBipFinder.class);
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
-	public static void main(String[] args) throws Exception {
-
-		String jsonConfiguration = IOUtils
-			.toString(
-				PrepareBipFinder.class
-					.getResourceAsStream(
-						"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_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);
-
-		final String sourcePath = parser.get("sourcePath");
-		log.info("sourcePath {}: ", sourcePath);
-
-		final String outputPath = parser.get("outputPath");
-		log.info("outputPath {}: ", outputPath);
-
-		SparkConf conf = new SparkConf();
-
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
-				prepareResults(spark, sourcePath, outputPath);
-			});
-	}
-
-	private static void prepareResults(SparkSession spark, String inputPath, String outputPath) {
-
-		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-
-		JavaRDD<BipResultModel> bipDeserializeJavaRDD = sc
-			.textFile(inputPath)
-			.map(item -> OBJECT_MAPPER.readValue(item, BipResultModel.class));
-
-		spark
-			.createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> {
-				BipScore bs = new BipScore();
-				bs.setId(key);
-				bs.setScoreList(entry.get(key));
-
-				return bs;
-			}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class))
-			.map((MapFunction<BipScore, Result>) v -> {
-				Result r = new Result();
-				final String cleanedPid = CleaningFunctions.normalizePidValue(DOI, v.getId());
-
-				r.setId(DHPUtils.generateUnresolvedIdentifier(v.getId(), DOI));
-				Instance inst = new Instance();
-				inst.setMeasures(getMeasure(v));
-
-				inst
-					.setPid(
-						Arrays
-							.asList(
-								OafMapperUtils
-									.structuredProperty(
-										cleanedPid,
-										OafMapperUtils
-											.qualifier(
-												DOI, DOI_CLASSNAME,
-												ModelConstants.DNET_PID_TYPES,
-												ModelConstants.DNET_PID_TYPES),
-										null)));
-				r.setInstance(Arrays.asList(inst));
-				r
-					.setDataInfo(
-						OafMapperUtils
-							.dataInfo(
-								false, null, true,
-								false,
-								OafMapperUtils
-									.qualifier(
-										ModelConstants.PROVENANCE_ENRICH,
-										null,
-										ModelConstants.DNET_PROVENANCE_ACTIONS,
-										ModelConstants.DNET_PROVENANCE_ACTIONS),
-								null));
-				return r;
-			}, Encoders.bean(Result.class))
-			.write()
-			.mode(SaveMode.Overwrite)
-			.option("compression", "gzip")
-			.json(outputPath + "/bip");
-	}
-
-	private static List<Measure> getMeasure(BipScore value) {
-		return value
-			.getScoreList()
-			.stream()
-			.map(score -> {
-				Measure m = new Measure();
-				m.setId(score.getId());
-				m
-					.setUnit(
-						score
-							.getUnit()
-							.stream()
-							.map(unit -> {
-								KeyValue kv = new KeyValue();
-								kv.setValue(unit.getValue());
-								kv.setKey(unit.getKey());
-								kv
-									.setDataInfo(
-										OafMapperUtils
-											.dataInfo(
-												false,
-												UPDATE_DATA_INFO_TYPE,
-												true,
-												false,
-												OafMapperUtils
-													.qualifier(
-														UPDATE_MEASURE_BIP_CLASS_ID,
-														UPDATE_CLASS_NAME,
-														ModelConstants.DNET_PROVENANCE_ACTIONS,
-														ModelConstants.DNET_PROVENANCE_ACTIONS),
-												""));
-								return kv;
-							})
-							.collect(Collectors.toList()));
-				return m;
-			})
-			.collect(Collectors.toList());
-	}
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java

@@ -78,12 +78,20 @@ public class PrepareFOSSparkJob implements Serializable {
 				HashSet<String> level1 = new HashSet<>();
 				HashSet<String> level2 = new HashSet<>();
 				HashSet<String> level3 = new HashSet<>();
-				addLevels(level1, level2, level3, first);
+				HashSet<String> level4 = new HashSet<>();
-				it.forEachRemaining(v -> addLevels(level1, level2, level3, v));
+				addLevels(level1, level2, level3, level4, first);
+				it.forEachRemaining(v -> addLevels(level1, level2, level3, level4, v));
 				List<Subject> sbjs = new ArrayList<>();
-				level1.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
+				level1
-				level2.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
+					.forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
-				level3.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
+				level2
+					.forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
+				level3
+					.forEach(
+						l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true)));
+				level4
+					.forEach(
+						l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true)));
 				r.setSubject(sbjs);
 				r
 					.setDataInfo(
@@ -106,11 +114,18 @@ public class PrepareFOSSparkJob implements Serializable {
 			.json(outputPath + "/fos");
 	}
 
+	private static void add(List<Subject> sbsjs, Subject sbj) {
+		if (sbj != null)
+			sbsjs.add(sbj);
+	}
+
 	private static void addLevels(HashSet<String> level1, HashSet<String> level2, HashSet<String> level3,
+		HashSet<String> level4,
 		FOSDataModel first) {
 		level1.add(first.getLevel1());
 		level2.add(first.getLevel2());
-		level3.add(first.getLevel3());
+		level3.add(first.getLevel3() + "@@" + first.getScoreL3());
+		level4.add(first.getLevel4() + "@@" + first.getScoreL4());
 	}
 
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java

@@ -69,9 +69,9 @@ public class SparkSaveUnresolved implements Serializable {
 			.mapGroups((MapGroupsFunction<String, Result, Result>) (k, it) -> {
 				Result ret = it.next();
 				it.forEachRemaining(r -> {
-					if (r.getInstance() != null) {
+//					if (r.getInstance() != null) {
-						ret.setInstance(r.getInstance());
+//						ret.setInstance(r.getInstance());
-					}
+//					}
 					if (r.getSubject() != null) {
 						if (ret.getSubject() != null)
 							ret.getSubject().addAll(r.getSubject());

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/FOSDataModel.java

@@ -11,21 +11,43 @@ public class FOSDataModel implements Serializable {
 	private String doi;
 
 	@CsvBindByPosition(position = 1)
+//    @CsvBindByName(column = "doi")
+	private String oaid;
+	@CsvBindByPosition(position = 2)
 //    @CsvBindByName(column = "level1")
 	private String level1;
 
-	@CsvBindByPosition(position = 2)
+	@CsvBindByPosition(position = 3)
 //    @CsvBindByName(column = "level2")
 	private String level2;
 
-	@CsvBindByPosition(position = 3)
+	@CsvBindByPosition(position = 4)
 //    @CsvBindByName(column = "level3")
 	private String level3;
 
+	@CsvBindByPosition(position = 5)
+//    @CsvBindByName(column = "level3")
+	private String level4;
+	@CsvBindByPosition(position = 6)
+	private String scoreL3;
+	@CsvBindByPosition(position = 7)
+	private String scoreL4;
+
 	public FOSDataModel() {
 
 	}
 
+	public FOSDataModel(String doi, String level1, String level2, String level3, String level4, String l3score,
+		String l4score) {
+		this.doi = doi;
+		this.level1 = level1;
+		this.level2 = level2;
+		this.level3 = level3;
+		this.level4 = level4;
+		this.scoreL3 = l3score;
+		this.scoreL4 = l4score;
+	}
+
 	public FOSDataModel(String doi, String level1, String level2, String level3) {
 		this.doi = doi;
 		this.level1 = level1;
@@ -33,8 +55,41 @@ public class FOSDataModel implements Serializable {
 		this.level3 = level3;
 	}
 
-	public static FOSDataModel newInstance(String d, String level1, String level2, String level3) {
+	public static FOSDataModel newInstance(String d, String level1, String level2, String level3, String level4,
-		return new FOSDataModel(d, level1, level2, level3);
+		String scorel3, String scorel4) {
+		return new FOSDataModel(d, level1, level2, level3, level4, scorel3, scorel4);
+	}
+
+	public String getOaid() {
+		return oaid;
+	}
+
+	public void setOaid(String oaid) {
+		this.oaid = oaid;
+	}
+
+	public String getLevel4() {
+		return level4;
+	}
+
+	public void setLevel4(String level4) {
+		this.level4 = level4;
+	}
+
+	public String getScoreL3() {
+		return scoreL3;
+	}
+
+	public void setScoreL3(String scoreL3) {
+		this.scoreL3 = scoreL3;
+	}
+
+	public String getScoreL4() {
+		return scoreL4;
+	}
+
+	public void setScoreL4(String scoreL4) {
+		this.scoreL4 = scoreL4;
 	}
 
 	public String getDoi() {

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java

@@ -10,8 +10,10 @@ import java.util.*;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaPairRDD;
 import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.api.java.function.MapFunction;
@@ -26,19 +28,29 @@ import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
+import eu.dnetlib.dhp.schema.oaf.utils.*;
-import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.utils.DHPUtils;
 import scala.Tuple2;
 
 public class CreateActionSetSparkJob implements Serializable {
 	public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
 	public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
-	private static final String ID_PREFIX = "50|doi_________::";
+
+	// DOI-to-DOI citations
+	public static final String COCI = "COCI";
+
+	// PMID-to-PMID citations
+	public static final String POCI = "POCI";
+
+	private static final String DOI_PREFIX = "50|doi_________::";
+
+	private static final String PMID_PREFIX = "50|pmid________::";
+
 	private static final String TRUST = "0.91";
 
 	private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
+
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
 	public static void main(final String[] args) throws IOException, ParseException {
@@ -62,7 +74,7 @@ public class CreateActionSetSparkJob implements Serializable {
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
 		final String inputPath = parser.get("inputPath");
-		log.info("inputPath {}", inputPath.toString());
+		log.info("inputPath {}", inputPath);
 
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath {}", outputPath);
@@ -76,41 +88,68 @@ public class CreateActionSetSparkJob implements Serializable {
 		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
-			spark -> {
+			spark -> extractContent(spark, inputPath, outputPath, shouldDuplicateRels));
-				extractContent(spark, inputPath, outputPath, shouldDuplicateRels);
-			});
 
 	}
 
 	private static void extractContent(SparkSession spark, String inputPath, String outputPath,
 		boolean shouldDuplicateRels) {
-		spark
+
+		getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, COCI)
+			.union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, POCI))
+			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+	}
+
+	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath,
+		boolean shouldDuplicateRels, String prefix) {
+		return spark
 			.read()
-			.textFile(inputPath + "/*")
+			.textFile(inputPath + "/" + prefix + "/" + prefix + "_JSON/*")
 			.map(
 				(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
 				Encoders.bean(COCI.class))
 			.flatMap(
-				(FlatMapFunction<COCI, Relation>) value -> createRelation(value, shouldDuplicateRels).iterator(),
+				(FlatMapFunction<COCI, Relation>) value -> createRelation(
+					value, shouldDuplicateRels, prefix)
+						.iterator(),
 				Encoders.bean(Relation.class))
-			.filter((FilterFunction<Relation>) value -> value != null)
+			.filter((FilterFunction<Relation>) Objects::nonNull)
 			.toJavaRDD()
 			.map(p -> new AtomicAction(p.getClass(), p))
 			.mapToPair(
 				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
-			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
-
 	}
 
-	private static List<Relation> createRelation(COCI value, boolean duplicate) {
+	private static List<Relation> createRelation(COCI value, boolean duplicate, String p) {
 
 		List<Relation> relationList = new ArrayList<>();
+		String prefix;
+		String citing;
+		String cited;
 
-		String citing = ID_PREFIX
+		switch (p) {
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCiting()));
+			case COCI:
-		final String cited = ID_PREFIX
+				prefix = DOI_PREFIX;
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCited()));
+				citing = prefix
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting()));
+				cited = prefix
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCited()));
+				break;
+			case POCI:
+				prefix = PMID_PREFIX;
+				citing = prefix
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCiting()));
+				cited = prefix
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCited()));
+				break;
+			default:
+				throw new IllegalStateException("Invalid prefix: " + p);
+		}
 
 		if (!citing.equals(cited)) {
 			relationList
@@ -120,7 +159,7 @@ public class CreateActionSetSparkJob implements Serializable {
 						cited, ModelConstants.CITES));
 
 			if (duplicate && value.getCiting().endsWith(".refs")) {
-				citing = ID_PREFIX + IdentifierFactory
+				citing = prefix + IdentifierFactory
 					.md5(
 						CleaningFunctions
 							.normalizePidValue(
@@ -132,59 +171,30 @@ public class CreateActionSetSparkJob implements Serializable {
 		return relationList;
 	}
 
-	private static Collection<Relation> getRelations(String citing, String cited) {
-
-		return Arrays
-			.asList(
-				getRelation(citing, cited, ModelConstants.CITES),
-				getRelation(cited, citing, ModelConstants.IS_CITED_BY));
-	}
-
 	public static Relation getRelation(
 		String source,
 		String target,
-		String relclass) {
+		String relClass) {
-		Relation r = new Relation();
-		r.setCollectedfrom(getCollectedFrom());
-		r.setSource(source);
-		r.setTarget(target);
-		r.setRelClass(relclass);
-		r.setRelType(ModelConstants.RESULT_RESULT);
-		r.setSubRelType(ModelConstants.CITATION);
-		r
-			.setDataInfo(
-				getDataInfo());
-		return r;
-	}
 
-	public static List<KeyValue> getCollectedFrom() {
+		return OafMapperUtils
-		KeyValue kv = new KeyValue();
+			.getRelation(
-		kv.setKey(ModelConstants.OPENOCITATIONS_ID);
+				source,
-		kv.setValue(ModelConstants.OPENOCITATIONS_NAME);
+				target,
-
+				ModelConstants.RESULT_RESULT,
-		return Arrays.asList(kv);
+				ModelConstants.CITATION,
-	}
+				relClass,
-
+				Arrays
-	public static DataInfo getDataInfo() {
+					.asList(
-		DataInfo di = new DataInfo();
+						OafMapperUtils.keyValue(ModelConstants.OPENOCITATIONS_ID, ModelConstants.OPENOCITATIONS_NAME)),
-		di.setInferred(false);
+				OafMapperUtils
-		di.setDeletedbyinference(false);
+					.dataInfo(
-		di.setTrust(TRUST);
+						false, null, false, false,
-
+						OafMapperUtils
-		di
+							.qualifier(
-			.setProvenanceaction(
+								OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME,
-				getQualifier(OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS));
+								ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
-		return di;
+						TRUST),
-	}
+				null);
-
-	public static Qualifier getQualifier(String class_id, String class_name,
-		String qualifierSchema) {
-		Qualifier pa = new Qualifier();
-		pa.setClassid(class_id);
-		pa.setClassname(class_name);
-		pa.setSchemeid(qualifierSchema);
-		pa.setSchemename(qualifierSchema);
-		return pa;
 	}
 
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java

@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.actionmanager.opencitations;
 
 import java.io.*;
 import java.io.Serializable;
+import java.util.Arrays;
 import java.util.Objects;
 import java.util.zip.GZIPOutputStream;
 import java.util.zip.ZipEntry;
@@ -37,7 +38,7 @@ public class GetOpenCitationsRefs implements Serializable {
 		parser.parseArgument(args);
 
 		final String[] inputFile = parser.get("inputFile").split(";");
-		log.info("inputFile {}", inputFile.toString());
+		log.info("inputFile {}", Arrays.asList(inputFile));
 
 		final String workingPath = parser.get("workingPath");
 		log.info("workingPath {}", workingPath);
@@ -45,6 +46,9 @@ public class GetOpenCitationsRefs implements Serializable {
 		final String hdfsNameNode = parser.get("hdfsNameNode");
 		log.info("hdfsNameNode {}", hdfsNameNode);
 
+		final String prefix = parser.get("prefix");
+		log.info("prefix {}", prefix);
+
 		Configuration conf = new Configuration();
 		conf.set("fs.defaultFS", hdfsNameNode);
 
@@ -53,30 +57,31 @@ public class GetOpenCitationsRefs implements Serializable {
 		GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
 
 		for (String file : inputFile) {
-			ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem);
+			ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem, prefix);
 		}
 
 	}
 
-	private void doExtract(String inputFile, String workingPath, FileSystem fileSystem)
+	private void doExtract(String inputFile, String workingPath, FileSystem fileSystem, String prefix)
 		throws IOException {
 
 		final Path path = new Path(inputFile);
 
 		FSDataInputStream oc_zip = fileSystem.open(path);
 
-		int count = 1;
+		// int count = 1;
 		try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
 			ZipEntry entry = null;
 			while ((entry = zis.getNextEntry()) != null) {
 
 				if (!entry.isDirectory()) {
 					String fileName = entry.getName();
-					fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
+					// fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
-					count++;
+					fileName = fileName.substring(0, fileName.lastIndexOf("."));
+					// count++;
 					try (
 						FSDataOutputStream out = fileSystem
-							.create(new Path(workingPath + "/COCI/" + fileName + ".gz"));
+							.create(new Path(workingPath + "/" + prefix + "/" + fileName + ".gz"));
 						GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
 
 						IOUtils.copy(zis, gzipOs);

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java

@@ -7,6 +7,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.IOException;
 import java.io.Serializable;
+import java.util.Arrays;
 import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
@@ -42,13 +43,16 @@ public class ReadCOCI implements Serializable {
 		log.info("outputPath: {}", outputPath);
 
 		final String[] inputFile = parser.get("inputFile").split(";");
-		log.info("inputFile {}", inputFile.toString());
+		log.info("inputFile {}", Arrays.asList(inputFile));
 		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
 		final String workingPath = parser.get("workingPath");
 		log.info("workingPath {}", workingPath);
 
+		final String format = parser.get("format");
+		log.info("format {}", format);
+
 		SparkConf sconf = new SparkConf();
 
 		final String delimiter = Optional
@@ -64,16 +68,17 @@ public class ReadCOCI implements Serializable {
 					workingPath,
 					inputFile,
 					outputPath,
-					delimiter);
+					delimiter,
+					format);
 			});
 	}
 
 	private static void doRead(SparkSession spark, String workingPath, String[] inputFiles,
 		String outputPath,
-		String delimiter) throws IOException {
+		String delimiter, String format) {
 
 		for (String inputFile : inputFiles) {
-			String p_string = workingPath + "/" + inputFile + ".gz";
+			String pString = workingPath + "/" + inputFile + ".gz";
 
 			Dataset<Row> cociData = spark
 				.read()
@@ -82,14 +87,20 @@ public class ReadCOCI implements Serializable {
 				.option("inferSchema", "true")
 				.option("header", "true")
 				.option("quotes", "\"")
-				.load(p_string)
+				.load(pString)
 				.repartition(100);
 
 			cociData.map((MapFunction<Row, COCI>) row -> {
 				COCI coci = new COCI();
+				if (format.equals("COCI")) {
+					coci.setCiting(row.getString(1));
+					coci.setCited(row.getString(2));
+				} else {
+					coci.setCiting(String.valueOf(row.getInt(1)));
+					coci.setCited(String.valueOf(row.getInt(2)));
+				}
 				coci.setOci(row.getString(0));
-				coci.setCiting(row.getString(1));
+
-				coci.setCited(row.getString(2));
 				return coci;
 			}, Encoders.bean(COCI.class))
 				.write()

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml

@@ -5,11 +5,6 @@
             <name>fosPath</name>
             <description>the input path of the resources to be extended</description>
         </property>
-
-        <property>
-            <name>bipScorePath</name>
-            <description>the path where to find the bipFinder scores</description>
-        </property>
         <property>
             <name>outputPath</name>
             <description>the path where to store the actionset</description>
@@ -77,35 +72,10 @@
 
 
     <fork name="prepareInfo">
-        <path start="prepareBip"/>
         <path start="getFOS"/>
         <path start="getSDG"/>
     </fork>
 
-    <action name="prepareBip">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Produces the unresolved from BIP! Finder</name>
-            <class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareBipFinder</class>
-            <jar>dhp-aggregation-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
-                --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}${spark2EventLogDir}
-                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
-            </spark-opts>
-            <arg>--sourcePath</arg><arg>${bipScorePath}</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/prepared</arg>
-        </spark>
-        <ok to="join"/>
-        <error to="Kill"/>
-    </action>
-
     <action name="getFOS">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -125,6 +95,7 @@
             </spark-opts>
             <arg>--sourcePath</arg><arg>${fosPath}</arg>
             <arg>--outputPath</arg><arg>${workingDir}/input/fos</arg>
+            <arg>--delimiter</arg><arg>${delimiter}</arg>
         </spark>
         <ok to="prepareFos"/>
         <error to="Kill"/>
@@ -213,7 +184,7 @@
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
             <mode>cluster</mode>
-            <name>Saves the result produced for bip and fos by grouping results with the same id</name>
+            <name>Save the unresolved entities grouping results with the same id</name>
             <class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.SparkSaveUnresolved</class>
             <jar>dhp-aggregation-${projectVersion}.jar</jar>
             <spark-opts>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json

@@ -16,10 +16,11 @@
     "paramLongName": "isSparkSessionManaged",
     "paramDescription": "the hdfs name node",
     "paramRequired": false
-  },  {
+  },
-  "paramName": "sdr",
+  {
-  "paramLongName": "shouldDuplicateRels",
+    "paramName": "sdr",
-  "paramDescription": "the hdfs name node",
+    "paramLongName": "shouldDuplicateRels",
-  "paramRequired": false
+    "paramDescription": "activates/deactivates the construction of bidirectional relations Cites/IsCitedBy",
-}
+    "paramRequired": false
+  }
 ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json

@@ -16,5 +16,11 @@
     "paramLongName": "hdfsNameNode",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
+  },
+  {
+    "paramName": "p",
+    "paramLongName": "prefix",
+    "paramDescription": "COCI or POCI",
+    "paramRequired": true
   }
 ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json

@@ -30,7 +30,12 @@
     "paramLongName": "inputFile",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
-  }
+  }, {
+  "paramName": "f",
+  "paramLongName": "format",
+  "paramDescription": "the hdfs name node",
+  "paramRequired": true
+}
 ]
 
 

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml

@@ -34,6 +34,7 @@
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
+
     <action name="download">
         <shell xmlns="uri:oozie:shell-action:0.2">
             <job-tracker>${jobTracker}</job-tracker>
@@ -46,7 +47,7 @@
             </configuration>
             <exec>download.sh</exec>
             <argument>${filelist}</argument>
-            <argument>${workingPath}/Original</argument>
+            <argument>${workingPath}/${prefix}/Original</argument>
             <env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
             <file>download.sh</file>
             <capture-output/>
@@ -54,12 +55,14 @@
         <ok to="extract"/>
         <error to="Kill"/>
     </action>
+
     <action name="extract">
         <java>
             <main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
             <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
             <arg>--inputFile</arg><arg>${inputFile}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingPath</arg><arg>${workingPath}/${prefix}</arg>
+            <arg>--prefix</arg><arg>${prefix}</arg>
         </java>
         <ok to="read"/>
         <error to="Kill"/>
@@ -82,10 +85,11 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
             </spark-opts>
-            <arg>--workingPath</arg><arg>${workingPath}/COCI</arg>
+            <arg>--workingPath</arg><arg>${workingPath}/${prefix}/${prefix}</arg>
-            <arg>--outputPath</arg><arg>${workingPath}/COCI_JSON/</arg>
+            <arg>--outputPath</arg><arg>${workingPath}/${prefix}/${prefix}_JSON/</arg>
             <arg>--delimiter</arg><arg>${delimiter}</arg>
             <arg>--inputFile</arg><arg>${inputFileCoci}</arg>
+            <arg>--format</arg><arg>${prefix}</arg>
         </spark>
         <ok to="create_actionset"/>
         <error to="Kill"/>
@@ -108,7 +112,7 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
             </spark-opts>
-            <arg>--inputPath</arg><arg>${workingPath}/COCI_JSON</arg>
+            <arg>--inputPath</arg><arg>${workingPath}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFosTest.java

@@ -13,10 +13,7 @@ import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.sql.SparkSession;
-import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.*;
-import org.junit.jupiter.api.Assertions;
-import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -68,6 +65,7 @@ public class GetFosTest {
 	}
 
 	@Test
+	@Disabled
 	void test3() throws Exception {
 		final String sourcePath = getClass()
 			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs.tsv")
@@ -96,4 +94,37 @@ public class GetFosTest {
 		tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
 
 	}
+
+	@Test
+	void test4() throws Exception {
+		final String sourcePath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs2.csv")
+			.getPath();
+
+		final String outputPath = workingDir.toString() + "/fos.json";
+		GetFOSSparkJob
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--sourcePath", sourcePath,
+					"--delimiter", ",",
+					"-outputPath", outputPath
+
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<FOSDataModel> tmp = sc
+			.textFile(outputPath)
+			.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
+
+		tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getLevel4() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getScoreL3() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getScoreL4() != null));
+
+	}
 }

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java

@@ -67,92 +67,6 @@ public class PrepareTest {
 		spark.stop();
 	}
 
-	@Test
-	void bipPrepareTest() throws Exception {
-		final String sourcePath = getClass()
-			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
-			.getPath();
-
-		PrepareBipFinder
-			.main(
-				new String[] {
-					"--isSparkSessionManaged", Boolean.FALSE.toString(),
-					"--sourcePath", sourcePath,
-					"--outputPath", workingDir.toString() + "/work"
-
-				});
-
-		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-
-		JavaRDD<Result> tmp = sc
-			.textFile(workingDir.toString() + "/work/bip")
-			.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
-
-		Assertions.assertEquals(86, tmp.count());
-
-		String doi1 = "unresolved::10.0000/096020199389707::doi";
-
-		Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).count());
-		Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().size());
-		Assertions
-			.assertEquals(
-				3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().get(0).getMeasures().size());
-		Assertions
-			.assertEquals(
-				"6.34596412687e-09", tmp
-					.filter(r -> r.getId().equals(doi1))
-					.collect()
-					.get(0)
-					.getInstance()
-					.get(0)
-					.getMeasures()
-					.stream()
-					.filter(sl -> sl.getId().equals("influence"))
-					.collect(Collectors.toList())
-					.get(0)
-					.getUnit()
-					.get(0)
-					.getValue());
-		Assertions
-			.assertEquals(
-				"0.641151896994", tmp
-					.filter(r -> r.getId().equals(doi1))
-					.collect()
-					.get(0)
-					.getInstance()
-					.get(0)
-					.getMeasures()
-					.stream()
-					.filter(sl -> sl.getId().equals("popularity_alt"))
-					.collect(Collectors.toList())
-					.get(0)
-					.getUnit()
-					.get(0)
-					.getValue());
-		Assertions
-			.assertEquals(
-				"2.33375102921e-09", tmp
-					.filter(r -> r.getId().equals(doi1))
-					.collect()
-					.get(0)
-					.getInstance()
-					.get(0)
-					.getMeasures()
-					.stream()
-					.filter(sl -> sl.getId().equals("popularity"))
-					.collect(Collectors.toList())
-					.get(0)
-					.getUnit()
-					.get(0)
-					.getValue());
-
-		final String doi2 = "unresolved::10.3390/s18072310::doi";
-
-		Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).count());
-		Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).collect().get(0).getInstance().size());
-
-	}
-
 	@Test
 	void fosPrepareTest() throws Exception {
 		final String sourcePath = getClass()
@@ -222,6 +136,76 @@ public class PrepareTest {
 
 	}
 
+	@Test
+	void fosPrepareTest2() throws Exception {
+		final String sourcePath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs_2.json")
+			.getPath();
+
+		PrepareFOSSparkJob
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--sourcePath", sourcePath,
+
+					"-outputPath", workingDir.toString() + "/work"
+
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Result> tmp = sc
+			.textFile(workingDir.toString() + "/work/fos")
+			.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
+
+		String doi1 = "unresolved::10.1016/j.revmed.2006.07.012::doi";
+
+		assertEquals(13, tmp.count());
+		assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count());
+
+		Result result = tmp
+			.filter(r -> r.getId().equals(doi1))
+			.first();
+
+		result.getSubject().forEach(s -> System.out.println(s.getValue() + " trust = " + s.getDataInfo().getTrust()));
+		Assertions.assertEquals(6, result.getSubject().size());
+
+		assertTrue(
+			result
+				.getSubject()
+				.stream()
+				.anyMatch(
+					s -> s.getValue().contains("03 medical and health sciences")
+						&& s.getDataInfo().getTrust().equals("")));
+
+		assertTrue(
+			result
+				.getSubject()
+				.stream()
+				.anyMatch(
+					s -> s.getValue().contains("0302 clinical medicine") && s.getDataInfo().getTrust().equals("")));
+
+		assertTrue(
+			result
+				.getSubject()
+				.stream()
+				.anyMatch(
+					s -> s
+						.getValue()
+						.contains("030204 cardiovascular system & hematology")
+						&& s.getDataInfo().getTrust().equals("0.5101401805877686")));
+		assertTrue(
+			result
+				.getSubject()
+				.stream()
+				.anyMatch(
+					s -> s
+						.getValue()
+						.contains("03020409 Hematology/Coagulopathies")
+						&& s.getDataInfo().getTrust().equals("0.0546871414174914")));
+
+	}
+
 	@Test
 	void sdgPrepareTest() throws Exception {
 		final String sourcePath = getClass()
@@ -268,57 +252,4 @@ public class PrepareTest {
 
 	}
 
-//	@Test
-//	void test3() throws Exception {
-//		final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_fos_results_20_12_2021.csv.gz";
-//
-//		final String outputPath = workingDir.toString() + "/fos.json";
-//		GetFOSSparkJob
-//			.main(
-//				new String[] {
-//					"--isSparkSessionManaged", Boolean.FALSE.toString(),
-//					"--sourcePath", sourcePath,
-//
-//					"-outputPath", outputPath
-//
-//				});
-//
-//		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-//
-//		JavaRDD<FOSDataModel> tmp = sc
-//			.textFile(outputPath)
-//			.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
-//
-//		tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
-//		tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null));
-//		tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null));
-//		tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
-//
-//	}
-//
-//	@Test
-//	void test4() throws Exception {
-//		final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_sdg_results_20_12_21.csv.gz";
-//
-//		final String outputPath = workingDir.toString() + "/sdg.json";
-//		GetSDGSparkJob
-//			.main(
-//				new String[] {
-//					"--isSparkSessionManaged", Boolean.FALSE.toString(),
-//					"--sourcePath", sourcePath,
-//
-//					"-outputPath", outputPath
-//
-//				});
-//
-//		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-//
-//		JavaRDD<SDGDataModel> tmp = sc
-//			.textFile(outputPath)
-//			.map(item -> OBJECT_MAPPER.readValue(item, SDGDataModel.class));
-//
-//		tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
-//		tmp.foreach(t -> Assertions.assertTrue(t.getSbj() != null));
-//
-//	}
 }

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java

@@ -340,18 +340,7 @@ public class ProduceTest {
 	}
 
 	private JavaRDD<Result> getResultJavaRDD() throws Exception {
-		final String bipPath = getClass()
-			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
-			.getPath();
 
-		PrepareBipFinder
-			.main(
-				new String[] {
-					"--isSparkSessionManaged", Boolean.FALSE.toString(),
-					"--sourcePath", bipPath,
-					"--outputPath", workingDir.toString() + "/work"
-
-				});
 		final String fosPath = getClass()
 			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json")
 			.getPath();
@@ -379,6 +368,40 @@ public class ProduceTest {
 			.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
 	}
 
+	@Test
+	public JavaRDD<Result> getResultFosJavaRDD() throws Exception {
+
+		final String fosPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs_2.json")
+			.getPath();
+
+		PrepareFOSSparkJob
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--sourcePath", fosPath,
+					"-outputPath", workingDir.toString() + "/work"
+				});
+
+		SparkSaveUnresolved.main(new String[] {
+			"--isSparkSessionManaged", Boolean.FALSE.toString(),
+			"--sourcePath", workingDir.toString() + "/work",
+
+			"-outputPath", workingDir.toString() + "/unresolved"
+
+		});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Result> tmp = sc
+			.textFile(workingDir.toString() + "/unresolved")
+			.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
+		tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
+
+		return tmp;
+
+	}
+
 	@Test
 	void prepareTest5Subjects() throws Exception {
 		final String doi = "unresolved::10.1063/5.0032658::doi";
@@ -415,18 +438,7 @@ public class ProduceTest {
 	}
 
 	private JavaRDD<Result> getResultJavaRDDPlusSDG() throws Exception {
-		final String bipPath = getClass()
-			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
-			.getPath();
 
-		PrepareBipFinder
-			.main(
-				new String[] {
-					"--isSparkSessionManaged", Boolean.FALSE.toString(),
-					"--sourcePath", bipPath,
-					"--outputPath", workingDir.toString() + "/work"
-
-				});
 		final String fosPath = getClass()
 			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json")
 			.getPath();
@@ -483,14 +495,6 @@ public class ProduceTest {
 					.filter(row -> row.getSubject() != null)
 					.count());
 
-		Assertions
-			.assertEquals(
-				85,
-				tmp
-					.filter(row -> !row.getId().equals(doi))
-					.filter(r -> r.getInstance() != null && r.getInstance().size() > 0)
-					.count());
-
 	}
 
 	@Test

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs2.csv

@@ -0,0 +1,26 @@
+DOI,OAID,level1,level2,level3,level4,score_for_L3,score_for_L4
+10.1016/j.anucene.2006.02.004,doi_________::00059d9963edf633bec756fb21b5bd72,02 engineering and technology,"0202 electrical engineering, electronic engineering, information engineering",020209 energy,02020908 Climate change policy/Ethanol fuel,0.5,0.5
+10.1016/j.anucene.2006.02.004,doi_________::00059d9963edf633bec756fb21b5bd72,02 engineering and technology,0211 other engineering and technologies,021108 energy,02110808 Climate change policy/Ethanol fuel,0.5,0.5
+10.1016/j.revmed.2006.07.010,doi_________::0026476c1651a92c933d752ff12496c7,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,N/A,0.5036656856536865,0.0
+10.1016/j.revmed.2006.07.010,doi_________::0026476c1651a92c933d752ff12496c7,03 medical and health sciences,0302 clinical medicine,030212 general & internal medicine,N/A,0.4963343143463135,0.0
+10.20965/jrm.2006.p0312,doi_________::0028336a2f3826cc83c47dbefac71543,02 engineering and technology,0209 industrial biotechnology,020901 industrial engineering & automation,02090104 Robotics/Robots,0.6111094951629639,0.5053805979936855
+10.20965/jrm.2006.p0312,doi_________::0028336a2f3826cc83c47dbefac71543,01 natural sciences,0104 chemical sciences,010401 analytical chemistry,N/A,0.3888905048370361,0.0
+10.1111/j.1747-7379.2006.040_1.x,doi_________::002c7077e7c114a8304eb90f59e45fa4,05 social sciences,0506 political science,050602 political science & public administration,05060202 Ethnic groups/Ethnicity,0.6159052848815918,0.7369035568037298
+10.1111/j.1747-7379.2006.040_1.x,doi_________::002c7077e7c114a8304eb90f59e45fa4,05 social sciences,0502 economics and business,050207 economics,N/A,0.3840946555137634,0.0
+10.1007/s10512-006-0049-9,doi_________::003f29f9254819cf4c78558b1bc25f10,02 engineering and technology,"0202 electrical engineering, electronic engineering, information engineering",020209 energy,02020908 Climate change policy/Ethanol fuel,0.5,0.5
+10.1007/s10512-006-0049-9,doi_________::003f29f9254819cf4c78558b1bc25f10,02 engineering and technology,0211 other engineering and technologies,021108 energy,02110808 Climate change policy/Ethanol fuel,0.5,0.5
+10.1111/j.1365-2621.2005.01045.x,doi_________::00419355b4c3e0646bd0e1b301164c8e,04 agricultural and veterinary sciences,0404 agricultural biotechnology,040401 food science,04040102 Food science/Food industry,0.5,0.5
+10.1111/j.1365-2621.2005.01045.x,doi_________::00419355b4c3e0646bd0e1b301164c8e,04 agricultural and veterinary sciences,0405 other agricultural sciences,040502 food science,04050202 Food science/Food industry,0.5,0.5
+10.1002/chin.200617262,doi_________::004c8cef80668904961b9e62841793c8,01 natural sciences,0104 chemical sciences,010405 organic chemistry,01040508 Functional groups/Ethers,0.5566747188568115,0.5582916736602783
+10.1002/chin.200617262,doi_________::004c8cef80668904961b9e62841793c8,01 natural sciences,0104 chemical sciences,010402 general chemistry,01040207 Chemical synthesis/Total synthesis,0.4433253407478332,0.4417082965373993
+10.1016/j.revmed.2006.07.012,doi_________::005b1d0fb650b680abaf6cfe26a21604,03 medical and health sciences,0302 clinical medicine,030204 cardiovascular system & hematology,03020409 Hematology/Coagulopathies,0.5101401805877686,0.0546871414174914
+10.1016/j.revmed.2006.07.012,doi_________::005b1d0fb650b680abaf6cfe26a21604,03 medical and health sciences,0301 basic medicine,030105 genetics & heredity,N/A,0.4898599088191986,0.0
+10.4109/jslab.17.132,doi_________::00889baa06de363e37930daaf8e800c0,03 medical and health sciences,0301 basic medicine,030104 developmental biology,N/A,0.5,0.0
+10.4109/jslab.17.132,doi_________::00889baa06de363e37930daaf8e800c0,03 medical and health sciences,0303 health sciences,030304 developmental biology,N/A,0.5,0.0
+10.1108/00251740610715687,doi_________::0092cb1b1920d556719385a26363ecaa,05 social sciences,0502 economics and business,050203 business & management,05020311 International business/International trade,0.605047881603241,0.2156608108845153
+10.1108/00251740610715687,doi_________::0092cb1b1920d556719385a26363ecaa,05 social sciences,0502 economics and business,050211 marketing,N/A,0.394952118396759,0.0
+10.1080/03067310500248098,doi_________::00a76678d230e3f20b6356804448028f,04 agricultural and veterinary sciences,0404 agricultural biotechnology,040401 food science,04040102 Food science/Food industry,0.5,0.5
+10.1080/03067310500248098,doi_________::00a76678d230e3f20b6356804448028f,04 agricultural and veterinary sciences,0405 other agricultural sciences,040502 food science,04050202 Food science/Food industry,0.5,0.5
+10.3152/147154306781778533,doi_________::00acc520f3939e5a6675343881fed4f2,05 social sciences,0502 economics and business,050203 business & management,05020307 Innovation/Product management,0.5293408632278442,0.5326762795448303
+10.3152/147154306781778533,doi_________::00acc520f3939e5a6675343881fed4f2,05 social sciences,0509 other social sciences,050905 science studies,05090502 Social philosophy/Capitalism,0.4706590473651886,0.4673237204551697
+10.1785/0120050806,doi_________::00d5831d329e7ae4523d78bfc3042e98,02 engineering and technology,0211 other engineering and technologies,021101 geological & geomatics engineering,02110103 Concrete/Building materials,0.5343400835990906,0.3285667930180677

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs_2.json

@@ -0,0 +1,25 @@
+{"doi":"10.1016/j.anucene.2006.02.004","level1":"02 engineering and technology","level2":"0202 electrical engineering, electronic engineering, information engineering","level3":"020209 energy","level4":"02020908 Climate change policy/Ethanol fuel","scoreL3":"0.5","scoreL4":"0.5"}
+{"doi":"10.1016/j.anucene.2006.02.004","level1":"02 engineering and technology","level2":"0211 other engineering and technologies","level3":"021108 energy","level4":"02110808 Climate change policy/Ethanol fuel","scoreL3":"0.5","scoreL4":"0.5"}
+{"doi":"10.1016/j.revmed.2006.07.010","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030220 oncology & carcinogenesis","level4":"N/A","scoreL3":"0.5036656856536865","scoreL4":"0.0"}
+{"doi":"10.1016/j.revmed.2006.07.010","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030212 general & internal medicine","level4":"N/A","scoreL3":"0.4963343143463135","scoreL4":"0.0"}
+{"doi":"10.20965/jrm.2006.p0312","level1":"02 engineering and technology","level2":"0209 industrial biotechnology","level3":"020901 industrial engineering & automation","level4":"02090104 Robotics/Robots","scoreL3":"0.6111094951629639","scoreL4":"0.5053805979936855"}
+{"doi":"10.20965/jrm.2006.p0312","level1":"01 natural sciences","level2":"0104 chemical sciences","level3":"010401 analytical chemistry","level4":"N/A","scoreL3":"0.3888905048370361","scoreL4":"0.0"}
+{"doi":"10.1111/j.1747-7379.2006.040_1.x","level1":"05 social sciences","level2":"0506 political science","level3":"050602 political science & public administration","level4":"05060202 Ethnic groups/Ethnicity","scoreL3":"0.6159052848815918","scoreL4":"0.7369035568037298"}
+{"doi":"10.1111/j.1747-7379.2006.040_1.x","level1":"05 social sciences","level2":"0502 economics and business","level3":"050207 economics","level4":"N/A","scoreL3":"0.3840946555137634","scoreL4":"0.0"}
+{"doi":"10.1007/s10512-006-0049-9","level1":"02 engineering and technology","level2":"0202 electrical engineering, electronic engineering, information engineering","level3":"020209 energy","level4":"02020908 Climate change policy/Ethanol fuel","scoreL3":"0.5","scoreL4":"0.5"}
+{"doi":"10.1007/s10512-006-0049-9","level1":"02 engineering and technology","level2":"0211 other engineering and technologies","level3":"021108 energy","level4":"02110808 Climate change policy/Ethanol fuel","scoreL3":"0.5","scoreL4":"0.5"}
+{"doi":"10.1111/j.1365-2621.2005.01045.x","level1":"04 agricultural and veterinary sciences","level2":"0404 agricultural biotechnology","level3":"040401 food science","level4":"04040102 Food science/Food industry","scoreL3":"0.5","scoreL4":"0.5"}
+{"doi":"10.1111/j.1365-2621.2005.01045.x","level1":"04 agricultural and veterinary sciences","level2":"0405 other agricultural sciences","level3":"040502 food science","level4":"04050202 Food science/Food industry","scoreL3":"0.5","scoreL4":"0.5"}
+{"doi":"10.1002/chin.200617262","level1":"01 natural sciences","level2":"0104 chemical sciences","level3":"010405 organic chemistry","level4":"01040508 Functional groups/Ethers","scoreL3":"0.5566747188568115","scoreL4":"0.5582916736602783"}
+{"doi":"10.1002/chin.200617262","level1":"01 natural sciences","level2":"0104 chemical sciences","level3":"010402 general chemistry","level4":"01040207 Chemical synthesis/Total synthesis","scoreL3":"0.4433253407478332","scoreL4":"0.4417082965373993"}
+{"doi":"10.1016/j.revmed.2006.07.012","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030204 cardiovascular system & hematology","level4":"03020409 Hematology/Coagulopathies","scoreL3":"0.5101401805877686","scoreL4":"0.0546871414174914"}
+{"doi":"10.1016/j.revmed.2006.07.012","level1":"03 medical and health sciences","level2":"0301 basic medicine","level3":"030105 genetics & heredity","level4":"N/A","scoreL3":"0.4898599088191986","scoreL4":"0.0"}
+{"doi":"10.4109/jslab.17.132","level1":"03 medical and health sciences","level2":"0301 basic medicine","level3":"030104 developmental biology","level4":"N/A","scoreL3":"0.5","scoreL4":"0.0"}
+{"doi":"10.4109/jslab.17.132","level1":"03 medical and health sciences","level2":"0303 health sciences","level3":"030304 developmental biology","level4":"N/A","scoreL3":"0.5","scoreL4":"0.0"}
+{"doi":"10.1108/00251740610715687","level1":"05 social sciences","level2":"0502 economics and business","level3":"050203 business & management","level4":"05020311 International business/International trade","scoreL3":"0.605047881603241","scoreL4":"0.2156608108845153"}
+{"doi":"10.1108/00251740610715687","level1":"05 social sciences","level2":"0502 economics and business","level3":"050211 marketing","level4":"N/A","scoreL3":"0.394952118396759","scoreL4":"0.0"}
+{"doi":"10.1080/03067310500248098","level1":"04 agricultural and veterinary sciences","level2":"0404 agricultural biotechnology","level3":"040401 food science","level4":"04040102 Food science/Food industry","scoreL3":"0.5","scoreL4":"0.5"}
+{"doi":"10.1080/03067310500248098","level1":"04 agricultural and veterinary sciences","level2":"0405 other agricultural sciences","level3":"040502 food science","level4":"04050202 Food science/Food industry","scoreL3":"0.5","scoreL4":"0.5"}
+{"doi":"10.3152/147154306781778533","level1":"05 social sciences","level2":"0502 economics and business","level3":"050203 business & management","level4":"05020307 Innovation/Product management","scoreL3":"0.5293408632278442","scoreL4":"0.5326762795448303"}
+{"doi":"10.3152/147154306781778533","level1":"05 social sciences","level2":"0509 other social sciences","level3":"050905 science studies","level4":"05090502 Social philosophy/Capitalism","scoreL3":"0.4706590473651886","scoreL4":"0.4673237204551697"}
+{"doi":"10.1785/0120050806","level1":"02 engineering and technology","level2":"0211 other engineering and technologies","level3":"021101 geological & geomatics engineering","level4":"02110103 Concrete/Building materials","scoreL3":"0.5343400835990906","scoreL4":"0.3285667930180677"}

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/SparkCopyOpenorgsMergeRels.java

@@ -7,6 +7,7 @@ import java.util.Optional;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SaveMode;
 import org.apache.spark.sql.SparkSession;
@@ -77,13 +78,12 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
 
 		log.info("Number of Openorgs Merge Relations collected: {}", mergeRelsRDD.count());
 
-		spark
+		final Dataset<Relation> relations = spark
 			.createDataset(
 				mergeRelsRDD.rdd(),
-				Encoders.bean(Relation.class))
+				Encoders.bean(Relation.class));
-			.write()
+
-			.mode(SaveMode.Append)
+		saveParquet(relations, outputPath, SaveMode.Append);
-			.parquet(outputPath);
 	}
 
 	private boolean isMergeRel(Relation rel) {

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

@@ -67,12 +67,7 @@ public class SparkCopyRelationsNoOpenorgs extends AbstractSparkAction {
 			log.debug("Number of non-Openorgs relations collected: {}", simRels.count());
 		}
 
-		spark
+		save(spark.createDataset(simRels.rdd(), Encoders.bean(Relation.class)), outputPath, SaveMode.Overwrite);
-			.createDataset(simRels.rdd(), Encoders.bean(Relation.class))
-			.write()
-			.mode(SaveMode.Overwrite)
-			.json(outputPath);
-
 	}
 
 }

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

@@ -155,7 +155,7 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
 					(FlatMapFunction<ConnectedComponent, Relation>) cc -> ccToMergeRel(cc, dedupConf),
 					Encoders.bean(Relation.class));
 
-			mergeRels.write().mode(SaveMode.Overwrite).parquet(mergeRelPath);
+			saveParquet(mergeRels, mergeRelPath, SaveMode.Overwrite);
 
 		}
 	}

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

@@ -72,11 +72,7 @@ public class SparkCreateOrgsDedupRecord extends AbstractSparkAction {
 
 		final String mergeRelsPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, "organization");
 
-		rootOrganization(spark, entityPath, mergeRelsPath)
+		save(rootOrganization(spark, entityPath, mergeRelsPath), outputPath, SaveMode.Overwrite);
-			.write()
-			.mode(SaveMode.Overwrite)
-			.option("compression", "gzip")
-			.json(outputPath);
 
 	}
 

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

@@ -82,8 +82,6 @@ public class SparkCreateSimRels extends AbstractSparkAction {
 			final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity);
 			removeOutputDir(spark, outputPath);
 
-			JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-
 			SparkDeduper deduper = new SparkDeduper(dedupConf);
 
 			Dataset<?> simRels = spark

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();
+				String newSource = t._2();
+				String newTarget = t._3();
 
-		Dataset<Relation> processedRelations = distinctRelations(
+				if (rel.getDataInfo() == null) {
-			dedupedRels.union(mergeRels.map((MapFunction<Relation, Relation>) r -> r, REL_KRYO_ENC)))
+					rel.setDataInfo(new DataInfo());
-				.filter((FilterFunction<Relation>) r -> !Objects.equals(r.getSource(), r.getTarget()));
+				}
 
-		save(processedRelations, outputRelationPath, SaveMode.Overwrite);
+				if (newSource != null || newTarget != null) {
-	}
+					rel.getDataInfo().setDeletedbyinference(false);
 
-	private static Iterator<Relation> addInferredRelations(Tuple3<Relation, String, String> t) throws Exception {
+					if (newSource != null)
-		Relation existingRel = t._1();
+						rel.setSource(newSource);
-		String newSource = t._2();
-		String newTarget = t._3();
 
-		if (newSource == null && newTarget == null) {
+					if (newTarget != null)
-			return Collections.singleton(t._1()).iterator();
+						rel.setTarget(newTarget);
-		}
+				}
 
-		// update existing relation
+				return rel;
-		if (existingRel.getDataInfo() == null) {
+			}, REL_BEAN_ENC);
-			existingRel.setDataInfo(new DataInfo());
-		}
-		existingRel.getDataInfo().setDeletedbyinference(true);
 
-		// Create new relation inferred by dedupIDs
+		// ids of records that are both not deletedbyinference and not invisible
-		Relation inferredRel = (Relation) BeanUtils.cloneBean(existingRel);
+		Dataset<Row> ids = validIds(spark, graphBasePath);
 
-		inferredRel.setDataInfo((DataInfo) BeanUtils.cloneBean(existingRel.getDataInfo()));
+		// filter relations that point to valid records, can force them to be visible
-		inferredRel.getDataInfo().setDeletedbyinference(false);
+		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);
 
-		if (newSource != null)
+		Dataset<Relation> distinctRels = cleanedRels
-			inferredRel.setSource(newSource);
-
-		if (newTarget != null)
-			inferredRel.setTarget(newTarget);
-
-		return Arrays.asList(existingRel, inferredRel).iterator();
-	}
-
-	private Dataset<Relation> distinctRelations(Dataset<Relation> rels) {
-		return rels
-			.filter(getRelationFilterFunction())
 			.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/java/eu/dnetlib/dhp/oa/dedup/SparkWhitelistSimRels.java

@@ -67,8 +67,6 @@ public class SparkWhitelistSimRels extends AbstractSparkAction {
 		log.info("workingPath:   '{}'", workingPath);
 		log.info("whiteListPath: '{}'", whiteListPath);
 
-		JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-
 		// file format: source####target
 		Dataset<Row> whiteListRels = spark
 			.read()

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-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json

@@ -0,0 +1,940 @@
+[
+  {
+    "id": "100007630",
+    "uri": "http://dx.doi.org/10.13039/100007630",
+    "name": "College of Engineering and Informatics, National University of Ireland, Galway",
+    "synonym": []
+  },
+  {
+    "id": "100007731",
+    "uri": "http://dx.doi.org/10.13039/100007731",
+    "name": "Endo International",
+    "synonym": []
+  },
+  {
+    "id": "100008099",
+    "uri": "http://dx.doi.org/10.13039/100008099",
+    "name": "Food Safety Authority of Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100008124",
+    "uri": "http://dx.doi.org/10.13039/100008124",
+    "name": "Department of Jobs, Enterprise and Innovation",
+    "synonym": []
+  },
+  {
+    "id": "100009098",
+    "uri": "http://dx.doi.org/10.13039/100009098",
+    "name": "Department of Foreign Affairs and Trade, Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100009099",
+    "uri": "http://dx.doi.org/10.13039/100009099",
+    "name": "Irish Aid",
+    "synonym": []
+  },
+  {
+    "id": "100009770",
+    "uri": "http://dx.doi.org/10.13039/100009770",
+    "name": "National University of Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100009985",
+    "uri": "http://dx.doi.org/10.13039/100009985",
+    "name": "Parkinson's Association of Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100010399",
+    "uri": "http://dx.doi.org/10.13039/100010399",
+    "name": "European Society of Cataract and Refractive Surgeons",
+    "synonym": []
+  },
+  {
+    "id": "100010414",
+    "uri": "http://dx.doi.org/10.13039/100010414",
+    "name": "Health Research Board",
+    "synonym": [
+      "501100001590"
+    ]
+  },
+  {
+    "id": "100010546",
+    "uri": "http://dx.doi.org/10.13039/100010546",
+    "name": "Deparment of Children and Youth Affairs, Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100010993",
+    "uri": "http://dx.doi.org/10.13039/100010993",
+    "name": "Irish Nephrology Society",
+    "synonym": []
+  },
+  {
+    "id": "100011062",
+    "uri": "http://dx.doi.org/10.13039/100011062",
+    "name": "Asian Spinal Cord Network",
+    "synonym": []
+  },
+  {
+    "id": "100011096",
+    "uri": "http://dx.doi.org/10.13039/100011096",
+    "name": "Jazz Pharmaceuticals",
+    "synonym": []
+  },
+  {
+    "id": "100011396",
+    "uri": "http://dx.doi.org/10.13039/100011396",
+    "name": "Irish College of General Practitioners",
+    "synonym": []
+  },
+  {
+    "id": "100012734",
+    "uri": "http://dx.doi.org/10.13039/100012734",
+    "name": "Department for Culture, Heritage and the Gaeltacht, Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100012754",
+    "uri": "http://dx.doi.org/10.13039/100012754",
+    "name": "Horizon Pharma",
+    "synonym": []
+  },
+  {
+    "id": "100012891",
+    "uri": "http://dx.doi.org/10.13039/100012891",
+    "name": "Medical Research Charities Group",
+    "synonym": []
+  },
+  {
+    "id": "100012919",
+    "uri": "http://dx.doi.org/10.13039/100012919",
+    "name": "Epilepsy Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100012920",
+    "uri": "http://dx.doi.org/10.13039/100012920",
+    "name": "GLEN",
+    "synonym": []
+  },
+  {
+    "id": "100012921",
+    "uri": "http://dx.doi.org/10.13039/100012921",
+    "name": "Royal College of Surgeons in Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100013029",
+    "uri": "http://dx.doi.org/10.13039/100013029",
+    "name": "Iris O'Brien Foundation",
+    "synonym": []
+  },
+  {
+    "id": "100013206",
+    "uri": "http://dx.doi.org/10.13039/100013206",
+    "name": "Food Institutional Research Measure",
+    "synonym": []
+  },
+  {
+    "id": "100013381",
+    "uri": "http://dx.doi.org/10.13039/100013381",
+    "name": "Irish Phytochemical Food Network",
+    "synonym": []
+  },
+  {
+    "id": "100013433",
+    "uri": "http://dx.doi.org/10.13039/100013433",
+    "name": "Transport Infrastructure Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100013461",
+    "uri": "http://dx.doi.org/10.13039/100013461",
+    "name": "Arts and Disability Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100013548",
+    "uri": "http://dx.doi.org/10.13039/100013548",
+    "name": "Filmbase",
+    "synonym": []
+  },
+  {
+    "id": "100013917",
+    "uri": "http://dx.doi.org/10.13039/100013917",
+    "name": "Society for Musicology in Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100014251",
+    "uri": "http://dx.doi.org/10.13039/100014251",
+    "name": "Humanities in the European Research Area",
+    "synonym": []
+  },
+  {
+    "id": "100014364",
+    "uri": "http://dx.doi.org/10.13039/100014364",
+    "name": "National Children's Research Centre",
+    "synonym": []
+  },
+  {
+    "id": "100014384",
+    "uri": "http://dx.doi.org/10.13039/100014384",
+    "name": "Amarin Corporation",
+    "synonym": []
+  },
+  {
+    "id": "100014902",
+    "uri": "http://dx.doi.org/10.13039/100014902",
+    "name": "Irish Association for Cancer Research",
+    "synonym": []
+  },
+  {
+    "id": "100015023",
+    "uri": "http://dx.doi.org/10.13039/100015023",
+    "name": "Ireland Funds",
+    "synonym": []
+  },
+  {
+    "id": "100015037",
+    "uri": "http://dx.doi.org/10.13039/100015037",
+    "name": "Simon Cumbers Media Fund",
+    "synonym": []
+  },
+  {
+    "id": "100015319",
+    "uri": "http://dx.doi.org/10.13039/100015319",
+    "name": "Sport Ireland Institute",
+    "synonym": []
+  },
+  {
+    "id": "100015320",
+    "uri": "http://dx.doi.org/10.13039/100015320",
+    "name": "Paralympics Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100015442",
+    "uri": "http://dx.doi.org/10.13039/100015442",
+    "name": "Global Brain Health Institute",
+    "synonym": []
+  },
+  {
+    "id": "100015776",
+    "uri": "http://dx.doi.org/10.13039/100015776",
+    "name": "Health and Social Care Board",
+    "synonym": []
+  },
+  {
+    "id": "100015992",
+    "uri": "http://dx.doi.org/10.13039/100015992",
+    "name": "St. Luke's Institute of Cancer Research",
+    "synonym": []
+  },
+  {
+    "id": "100017897",
+    "uri": "http://dx.doi.org/10.13039/100017897",
+    "name": "Friedreich\u2019s Ataxia Research Alliance Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100018064",
+    "uri": "http://dx.doi.org/10.13039/100018064",
+    "name": "Department of Tourism, Culture, Arts, Gaeltacht, Sport and Media",
+    "synonym": []
+  },
+  {
+    "id": "100018172",
+    "uri": "http://dx.doi.org/10.13039/100018172",
+    "name": "Department of the Environment, Climate and Communications",
+    "synonym": []
+  },
+  {
+    "id": "100018175",
+    "uri": "http://dx.doi.org/10.13039/100018175",
+    "name": "Dairy Processing Technology Centre",
+    "synonym": []
+  },
+  {
+    "id": "100018270",
+    "uri": "http://dx.doi.org/10.13039/100018270",
+    "name": "Health Service Executive",
+    "synonym": []
+  },
+  {
+    "id": "100018529",
+    "uri": "http://dx.doi.org/10.13039/100018529",
+    "name": "Alkermes",
+    "synonym": []
+  },
+  {
+    "id": "100018542",
+    "uri": "http://dx.doi.org/10.13039/100018542",
+    "name": "Irish Endocrine Society",
+    "synonym": []
+  },
+  {
+    "id": "100018754",
+    "uri": "http://dx.doi.org/10.13039/100018754",
+    "name": "An Roinn Sl\u00e1inte",
+    "synonym": []
+  },
+  {
+    "id": "100018998",
+    "uri": "http://dx.doi.org/10.13039/100018998",
+    "name": "Irish Research eLibrary",
+    "synonym": []
+  },
+  {
+    "id": "100019428",
+    "uri": "http://dx.doi.org/10.13039/100019428",
+    "name": "Nabriva Therapeutics",
+    "synonym": []
+  },
+  {
+    "id": "100019637",
+    "uri": "http://dx.doi.org/10.13039/100019637",
+    "name": "Horizon Therapeutics",
+    "synonym": []
+  },
+  {
+    "id": "100020174",
+    "uri": "http://dx.doi.org/10.13039/100020174",
+    "name": "Health Research Charities Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100020202",
+    "uri": "http://dx.doi.org/10.13039/100020202",
+    "name": "UCD Foundation",
+    "synonym": []
+  },
+  {
+    "id": "100020233",
+    "uri": "http://dx.doi.org/10.13039/100020233",
+    "name": "Ireland Canada University Foundation",
+    "synonym": []
+  },
+  {
+    "id": "100022943",
+    "uri": "http://dx.doi.org/10.13039/100022943",
+    "name": "National Cancer Registry Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100001581",
+    "uri": "http://dx.doi.org/10.13039/501100001581",
+    "name": "Arts Council of Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100001582",
+    "uri": "http://dx.doi.org/10.13039/501100001582",
+    "name": "Centre for Ageing Research and Development in Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100001583",
+    "uri": "http://dx.doi.org/10.13039/501100001583",
+    "name": "Cystinosis Foundation Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100001584",
+    "uri": "http://dx.doi.org/10.13039/501100001584",
+    "name": "Department of Agriculture, Food and the Marine, Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100001586",
+    "uri": "http://dx.doi.org/10.13039/501100001586",
+    "name": "Department of Education and Skills, Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100001587",
+    "uri": "http://dx.doi.org/10.13039/501100001587",
+    "name": "Economic and Social Research Institute",
+    "synonym": []
+  },
+  {
+    "id": "501100001588",
+    "uri": "http://dx.doi.org/10.13039/501100001588",
+    "name": "Enterprise Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100001589",
+    "uri": "http://dx.doi.org/10.13039/501100001589",
+    "name": "Environmental Protection Agency",
+    "synonym": []
+  },
+  {
+    "id": "501100001591",
+    "uri": "http://dx.doi.org/10.13039/501100001591",
+    "name": "Heritage Council",
+    "synonym": []
+  },
+  {
+    "id": "501100001592",
+    "uri": "http://dx.doi.org/10.13039/501100001592",
+    "name": "Higher Education Authority",
+    "synonym": []
+  },
+  {
+    "id": "501100001593",
+    "uri": "http://dx.doi.org/10.13039/501100001593",
+    "name": "Irish Cancer Society",
+    "synonym": []
+  },
+  {
+    "id": "501100001594",
+    "uri": "http://dx.doi.org/10.13039/501100001594",
+    "name": "Irish Heart Foundation",
+    "synonym": []
+  },
+  {
+    "id": "501100001595",
+    "uri": "http://dx.doi.org/10.13039/501100001595",
+    "name": "Irish Hospice Foundation",
+    "synonym": []
+  },
+  {
+    "id": "501100001596",
+    "uri": "http://dx.doi.org/10.13039/501100001596",
+    "name": "Irish Research Council for Science, Engineering and Technology",
+    "synonym": []
+  },
+  {
+    "id": "501100001597",
+    "uri": "http://dx.doi.org/10.13039/501100001597",
+    "name": "Irish Research Council for the Humanities and Social Sciences",
+    "synonym": []
+  },
+  {
+    "id": "501100001598",
+    "uri": "http://dx.doi.org/10.13039/501100001598",
+    "name": "Mental Health Commission",
+    "synonym": []
+  },
+  {
+    "id": "501100001600",
+    "uri": "http://dx.doi.org/10.13039/501100001600",
+    "name": "Research and Education Foundation, Sligo General Hospital",
+    "synonym": []
+  },
+  {
+    "id": "501100001601",
+    "uri": "http://dx.doi.org/10.13039/501100001601",
+    "name": "Royal Irish Academy",
+    "synonym": []
+  },
+  {
+    "id": "501100001603",
+    "uri": "http://dx.doi.org/10.13039/501100001603",
+    "name": "Sustainable Energy Authority of Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100001604",
+    "uri": "http://dx.doi.org/10.13039/501100001604",
+    "name": "Teagasc",
+    "synonym": []
+  },
+  {
+    "id": "501100001627",
+    "uri": "http://dx.doi.org/10.13039/501100001627",
+    "name": "Marine Institute",
+    "synonym": []
+  },
+  {
+    "id": "501100001628",
+    "uri": "http://dx.doi.org/10.13039/501100001628",
+    "name": "Central Remedial Clinic",
+    "synonym": []
+  },
+  {
+    "id": "501100001629",
+    "uri": "http://dx.doi.org/10.13039/501100001629",
+    "name": "Royal Dublin Society",
+    "synonym": []
+  },
+  {
+    "id": "501100001630",
+    "uri": "http://dx.doi.org/10.13039/501100001630",
+    "name": "Dublin Institute for Advanced Studies",
+    "synonym": []
+  },
+  {
+    "id": "501100001631",
+    "uri": "http://dx.doi.org/10.13039/501100001631",
+    "name": "University College Dublin",
+    "synonym": []
+  },
+  {
+    "id": "501100001633",
+    "uri": "http://dx.doi.org/10.13039/501100001633",
+    "name": "National University of Ireland, Maynooth",
+    "synonym": []
+  },
+  {
+    "id": "501100001634",
+    "uri": "http://dx.doi.org/10.13039/501100001634",
+    "name": "University of Galway",
+    "synonym": []
+  },
+  {
+    "id": "501100001635",
+    "uri": "http://dx.doi.org/10.13039/501100001635",
+    "name": "University of Limerick",
+    "synonym": []
+  },
+  {
+    "id": "501100001636",
+    "uri": "http://dx.doi.org/10.13039/501100001636",
+    "name": "University College Cork",
+    "synonym": []
+  },
+  {
+    "id": "501100001637",
+    "uri": "http://dx.doi.org/10.13039/501100001637",
+    "name": "Trinity College Dublin",
+    "synonym": []
+  },
+  {
+    "id": "501100001638",
+    "uri": "http://dx.doi.org/10.13039/501100001638",
+    "name": "Dublin City University",
+    "synonym": []
+  },
+  {
+    "id": "501100002081",
+    "uri": "http://dx.doi.org/10.13039/501100002081",
+    "name": "Irish Research Council",
+    "synonym": []
+  },
+  {
+    "id": "501100002736",
+    "uri": "http://dx.doi.org/10.13039/501100002736",
+    "name": "Covidien",
+    "synonym": []
+  },
+  {
+    "id": "501100002755",
+    "uri": "http://dx.doi.org/10.13039/501100002755",
+    "name": "Brennan and Company",
+    "synonym": []
+  },
+  {
+    "id": "501100002919",
+    "uri": "http://dx.doi.org/10.13039/501100002919",
+    "name": "Cork Institute of Technology",
+    "synonym": []
+  },
+  {
+    "id": "501100002959",
+    "uri": "http://dx.doi.org/10.13039/501100002959",
+    "name": "Dublin City Council",
+    "synonym": []
+  },
+  {
+    "id": "501100003036",
+    "uri": "http://dx.doi.org/10.13039/501100003036",
+    "name": "Perrigo Company Charitable Foundation",
+    "synonym": []
+  },
+  {
+    "id": "501100003037",
+    "uri": "http://dx.doi.org/10.13039/501100003037",
+    "name": "Elan",
+    "synonym": []
+  },
+  {
+    "id": "501100003496",
+    "uri": "http://dx.doi.org/10.13039/501100003496",
+    "name": "HeyStaks Technologies",
+    "synonym": []
+  },
+  {
+    "id": "501100003553",
+    "uri": "http://dx.doi.org/10.13039/501100003553",
+    "name": "Gaelic Athletic Association",
+    "synonym": []
+  },
+  {
+    "id": "501100003840",
+    "uri": "http://dx.doi.org/10.13039/501100003840",
+    "name": "Irish Institute of Clinical Neuroscience",
+    "synonym": []
+  },
+  {
+    "id": "501100003956",
+    "uri": "http://dx.doi.org/10.13039/501100003956",
+    "name": "Aspect Medical Systems",
+    "synonym": []
+  },
+  {
+    "id": "501100004162",
+    "uri": "http://dx.doi.org/10.13039/501100004162",
+    "name": "Meath Foundation",
+    "synonym": []
+  },
+  {
+    "id": "501100004210",
+    "uri": "http://dx.doi.org/10.13039/501100004210",
+    "name": "Our Lady's Children's Hospital, Crumlin",
+    "synonym": []
+  },
+  {
+    "id": "501100004321",
+    "uri": "http://dx.doi.org/10.13039/501100004321",
+    "name": "Shire",
+    "synonym": []
+  },
+  {
+    "id": "501100004981",
+    "uri": "http://dx.doi.org/10.13039/501100004981",
+    "name": "Athlone Institute of Technology",
+    "synonym": []
+  },
+  {
+    "id": "501100006518",
+    "uri": "http://dx.doi.org/10.13039/501100006518",
+    "name": "Department of Communications, Energy and Natural Resources, Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100006553",
+    "uri": "http://dx.doi.org/10.13039/501100006553",
+    "name": "Collaborative Centre for Applied Nanotechnology",
+    "synonym": []
+  },
+  {
+    "id": "501100006759",
+    "uri": "http://dx.doi.org/10.13039/501100006759",
+    "name": "CLARITY Centre for Sensor Web Technologies",
+    "synonym": []
+  },
+  {
+    "id": "501100009246",
+    "uri": "http://dx.doi.org/10.13039/501100009246",
+    "name": "Technological University Dublin",
+    "synonym": []
+  },
+  {
+    "id": "501100009269",
+    "uri": "http://dx.doi.org/10.13039/501100009269",
+    "name": "Programme of Competitive Forestry Research for Development",
+    "synonym": []
+  },
+  {
+    "id": "501100009315",
+    "uri": "http://dx.doi.org/10.13039/501100009315",
+    "name": "Cystinosis Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100010808",
+    "uri": "http://dx.doi.org/10.13039/501100010808",
+    "name": "Geological Survey of Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100011030",
+    "uri": "http://dx.doi.org/10.13039/501100011030",
+    "name": "Alimentary Glycoscience Research Cluster",
+    "synonym": []
+  },
+  {
+    "id": "501100011031",
+    "uri": "http://dx.doi.org/10.13039/501100011031",
+    "name": "Alimentary Health",
+    "synonym": []
+  },
+  {
+    "id": "501100011103",
+    "uri": "http://dx.doi.org/10.13039/501100011103",
+    "name": "Rann\u00eds",
+    "synonym": []
+  },
+  {
+    "id": "501100012354",
+    "uri": "http://dx.doi.org/10.13039/501100012354",
+    "name": "Inland Fisheries Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100014384",
+    "uri": "http://dx.doi.org/10.13039/501100014384",
+    "name": "X-Bolt Orthopaedics",
+    "synonym": []
+  },
+  {
+    "id": "501100014710",
+    "uri": "http://dx.doi.org/10.13039/501100014710",
+    "name": "PrecisionBiotics Group",
+    "synonym": []
+  },
+  {
+    "id": "501100014827",
+    "uri": "http://dx.doi.org/10.13039/501100014827",
+    "name": "Dormant Accounts Fund",
+    "synonym": []
+  },
+  {
+    "id": "501100016041",
+    "uri": "http://dx.doi.org/10.13039/501100016041",
+    "name": "St Vincents Anaesthesia Foundation",
+    "synonym": []
+  },
+  {
+    "id": "501100017501",
+    "uri": "http://dx.doi.org/10.13039/501100017501",
+    "name": "FotoNation",
+    "synonym": []
+  },
+  {
+    "id": "501100018641",
+    "uri": "http://dx.doi.org/10.13039/501100018641",
+    "name": "Dairy Research Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100018839",
+    "uri": "http://dx.doi.org/10.13039/501100018839",
+    "name": "Irish Centre for High-End Computing",
+    "synonym": []
+  },
+  {
+    "id": "501100019905",
+    "uri": "http://dx.doi.org/10.13039/501100019905",
+    "name": "Galway University Foundation",
+    "synonym": []
+  },
+  {
+    "id": "501100020036",
+    "uri": "http://dx.doi.org/10.13039/501100020036",
+    "name": "Dystonia Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100020221",
+    "uri": "http://dx.doi.org/10.13039/501100020221",
+    "name": "Irish Motor Neurone Disease Association",
+    "synonym": []
+  },
+  {
+    "id": "501100020270",
+    "uri": "http://dx.doi.org/10.13039/501100020270",
+    "name": "Advanced Materials and Bioengineering Research",
+    "synonym": []
+  },
+  {
+    "id": "501100020403",
+    "uri": "http://dx.doi.org/10.13039/501100020403",
+    "name": "Irish Composites Centre",
+    "synonym": []
+  },
+  {
+    "id": "501100020425",
+    "uri": "http://dx.doi.org/10.13039/501100020425",
+    "name": "Irish Thoracic Society",
+    "synonym": []
+  },
+  {
+    "id": "501100021102",
+    "uri": "http://dx.doi.org/10.13039/501100021102",
+    "name": "Waterford Institute of Technology",
+    "synonym": []
+  },
+  {
+    "id": "501100021110",
+    "uri": "http://dx.doi.org/10.13039/501100021110",
+    "name": "Irish MPS Society",
+    "synonym": []
+  },
+  {
+    "id": "501100021525",
+    "uri": "http://dx.doi.org/10.13039/501100021525",
+    "name": "Insight SFI Research Centre for Data Analytics",
+    "synonym": []
+  },
+  {
+    "id": "501100021694",
+    "uri": "http://dx.doi.org/10.13039/501100021694",
+    "name": "Elan Pharma International",
+    "synonym": []
+  },
+  {
+    "id": "501100021838",
+    "uri": "http://dx.doi.org/10.13039/501100021838",
+    "name": "Royal College of Physicians of Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100022542",
+    "uri": "http://dx.doi.org/10.13039/501100022542",
+    "name": "Breakthrough Cancer Research",
+    "synonym": []
+  },
+  {
+    "id": "501100022610",
+    "uri": "http://dx.doi.org/10.13039/501100022610",
+    "name": "Breast Cancer Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100022728",
+    "uri": "http://dx.doi.org/10.13039/501100022728",
+    "name": "Munster Technological University",
+    "synonym": []
+  },
+  {
+    "id": "501100022729",
+    "uri": "http://dx.doi.org/10.13039/501100022729",
+    "name": "Institute of Technology, Tralee",
+    "synonym": []
+  },
+  {
+    "id": "501100023273",
+    "uri": "http://dx.doi.org/10.13039/501100023273",
+    "name": "HRB Clinical Research Facility Galway",
+    "synonym": []
+  },
+  {
+    "id": "501100023378",
+    "uri": "http://dx.doi.org/10.13039/501100023378",
+    "name": "Lauritzson Foundation",
+    "synonym": []
+  },
+  {
+    "id": "501100023551",
+    "uri": "http://dx.doi.org/10.13039/501100023551",
+    "name": "Cystic Fibrosis Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100023970",
+    "uri": "http://dx.doi.org/10.13039/501100023970",
+    "name": "Tyndall National Institute",
+    "synonym": []
+  },
+  {
+    "id": "501100024094",
+    "uri": "http://dx.doi.org/10.13039/501100024094",
+    "name": "Raidi\u00f3 Teilif\u00eds \u00c9ireann",
+    "synonym": []
+  },
+  {
+    "id": "501100024242",
+    "uri": "http://dx.doi.org/10.13039/501100024242",
+    "name": "Synthesis and Solid State Pharmaceutical Centre",
+    "synonym": []
+  },
+  {
+    "id": "501100024313",
+    "uri": "http://dx.doi.org/10.13039/501100024313",
+    "name": "Irish Rugby Football Union",
+    "synonym": []
+  },
+  {
+    "id": "100007490",
+    "uri": "http://dx.doi.org/10.13039/100007490",
+    "name": "Bausch and Lomb Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100007819",
+    "uri": "http://dx.doi.org/10.13039/100007819",
+    "name": "Allergan",
+    "synonym": []
+  },
+  {
+    "id": "100010547",
+    "uri": "http://dx.doi.org/10.13039/100010547",
+    "name": "Irish Youth Justice Service",
+    "synonym": []
+  },
+  {
+    "id": "100012733",
+    "uri": "http://dx.doi.org/10.13039/100012733",
+    "name": "National Parks and Wildlife Service",
+    "synonym": []
+  },
+  {
+    "id": "100015278",
+    "uri": "http://dx.doi.org/10.13039/100015278",
+    "name": "Pfizer Healthcare Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100017144",
+    "uri": "http://dx.doi.org/10.13039/100017144",
+    "name": "Shell E and P Ireland",
+    "synonym": []
+  },
+  {
+    "id": "100022895",
+    "uri": "http://dx.doi.org/10.13039/100022895",
+    "name": "Health Research Institute, University of Limerick",
+    "synonym": []
+  },
+  {
+    "id": "501100001599",
+    "uri": "http://dx.doi.org/10.13039/501100001599",
+    "name": "National Council for Forest Research and Development",
+    "synonym": []
+  },
+  {
+    "id": "501100006554",
+    "uri": "http://dx.doi.org/10.13039/501100006554",
+    "name": "IDA Ireland",
+    "synonym": []
+  },
+  {
+    "id": "501100011626",
+    "uri": "http://dx.doi.org/10.13039/501100011626",
+    "name": "Energy Policy Research Centre, Economic and Social Research Institute",
+    "synonym": []
+  },
+  {
+    "id": "501100014531",
+    "uri": "http://dx.doi.org/10.13039/501100014531",
+    "name": "Physical Education and Sport Sciences Department, University of Limerick",
+    "synonym": []
+  },
+  {
+    "id": "501100014745",
+    "uri": "http://dx.doi.org/10.13039/501100014745",
+    "name": "APC Microbiome Institute",
+    "synonym": []
+  },
+  {
+    "id": "501100014826",
+    "uri": "http://dx.doi.org/10.13039/501100014826",
+    "name": "ADAPT - Centre for Digital Content Technology",
+    "synonym": []
+  },
+  {
+    "id": "501100020570",
+    "uri": "http://dx.doi.org/10.13039/501100020570",
+    "name": "College of Medicine, Nursing and Health Sciences, National University of Ireland, Galway",
+    "synonym": []
+  },
+  {
+    "id": "501100020871",
+    "uri": "http://dx.doi.org/10.13039/501100020871",
+    "name": "Bernal Institute, University of Limerick",
+    "synonym": []
+  },
+  {
+    "id": "501100023852",
+    "uri": "http://dx.doi.org/10.13039/501100023852",
+    "name": "Moore Institute for Research in the Humanities and Social Studies, University of Galway",
+    "synonym": []
+  }
+]

dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala

@@ -16,6 +16,7 @@ import org.slf4j.{Logger, LoggerFactory}
 import java.util
 import scala.collection.JavaConverters._
 import scala.collection.mutable
+import scala.io.Source
 import scala.util.matching.Regex
 
 case class CrossrefDT(doi: String, json: String, timestamp: Long) {}
@@ -30,11 +31,22 @@ case class mappingAuthor(
   affiliation: Option[mappingAffiliation]
 ) {}
 
+case class funderInfo(id: String, uri: String, name: String, synonym: List[String]) {}
+
 case class mappingFunder(name: String, DOI: Option[String], award: Option[List[String]]) {}
 
 case object Crossref2Oaf {
   val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
 
+  val irishFunder: List[funderInfo] = {
+    val s = Source
+      .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json"))
+      .mkString
+    implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
+    lazy val json: org.json4s.JValue = parse(s)
+    json.extract[List[funderInfo]]
+  }
+
   val mappingCrossrefType = Map(
     "book-section"        -> "publication",
     "book"                -> "publication",
@@ -88,6 +100,13 @@ case object Crossref2Oaf {
     "report"              -> "0017 Report"
   )
 
+  def getIrishId(doi: String): Option[String] = {
+    val id = doi.split("/").last
+    irishFunder
+      .find(f => id.equalsIgnoreCase(f.id) || (f.synonym.nonEmpty && f.synonym.exists(s => s.equalsIgnoreCase(id))))
+      .map(f => f.id)
+  }
+
   def mappingResult(result: Result, json: JValue, cobjCategory: String): Result = {
     implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
 
@@ -467,6 +486,14 @@ case object Crossref2Oaf {
     if (funders != null)
       funders.foreach(funder => {
         if (funder.DOI.isDefined && funder.DOI.get.nonEmpty) {
+
+          if (getIrishId(funder.DOI.get).isDefined) {
+            val nsPrefix = getIrishId(funder.DOI.get).get.padTo(12, '_')
+            val targetId = getProjectId(nsPrefix, "1e5e62235d094afd01cd56e65112fc63")
+            queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+            queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
+          }
+
           funder.DOI.get match {
             case "10.13039/100010663" | "10.13039/100010661" | "10.13039/501100007601" | "10.13039/501100000780" |
                 "10.13039/100010665" =>

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java

@@ -25,6 +25,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.bulktag.community.*;
 import eu.dnetlib.dhp.schema.oaf.Datasource;
 import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 
 public class SparkBulkTagJob {
 
@@ -170,10 +171,12 @@ public class SparkBulkTagJob {
 	// TODO remove this hack as soon as the values fixed by this method will be provided as NON null
 	private static <R extends Result> MapFunction<R, R> patchResult() {
 		return r -> {
-			if (r.getDataInfo().getDeletedbyinference() == null) {
+			if (Objects.isNull(r.getDataInfo())) {
+				r.setDataInfo(OafMapperUtils.dataInfo(false, "", false, false, OafMapperUtils.unknown("", ""), ""));
+			} else if (r.getDataInfo().getDeletedbyinference() == null) {
 				r.getDataInfo().setDeletedbyinference(false);
 			}
-			if (r.getContext() == null) {
+			if (Objects.isNull(r.getContext())) {
 				r.setContext(new ArrayList<>());
 			}
 			return r;

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java

@@ -5,10 +5,7 @@ import static eu.dnetlib.dhp.PropagationConstant.*;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
-import java.util.ArrayList;
+import java.util.*;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.Set;
 import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
@@ -88,14 +85,33 @@ public class PrepareResultCountrySet {
 		// selects all the results non deleted by inference and non invisible
 		Dataset<R> result = readPath(spark, inputPath, resultClazz)
 			.filter(
-				(FilterFunction<R>) r -> !r.getDataInfo().getDeletedbyinference() &&
+				(FilterFunction<R>) r -> Optional
-					!r.getDataInfo().getInvisible());
+					.ofNullable(r.getDataInfo())
+					.map(dataInfo -> !dataInfo.getDeletedbyinference() && !dataInfo.getInvisible())
+					.orElse(true));
 
 		// of the results collects the distinct keys for collected from (at the level of the result) and hosted by
 		// and produces pairs resultId, key for each distinct key associated to the result
 		result.flatMap((FlatMapFunction<R, EntityEntityRel>) r -> {
-			Set<String> cfhb = r.getCollectedfrom().stream().map(cf -> cf.getKey()).collect(Collectors.toSet());
+			Set<String> cfhb = Optional
-			cfhb.addAll(r.getInstance().stream().map(i -> i.getHostedby().getKey()).collect(Collectors.toSet()));
+				.ofNullable(r.getCollectedfrom())
+				.map(cf -> cf.stream().map(KeyValue::getKey).collect(Collectors.toSet()))
+				.orElse(new HashSet<>());
+			cfhb
+				.addAll(
+					Optional
+						.ofNullable(r.getInstance())
+						.map(
+							i -> i
+								.stream()
+								.map(
+									ii -> Optional
+										.ofNullable(ii.getHostedby())
+										.map(KeyValue::getKey)
+										.orElse(null))
+								.filter(Objects::nonNull)
+								.collect(Collectors.toSet()))
+						.orElse(new HashSet<>()));
 			return cfhb
 				.stream()
 				.map(value -> EntityEntityRel.newInstance(r.getId(), value))

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/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/config-default.xml

@@ -1,4 +1,12 @@
 <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>
@@ -7,4 +15,28 @@
         <name>oozie.action.sharelib.for.spark</name>
         <value>spark2</value>
     </property>
+    <property>
+        <name>hive_metastore_uris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>spark2YarnHistoryServerAddress</name>
+        <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
+    </property>
+    <property>
+        <name>spark2ExtraListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+    </property>
+    <property>
+        <name>spark2SqlQueryExecutionListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+    </property>
+    <property>
+        <name>sparkExecutorNumber</name>
+        <value>4</value>
+    </property>
+    <property>
+        <name>spark2EventLogDir</name>
+        <value>/user/spark/spark2ApplicationHistory</value>
+    </property>
 </configuration>

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

@@ -10,7 +10,6 @@ import java.nio.file.Path;
 import java.nio.file.Paths;
 
 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;
@@ -23,9 +22,9 @@ import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.common.HdfsSupport;
-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.OafEntity;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.utils.DHPUtils;
 
@@ -40,8 +39,9 @@ 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 +58,8 @@ 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
@@ -76,39 +76,28 @@ public class GroupEntitiesSparkJobTest {
 			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());

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh

@@ -24,13 +24,13 @@ function copydb() {
   # drop tables from db
   for i in `impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -d ${db} --delimited  -q "show tables"`;
     do
-        `impala-shell  -i impala-cluster-dn1.openaire.eu -d -d ${db} -q "drop table $i;"`;
+        `impala-shell  -i impala-cluster-dn1.openaire.eu -d ${db} -q "drop table $i;"`;
     done
 
   # drop views from db
   for i in `impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -d ${db} --delimited  -q "show tables"`;
     do
-        `impala-shell  -i impala-cluster-dn1.openaire.eu -d -d ${db} -q "drop view $i;"`;
+        `impala-shell  -i impala-cluster-dn1.openaire.eu -d ${db} -q "drop view $i;"`;
     done
 
   # delete the database
@@ -82,12 +82,12 @@ copydb $USAGE_STATS_DB
 copydb $PROD_USAGE_STATS_DB
 copydb $EXT_DB
 copydb $STATS_DB
-#copydb $MONITOR_DB
+copydb $MONITOR_DB
 copydb $OBSERVATORY_DB
 
 copydb $MONITOR_DB'_funded'
 copydb $MONITOR_DB'_institutions'
-copydb $MONITOR_DB'_RIs_tail'
+copydb $MONITOR_DB'_ris_tail'
 
 contexts="knowmad::other dh-ch::other enermaps::other gotriple::other neanias-atmospheric::other rural-digital-europe::other covid-19::other aurora::other neanias-space::other north-america-studies::other north-american-studies::other eutopia::other"
 for i in ${contexts}

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizeImpalaCluster.sh

@@ -13,7 +13,7 @@ function createShadowDB() {
   # drop views from db
   for i in `impala-shell -i impala-cluster-dn1.openaire.eu -d ${SHADOW} --delimited  -q "show tables"`;
     do
-        `impala-shell  -i impala-cluster-dn1.openaire.eu -d -d ${SHADOW} -q "drop view $i;"`;
+        `impala-shell  -i impala-cluster-dn1.openaire.eu -d ${SHADOW} -q "drop view $i;"`;
     done
 
   impala-shell -i impala-cluster-dn1.openaire.eu -q "drop database ${SHADOW} CASCADE";
@@ -36,13 +36,13 @@ createShadowDB $MONITOR_DB $MONITOR_DB_SHADOW
 createShadowDB $OBSERVATORY_DB $OBSERVATORY_DB_SHADOW
 createShadowDB USAGE_STATS_DB USAGE_STATS_DB_SHADOW
 
-createShadowDB $MONITOR_DB'_funded' $MONITOR_DB'_funded_shadow'
+createShadowDB $MONITOR_DB'_funded' $MONITOR_DB_SHADOW'_shadow_funded'
-createShadowDB $MONITOR_DB'_institutions' $MONITOR_DB'_institutions_shadow'
+createShadowDB $MONITOR_DB'_institutions' $MONITOR_DB_SHADOW'_shadow_institutions'
-createShadowDB $MONITOR_DB'_RIs_tail' $MONITOR_DB'_RIs_tail_shadow'
+createShadowDB $MONITOR_DB'_ris_tail' $MONITOR_DB_SHADOW'_shadow_ris_tail'
 
 contexts="knowmad::other dh-ch::other enermaps::other gotriple::other neanias-atmospheric::other rural-digital-europe::other covid-19::other aurora::other neanias-space::other north-america-studies::other north-american-studies::other eutopia::other"
 for i in ${contexts}
 do
    tmp=`echo "$i"  | sed 's/'-'/'_'/g' | sed 's/'::'/'_'/g'`
-  createShadowDB ${MONITOR_DB}'_'${tmp} ${MONITOR_DB}'_'${tmp}'_shadow'
+  createShadowDB ${MONITOR_DB}'_'${tmp} ${MONITOR_DB_SHADOW}'_shadow_'${tmp}
 done

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh

@@ -14,6 +14,7 @@ export SCRIPT_PATH2=$5
 export SCRIPT_PATH3=$6
 export SCRIPT_PATH4=$7
 export SCRIPT_PATH5=$8
+export SCRIPT_PATH6=$9
 
 export HIVE_OPTS="-hiveconf mapred.job.queue.name=analytics -hiveconf hive.spark.client.connect.timeout=120000ms -hiveconf hive.spark.client.server.connect.timeout=300000ms -hiveconf spark.executor.memory=19166291558 -hiveconf spark.yarn.executor.memoryOverhead=3225 -hiveconf spark.driver.memory=11596411699 -hiveconf spark.yarn.driver.memoryOverhead=1228"
 export HADOOP_USER_NAME="oozie"
@@ -33,12 +34,19 @@ hdfs dfs -copyToLocal $7
 echo "Getting file from " $8
 hdfs dfs -copyToLocal $8
 
+echo "Getting file from " $9
+hdfs dfs -copyToLocal $9
+
+
 echo "Creating monitor database"
+cat step20-createMonitorDBAll.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2/g1" > foo
+hive $HIVE_OPTS -f foo
+
 cat step20-createMonitorDB_funded.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_funded/g1" > foo
 hive $HIVE_OPTS -f foo
 cat step20-createMonitorDB.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_funded/g1" > foo
 hive $HIVE_OPTS -f foo
-#
+
 cat step20-createMonitorDB_institutions.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_institutions/g1" > foo
 hive $HIVE_OPTS -f foo
 cat step20-createMonitorDB.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_institutions/g1" > foo
@@ -56,14 +64,20 @@ do
   hive $HIVE_OPTS -f foo
 done
 
-
+cat step20-createMonitorDB_RIs_tail.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_ris_tail/g1" | sed "s/CONTEXTS/\"'knowmad::other','dh-ch::other', 'enermaps::other', 'gotriple::other', 'neanias-atmospheric::other', 'rural-digital-europe::other', 'covid-19::other', 'aurora::other', 'neanias-space::other', 'north-america-studies::other', 'north-american-studies::other', 'eutopia::other'\"/g" > foo
-cat step20-createMonitorDB_RIs_tail.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_RIs_tail/g1" | sed "s/CONTEXTS/\"'knowmad::other','dh-ch::other', 'enermaps::other', 'gotriple::other', 'neanias-atmospheric::other', 'rural-digital-europe::other', 'covid-19::other', 'aurora::other', 'neanias-space::other', 'north-america-studies::other', 'north-american-studies::other', 'eutopia::other'\"/g" > foo
 hive $HIVE_OPTS -f foo
-cat step20-createMonitorDB.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_RIs_tail/g1" > foo
+cat step20-createMonitorDB.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_ris_tail/g1" > foo
 hive $HIVE_OPTS -f foo
 
 echo "Hive shell finished"
 
+echo "Updating shadow monitor all database"
+hive -e "drop database if exists ${SHADOW} cascade"
+hive -e "create database if not exists ${SHADOW}"
+hive $HIVE_OPTS --database ${2} -e "show tables" | grep -v WARN | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${2}.\1;/" > foo
+hive -f foo
+echo "Updated shadow monitor all database"
+
 echo "Updating shadow monitor funded database"
 hive -e "drop database if exists ${SHADOW}_funded cascade"
 hive -e "create database if not exists ${SHADOW}_funded"

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql

@@ -37,8 +37,15 @@ select * from ${stats_db_name}.otherresearchproduct_refereed;
 
 create table if not exists ${stats_db_name}.indi_impact_measures STORED AS PARQUET as
 select substr(id, 4) as id, measures_ids.id impactmetric, cast(measures_ids.unit.value[0] as double) score,
-cast(measures_ids.unit.value[0] as decimal(6,3)) score_dec, measures_ids.unit.value[1] class
+cast(measures_ids.unit.value[0] as decimal(6,3)) score_dec, measures_ids.unit.value[1] impact_class
 from ${openaire_db_name}.result lateral view explode(measures) measures as measures_ids
 where measures_ids.id!='views' and measures_ids.id!='downloads';
 
-ANALYZE TABLE indi_impact_measures COMPUTE STATISTICS;
+create table if not exists ${stats_db_name}.result_apc_affiliations STORED AS PARQUET as
+select distinct substr(rel.target,4) id, substr(rel.source,4) organization, o.legalname.value name,
+cast(rel.properties[0].value as double) apc_amount,
+rel.properties[1].value apc_currency
+from ${openaire_db_name}.relation rel
+join ${openaire_db_name}.organization o on o.id=rel.source
+join ${openaire_db_name}.result r on r.id=rel.target
+where rel.subreltype = 'affiliation' and rel.datainfo.deletedbyinference = false and size(rel.properties)>0;

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql

@@ -35,6 +35,7 @@ create or replace view ${stats_db_name}.doctoratestudents as select * from stats
 create or replace view ${stats_db_name}.totalresearchers as select * from stats_ext.totalresearchers;
 create or replace view ${stats_db_name}.totalresearchersft as select * from stats_ext.totalresearchersft;
 create or replace view ${stats_db_name}.hrrst as select * from stats_ext.hrrst;
+create or replace view ${stats_db_name}.graduatedoctorates as select * from stats_ext.graduatedoctorates;
 
 create table if not exists ${stats_db_name}.result_instance stored as parquet as
 select distinct r.*

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql

@@ -88,85 +88,88 @@ create view if not exists TARGET.doctoratestudents as select * from SOURCE.docto
 create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers;
 create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft;
 create view if not exists TARGET.hrrst as select * from SOURCE.hrrst;
+create view if not exists TARGET.graduatedoctorates as select * from SOURCE.graduatedoctorates;
 
 create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_citations COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_citations COMPUTE STATISTICS;
 
 create table TARGET.result_references_oc stored as parquet as select * from SOURCE.result_references_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_references_oc COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_references_oc COMPUTE STATISTICS;
 
 create table TARGET.result_citations_oc stored as parquet as select * from SOURCE.result_citations_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_citations_oc COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_citations_oc COMPUTE STATISTICS;
 
 create table TARGET.result_classifications stored as parquet as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_classifications COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_classifications COMPUTE STATISTICS;
 
 create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_apc COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_apc COMPUTE STATISTICS;
 
 create table TARGET.result_concepts stored as parquet as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_concepts COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_concepts COMPUTE STATISTICS;
 
 create table TARGET.result_datasources stored as parquet as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_datasources COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_datasources COMPUTE STATISTICS;
 
 create table TARGET.result_fundercount stored as parquet as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_fundercount COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_fundercount COMPUTE STATISTICS;
 
 create table TARGET.result_gold stored as parquet as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_gold COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_gold COMPUTE STATISTICS;
 
 create table TARGET.result_greenoa stored as parquet as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_greenoa COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_greenoa COMPUTE STATISTICS;
 
 create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_languages COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_languages COMPUTE STATISTICS;
 
 create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_licenses COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_licenses COMPUTE STATISTICS;
 
 create table TARGET.licenses_normalized STORED AS PARQUET as select * from SOURCE.licenses_normalized;
-ANALYZE TABLE TARGET.licenses_normalized COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.licenses_normalized COMPUTE STATISTICS;
 
 create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_oids COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_oids COMPUTE STATISTICS;
 
 create table TARGET.result_organization stored as parquet as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_organization COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_organization COMPUTE STATISTICS;
 
 create table TARGET.result_peerreviewed stored as parquet as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_peerreviewed COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_peerreviewed COMPUTE STATISTICS;
 
 create table TARGET.result_pids stored as parquet as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_pids COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_pids COMPUTE STATISTICS;
 
 create table TARGET.result_projectcount stored as parquet as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_projectcount COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_projectcount COMPUTE STATISTICS;
 
 create table TARGET.result_projects stored as parquet as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_projects COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_projects COMPUTE STATISTICS;
 
 create table TARGET.result_refereed stored as parquet as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_refereed COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_refereed COMPUTE STATISTICS;
 
 create table TARGET.result_sources stored as parquet as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_sources COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_sources COMPUTE STATISTICS;
 
 create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_topics COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_topics COMPUTE STATISTICS;
 
 create table TARGET.result_fos stored as parquet as select * from SOURCE.result_fos orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_fos COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_fos COMPUTE STATISTICS;
 
 create table TARGET.result_accessroute stored as parquet as select * from SOURCE.result_accessroute orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.result_accessroute COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_accessroute COMPUTE STATISTICS;
+
+create table TARGET.result_orcid stored as parquet as select * from SOURCE.result_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
 
 create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result);
 create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result);
 create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou;
 drop view TARGET.foo1;
 drop view TARGET.foo2;
-ANALYZE TABLE TARGET.result_result COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result_result COMPUTE STATISTICS;
 
 -- datasources
 create view if not exists TARGET.datasource as select * from SOURCE.datasource;
@@ -175,7 +178,7 @@ create view if not exists TARGET.datasource_organizations as select * from SOURC
 create view if not exists TARGET.datasource_sources as select * from SOURCE.datasource_sources;
 
 create table TARGET.datasource_results stored as parquet as select id as result, datasource as id from TARGET.result_datasources;
-ANALYZE TABLE TARGET.datasource_results COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.datasource_results COMPUTE STATISTICS;
 
 -- organizations
 create view if not exists TARGET.organization as select * from SOURCE.organization;
@@ -193,28 +196,28 @@ create view if not exists TARGET.project_classification as select * from SOURCE.
 create view if not exists TARGET.project_organization_contribution as select * from SOURCE.project_organization_contribution;
 
 create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects;
-ANALYZE TABLE TARGET.project_results COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.project_results COMPUTE STATISTICS;
 
 -- indicators
 -- Sprint 1 ----
 create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_green_oa COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_green_oa COMPUTE STATISTICS;
 create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_grey_lit COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_grey_lit COMPUTE STATISTICS;
 create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_doi_from_crossref COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_doi_from_crossref COMPUTE STATISTICS;
 -- Sprint 2 ----
 create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_result_has_cc_licence COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_result_has_cc_licence COMPUTE STATISTICS;
 create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_result_has_cc_licence_url COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_result_has_cc_licence_url COMPUTE STATISTICS;
 create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_has_abstract COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_has_abstract COMPUTE STATISTICS;
 create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_result_with_orcid COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_result_with_orcid COMPUTE STATISTICS;
 ---- Sprint 3 ----
 create table TARGET.indi_funded_result_with_fundref stored as parquet as select * from SOURCE.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_funded_result_with_fundref COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_funded_result_with_fundref COMPUTE STATISTICS;
 create view TARGET.indi_result_org_collab as select * from SOURCE.indi_result_org_collab;
 create view TARGET.indi_result_org_country_collab as select * from SOURCE.indi_result_org_country_collab;
 create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org;
@@ -223,32 +226,32 @@ create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funde
 create view TARGET.indi_result_country_collab as select * from SOURCE.indi_result_country_collab;
 ---- Sprint 4 ----
 create table TARGET.indi_pub_diamond stored as parquet as select * from SOURCE.indi_pub_diamond orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_diamond COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_diamond COMPUTE STATISTICS;
 create table TARGET.indi_pub_in_transformative stored as parquet as select * from SOURCE.indi_pub_in_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_in_transformative COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_in_transformative COMPUTE STATISTICS;
 create table TARGET.indi_pub_closed_other_open stored as parquet as select * from SOURCE.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_closed_other_open COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_closed_other_open COMPUTE STATISTICS;
 ---- Sprint 5 ----
 create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_result_no_of_copies COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_result_no_of_copies COMPUTE STATISTICS;
 ---- Sprint 6 ----
 create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_hybrid_oa_with_cc COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_hybrid_oa_with_cc COMPUTE STATISTICS;
 create table TARGET.indi_pub_bronze_oa stored as parquet as select * from SOURCE.indi_pub_bronze_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_bronze_oa COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_bronze_oa COMPUTE STATISTICS;
 create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
-ANALYZE TABLE TARGET.indi_pub_downloads COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_downloads COMPUTE STATISTICS;
 create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
-ANALYZE TABLE TARGET.indi_pub_downloads_datasource COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_downloads_datasource COMPUTE STATISTICS;
 create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
-ANALYZE TABLE TARGET.indi_pub_downloads_year COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_downloads_year COMPUTE STATISTICS;
 create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
-ANALYZE TABLE TARGET.indi_pub_downloads_datasource_year COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_downloads_datasource_year COMPUTE STATISTICS;
 ---- Sprint 7 ----
 create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_gold_oa COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_gold_oa COMPUTE STATISTICS;
 create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_hybrid COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_hybrid COMPUTE STATISTICS;
 create view TARGET.indi_org_fairness as select * from SOURCE.indi_org_fairness;
 create view TARGET.indi_org_fairness_pub_pr as select * from SOURCE.indi_org_fairness_pub_pr;
 create view TARGET.indi_org_fairness_pub_year as select * from SOURCE.indi_org_fairness_pub_year;
@@ -259,12 +262,22 @@ create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable;
 create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess;
 create view TARGET.indi_org_openess_year as select * from SOURCE.indi_org_openess_year;
 create table TARGET.indi_pub_has_preprint stored as parquet as select * from SOURCE.indi_pub_has_preprint orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_has_preprint COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_has_preprint COMPUTE STATISTICS;
 create table TARGET.indi_pub_in_subscribed stored as parquet as select * from SOURCE.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_in_subscribed COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_in_subscribed COMPUTE STATISTICS;
 create table TARGET.indi_result_with_pid stored as parquet as select * from SOURCE.indi_result_with_pid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_result_with_pid COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_result_with_pid COMPUTE STATISTICS;
 create table TARGET.indi_impact_measures stored as parquet as select * from SOURCE.indi_impact_measures orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_impact_measures COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_impact_measures COMPUTE STATISTICS;
 create table TARGET.indi_pub_interdisciplinarity stored as parquet as select * from SOURCE.indi_pub_interdisciplinarity orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-ANALYZE TABLE TARGET.indi_pub_interdisciplinarity COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.indi_pub_interdisciplinarity COMPUTE STATISTICS;
+create table TARGET.result_apc_affiliations stored as parquet as select * from SOURCE.result_apc_affiliations orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_apc_affiliations COMPUTE STATISTICS;
+create table TARGET.indi_is_project_result_after stored as parquet as select * from SOURCE.indi_is_project_result_after orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
+create table TARGET.indi_is_funder_plan_s stored as parquet as select * from SOURCE.indi_is_funder_plan_s orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+create view TARGET.indi_funder_fairness as select * from SOURCE.indi_funder_fairness;
+create view TARGET.indi_funder_openess as select * from SOURCE.indi_funder_openess;
+create view TARGET.indi_funder_findable as select * from SOURCE.indi_funder_findable;
+create view TARGET.indi_ris_fairness as select * from SOURCE.indi_ris_fairness;
+create view TARGET.indi_ris_openess as select * from SOURCE.indi_ris_openess;
+create view TARGET.indi_ris_findable as select * from SOURCE.indi_ris_findable;

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql

@@ -0,0 +1,292 @@
+drop database if exists TARGET cascade;
+create database if not exists TARGET;
+
+create view if not exists TARGET.category as select * from SOURCE.category;
+create view if not exists TARGET.concept as select * from SOURCE.concept;
+create view if not exists TARGET.context as select * from SOURCE.context;
+create view if not exists TARGET.country as select * from SOURCE.country;
+create view if not exists TARGET.countrygdp as select * from SOURCE.countrygdp;
+create view if not exists TARGET.creation_date as select * from SOURCE.creation_date;
+create view if not exists TARGET.funder as select * from SOURCE.funder;
+create view if not exists TARGET.fundref as select * from SOURCE.fundref;
+create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture;
+create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure;
+create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents;
+create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers;
+create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft;
+create view if not exists TARGET.hrrst as select * from SOURCE.hrrst;
+create view if not exists TARGET.graduatedoctorates as select * from SOURCE.graduatedoctorates;
+
+create table TARGET.result stored as parquet as
+    select distinct * from (
+        select * from SOURCE.result r where exists (select 1 from SOURCE.result_projects rp join SOURCE.project p on rp.project=p.id where rp.id=r.id)
+        union all
+        select * from SOURCE.result r where exists (select 1 from SOURCE.result_concepts rc where rc.id=r.id)
+        union all
+        select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in (
+             'openorgs____::b84450f9864182c67b8611b5593f4250', --"Athena Research and Innovation Center In Information Communication & Knowledge Technologies', --ARC"
+             'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', --National Research Council
+             'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', --??? Not exists ??
+             'openorgs____::d169c7407dd417152596908d48c11460', --Masaryk University
+             'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', --University of Belgrade
+             'openorgs____::0ae431b820e4c33db8967fbb2b919150', --University of Helsinki
+             'openorgs____::759d59f05d77188faee99b7493b46805', --University of Minho
+             'openorgs____::cad284878801b9465fa51a95b1d779db', --Universidad Politécnica de Madrid
+             'openorgs____::eadc8da90a546e98c03f896661a2e4d4', --University of Göttingen
+             'openorgs____::c0286313e36479eff8676dba9b724b40', --National and Kapodistrian University of Athens
+             -- 'openorgs____::c80a8243a5e5c620d7931c88d93bf17a', --Université Paris Diderot
+             'openorgs____::c08634f0a6b0081c3dc6e6c93a4314f3', --Bielefeld University
+             'openorgs____::6fc85e4a8f7ecaf4b0c738d010e967ea', --University of Southern Denmark
+             'openorgs____::3d6122f87f9a97a99d8f6e3d73313720', --Humboldt-Universität zu Berlin
+             'openorgs____::16720ada63d0fa8ca41601feae7d1aa5', --TU Darmstadt
+             'openorgs____::ccc0a066b56d2cfaf90c2ae369df16f5', --KU Leuven
+             'openorgs____::4c6f119632adf789746f0a057ed73e90', --University of the Western Cape
+             'openorgs____::ec3665affa01aeafa28b7852c4176dbd', --Rudjer Boskovic Institute
+             'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University
+             'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg
+             'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII)
+             'openorgs____::b77c01aa15de3675da34277d48de2ec1', -- Valencia Catholic University Saint Vincent Martyr
+             'openorgs____::7fe2f66cdc43983c6b24816bfe9cf6a0', -- Unviersity of Warsaw
+             'openorgs____::15e7921fc50d9aa1229a82a84429419e', -- University Of Thessaly
+             'openorgs____::11f7919dadc8f8a7251af54bba60c956', -- Technical University of Crete
+             'openorgs____::84f0c5f5dbb6daf42748485924efde4b', -- University of Piraeus
+             'openorgs____::4ac562f0376fce3539504567649cb373', -- University of Patras
+             'openorgs____::3e8d1f8c3f6cd7f418b09f1f58b4873b', -- Aristotle University of Thessaloniki
+             'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank
+             'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech
+             'openorgs____::e15adb13c4dadd49de4d35c39b5da93a',  -- Nanyang Technological University
+             'openorgs____::4b34103bde246228fcd837f5f1bf4212',  -- Autonomous University of Barcelona
+             'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb',	-- McMaster University
+             'openorgs____::51c7fc556e46381734a25a6fbc3fd398',	-- University of Modena and Reggio Emilia
+             'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db',	-- Bilkent University
+             'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06',	-- Saints Cyril and Methodius University of Skopje
+             'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan
+             'openorgs____::b8b8ca674452579f3f593d9f5e557483',   -- University College Cork
+             'openorgs____::38d7097854736583dde879d12dacafca',	-- Brown University
+             'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech
+             'openorgs____::2530baca8a15936ba2e3297f2bce2e7e',	-- University of Cape Town
+             'openorgs____::d11f981828c485cd23d93f7f24f24db1',  -- Technological University Dublin
+             'openorgs____::5e6bf8962665cdd040341171e5c631d8',  -- Delft University of Technology
+             'openorgs____::846cb428d3f52a445f7275561a7beb5d',  -- University of Manitoba
+             'openorgs____::eb391317ed0dc684aa81ac16265de041',	-- Universitat Rovira i Virgili
+             'openorgs____::66aa9fc2fceb271423dfabcc38752dc0',  -- Lund University
+             'openorgs____::3cff625a4370d51e08624cc586138b2f',	-- IMT Atlantique
+             'openorgs____::c0b262bd6eab819e4c994914f9c010e2',   -- National Institute of Geophysics and Volcanology
+             'openorgs____::1624ff7c01bb641b91f4518539a0c28a',   -- Vrije Universiteit Amsterdam
+             'openorgs____::4d4051b56708688235252f1d8fddb8c1',	 --Iscte - Instituto Universitário de Lisboa
+             'openorgs____::ab4ac74c35fa5dada770cf08e5110fab',	-- Universidade Católica Portuguesa
+             'openorgs____::4d4051b56708688235252f1d8fddb8c1',	-- Iscte - Instituto Universitário de Lisboa
+             'openorgs____::5d55fb216b14691cf68218daf5d78cd9',  -- Munster Technological University
+             'openorgs____::0fccc7640f0cb44d5cd1b06b312a06b9',  -- Cardiff University
+             'openorgs____::8839b55dae0c84d56fd533f52d5d483a'   -- Leibniz Institute of Ecological Urban and Regional Development
+        ) )) foo;
+
+--ANALYZE TABLE TARGET.result COMPUTE STATISTICS;
+
+create view if not exists TARGET.category as select * from SOURCE.category;
+create view if not exists TARGET.concept as select * from SOURCE.concept;
+create view if not exists TARGET.context as select * from SOURCE.context;
+create view if not exists TARGET.country as select * from SOURCE.country;
+create view if not exists TARGET.countrygdp as select * from SOURCE.countrygdp;
+create view if not exists TARGET.creation_date as select * from SOURCE.creation_date;
+create view if not exists TARGET.funder as select * from SOURCE.funder;
+create view if not exists TARGET.fundref as select * from SOURCE.fundref;
+create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture;
+create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure;
+create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents;
+create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers;
+create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft;
+create view if not exists TARGET.hrrst as select * from SOURCE.hrrst;
+--create view if not exists TARGET.graduatedoctorates as select * from SOURCE.graduatedoctorates;
+
+create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_citations COMPUTE STATISTICS;
+
+create table TARGET.result_references_oc stored as parquet as select * from SOURCE.result_references_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_references_oc COMPUTE STATISTICS;
+
+create table TARGET.result_citations_oc stored as parquet as select * from SOURCE.result_citations_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_citations_oc COMPUTE STATISTICS;
+
+create table TARGET.result_classifications stored as parquet as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_classifications COMPUTE STATISTICS;
+
+create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_apc COMPUTE STATISTICS;
+
+create table TARGET.result_concepts stored as parquet as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_concepts COMPUTE STATISTICS;
+
+create table TARGET.result_datasources stored as parquet as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_datasources COMPUTE STATISTICS;
+
+create table TARGET.result_fundercount stored as parquet as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_fundercount COMPUTE STATISTICS;
+
+create table TARGET.result_gold stored as parquet as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_gold COMPUTE STATISTICS;
+
+create table TARGET.result_greenoa stored as parquet as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_greenoa COMPUTE STATISTICS;
+
+create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_languages COMPUTE STATISTICS;
+
+create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_licenses COMPUTE STATISTICS;
+
+create table TARGET.licenses_normalized STORED AS PARQUET as select * from SOURCE.licenses_normalized;
+--ANALYZE TABLE TARGET.licenses_normalized COMPUTE STATISTICS;
+
+create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_oids COMPUTE STATISTICS;
+
+create table TARGET.result_organization stored as parquet as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_organization COMPUTE STATISTICS;
+
+create table TARGET.result_peerreviewed stored as parquet as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_peerreviewed COMPUTE STATISTICS;
+
+create table TARGET.result_pids stored as parquet as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_pids COMPUTE STATISTICS;
+
+create table TARGET.result_projectcount stored as parquet as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_projectcount COMPUTE STATISTICS;
+
+create table TARGET.result_projects stored as parquet as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_projects COMPUTE STATISTICS;
+
+create table TARGET.result_refereed stored as parquet as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_refereed COMPUTE STATISTICS;
+
+create table TARGET.result_sources stored as parquet as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_sources COMPUTE STATISTICS;
+
+create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_topics COMPUTE STATISTICS;
+
+create table TARGET.result_fos stored as parquet as select * from SOURCE.result_fos orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_fos COMPUTE STATISTICS;
+
+create table TARGET.result_accessroute stored as parquet as select * from SOURCE.result_accessroute orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_accessroute COMPUTE STATISTICS;
+
+create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result);
+create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result);
+create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou;
+drop view TARGET.foo1;
+drop view TARGET.foo2;
+--ANALYZE TABLE TARGET.result_result COMPUTE STATISTICS;
+
+-- datasources
+create view if not exists TARGET.datasource as select * from SOURCE.datasource;
+create view if not exists TARGET.datasource_oids as select * from SOURCE.datasource_oids;
+create view if not exists TARGET.datasource_organizations as select * from SOURCE.datasource_organizations;
+create view if not exists TARGET.datasource_sources as select * from SOURCE.datasource_sources;
+
+create table TARGET.datasource_results stored as parquet as select id as result, datasource as id from TARGET.result_datasources;
+--ANALYZE TABLE TARGET.datasource_results COMPUTE STATISTICS;
+
+-- organizations
+create view if not exists TARGET.organization as select * from SOURCE.organization;
+create view if not exists TARGET.organization_datasources as select * from SOURCE.organization_datasources;
+create view if not exists TARGET.organization_pids as select * from SOURCE.organization_pids;
+create view if not exists TARGET.organization_projects as select * from SOURCE.organization_projects;
+create view if not exists TARGET.organization_sources as select * from SOURCE.organization_sources;
+
+-- projects
+create view if not exists TARGET.project as select * from SOURCE.project;
+create view if not exists TARGET.project_oids as select * from SOURCE.project_oids;
+create view if not exists TARGET.project_organizations as select * from SOURCE.project_organizations;
+create view if not exists TARGET.project_resultcount as select * from SOURCE.project_resultcount;
+create view if not exists TARGET.project_classification as select * from SOURCE.project_classification;
+create view if not exists TARGET.project_organization_contribution as select * from SOURCE.project_organization_contribution;
+
+create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects;
+--ANALYZE TABLE TARGET.project_results COMPUTE STATISTICS;
+
+-- indicators
+-- Sprint 1 ----
+create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_green_oa COMPUTE STATISTICS;
+create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_grey_lit COMPUTE STATISTICS;
+create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_doi_from_crossref COMPUTE STATISTICS;
+-- Sprint 2 ----
+create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_result_has_cc_licence COMPUTE STATISTICS;
+create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_result_has_cc_licence_url COMPUTE STATISTICS;
+create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_has_abstract COMPUTE STATISTICS;
+create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_result_with_orcid COMPUTE STATISTICS;
+---- Sprint 3 ----
+create table TARGET.indi_funded_result_with_fundref stored as parquet as select * from SOURCE.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_funded_result_with_fundref COMPUTE STATISTICS;
+create view TARGET.indi_result_org_collab as select * from SOURCE.indi_result_org_collab;
+create view TARGET.indi_result_org_country_collab as select * from SOURCE.indi_result_org_country_collab;
+create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org;
+create view TARGET.indi_project_collab_org_country as select * from SOURCE.indi_project_collab_org_country;
+create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab;
+create view TARGET.indi_result_country_collab as select * from SOURCE.indi_result_country_collab;
+---- Sprint 4 ----
+create table TARGET.indi_pub_diamond stored as parquet as select * from SOURCE.indi_pub_diamond orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_diamond COMPUTE STATISTICS;
+create table TARGET.indi_pub_in_transformative stored as parquet as select * from SOURCE.indi_pub_in_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_in_transformative COMPUTE STATISTICS;
+create table TARGET.indi_pub_closed_other_open stored as parquet as select * from SOURCE.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_closed_other_open COMPUTE STATISTICS;
+---- Sprint 5 ----
+create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_result_no_of_copies COMPUTE STATISTICS;
+---- Sprint 6 ----
+create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_hybrid_oa_with_cc COMPUTE STATISTICS;
+create table TARGET.indi_pub_bronze_oa stored as parquet as select * from SOURCE.indi_pub_bronze_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_bronze_oa COMPUTE STATISTICS;
+create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
+--ANALYZE TABLE TARGET.indi_pub_downloads COMPUTE STATISTICS;
+create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
+--ANALYZE TABLE TARGET.indi_pub_downloads_datasource COMPUTE STATISTICS;
+create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
+--ANALYZE TABLE TARGET.indi_pub_downloads_year COMPUTE STATISTICS;
+create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
+--ANALYZE TABLE TARGET.indi_pub_downloads_datasource_year COMPUTE STATISTICS;
+---- Sprint 7 ----
+create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_gold_oa COMPUTE STATISTICS;
+create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_hybrid COMPUTE STATISTICS;
+create view TARGET.indi_org_fairness as select * from SOURCE.indi_org_fairness;
+create view TARGET.indi_org_fairness_pub_pr as select * from SOURCE.indi_org_fairness_pub_pr;
+create view TARGET.indi_org_fairness_pub_year as select * from SOURCE.indi_org_fairness_pub_year;
+create view TARGET.indi_org_fairness_pub as select * from SOURCE.indi_org_fairness_pub;
+create view TARGET.indi_org_fairness_year as select * from SOURCE.indi_org_fairness_year;
+create view TARGET.indi_org_findable_year as select * from SOURCE.indi_org_findable_year;
+create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable;
+create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess;
+create view TARGET.indi_org_openess_year as select * from SOURCE.indi_org_openess_year;
+create table TARGET.indi_pub_has_preprint stored as parquet as select * from SOURCE.indi_pub_has_preprint orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_has_preprint COMPUTE STATISTICS;
+create table TARGET.indi_pub_in_subscribed stored as parquet as select * from SOURCE.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_in_subscribed COMPUTE STATISTICS;
+create table TARGET.indi_result_with_pid stored as parquet as select * from SOURCE.indi_result_with_pid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_result_with_pid COMPUTE STATISTICS;
+create table TARGET.indi_impact_measures stored as parquet as select * from SOURCE.indi_impact_measures orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_impact_measures COMPUTE STATISTICS;
+create table TARGET.indi_pub_interdisciplinarity stored as parquet as select * from SOURCE.indi_pub_interdisciplinarity orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.indi_pub_interdisciplinarity COMPUTE STATISTICS;
+create table TARGET.result_apc_affiliations stored as parquet as select * from SOURCE.result_apc_affiliations orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+--ANALYZE TABLE TARGET.result_apc_affiliations COMPUTE STATISTICS;
+create table TARGET.indi_is_project_result_after stored as parquet as select * from SOURCE.indi_is_project_result_after orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+create table TARGET.indi_is_funder_plan_s stored as parquet as select * from SOURCE.indi_is_funder_plan_s orig where exists (select 1 from TARGET.result r where r.id=orig.id);
+create view TARGET.indi_funder_fairness as select * from SOURCE.indi_funder_fairness;
+create view TARGET.indi_funder_openess as select * from SOURCE.indi_funder_openess;
+create view TARGET.indi_funder_findable as select * from SOURCE.indi_funder_findable;
+create view TARGET.indi_ris_fairness as select * from SOURCE.indi_ris_fairness;
+create view TARGET.indi_ris_openess as select * from SOURCE.indi_ris_openess;
+create view TARGET.indi_ris_findable as select * from SOURCE.indi_ris_findable;
+
+

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql

@@ -12,4 +12,4 @@ create table TARGET.result stored as parquet as
 --             join SOURCE.result
              where rc.id=r.id and conc.category like CONTEXT)
 )  foo;
-ANALYZE TABLE TARGET.result COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result COMPUTE STATISTICS;

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql

@@ -12,4 +12,4 @@ create table TARGET.result stored as parquet as
 --             join SOURCE.result
              where rc.id=r.id and conc.category not in (CONTEXTS))
 )  foo;
-ANALYZE TABLE TARGET.result COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result COMPUTE STATISTICS;

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql

@@ -6,4 +6,4 @@ create table TARGET.result stored as parquet as
         select * from SOURCE.result r where exists (select 1 from SOURCE.result_projects rp join SOURCE.project p on rp.project=p.id where rp.id=r.id)
     ) foo;
 
-ANALYZE TABLE TARGET.result COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result COMPUTE STATISTICS;

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql

@@ -34,16 +34,16 @@ create table TARGET.result stored as parquet as
              'openorgs____::3e8d1f8c3f6cd7f418b09f1f58b4873b', -- Aristotle University of Thessaloniki
              'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank
              'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech
-             'openorgs____::e15adb13c4dadd49de4d35c39b5da93a',  -- Nanyang Technological University
+             'openorgs____::e15adb13c4dadd49de4d35c39b5da93a', -- Nanyang Technological University
-             'openorgs____::4b34103bde246228fcd837f5f1bf4212',  -- Autonomous University of Barcelona
+             'openorgs____::4b34103bde246228fcd837f5f1bf4212', -- Autonomous University of Barcelona
-             'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb',	-- McMaster University
+             'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb', -- McMaster University
-             'openorgs____::51c7fc556e46381734a25a6fbc3fd398',	-- University of Modena and Reggio Emilia
+             'openorgs____::51c7fc556e46381734a25a6fbc3fd398', -- University of Modena and Reggio Emilia
-             'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db',	-- Bilkent University
+             'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db', -- Bilkent University
-             'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06',	-- Saints Cyril and Methodius University of Skopje
+             'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06', -- Saints Cyril and Methodius University of Skopje
              'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan
-             'openorgs____::b8b8ca674452579f3f593d9f5e557483',   -- University College Cork
+             'openorgs____::b8b8ca674452579f3f593d9f5e557483',  -- University College Cork
-             'openorgs____::38d7097854736583dde879d12dacafca'	-- Brown University
+             'openorgs____::38d7097854736583dde879d12dacafca',	-- Brown University
-             'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech
+             'openorgs____::57784c9e047e826fefdb1ef816120d92',  --Arts et Métiers ParisTech
              'openorgs____::2530baca8a15936ba2e3297f2bce2e7e',	-- University of Cape Town
              'openorgs____::d11f981828c485cd23d93f7f24f24db1',  -- Technological University Dublin
              'openorgs____::5e6bf8962665cdd040341171e5c631d8',  -- Delft University of Technology
@@ -52,7 +52,13 @@ create table TARGET.result stored as parquet as
              'openorgs____::66aa9fc2fceb271423dfabcc38752dc0',  -- Lund University
              'openorgs____::3cff625a4370d51e08624cc586138b2f',	-- IMT Atlantique
              'openorgs____::c0b262bd6eab819e4c994914f9c010e2',   -- National Institute of Geophysics and Volcanology
-             'openorgs____::1624ff7c01bb641b91f4518539a0c28a'     -- Vrije Universiteit Amsterdam
+             'openorgs____::1624ff7c01bb641b91f4518539a0c28a',   -- Vrije Universiteit Amsterdam
+             'openorgs____::4d4051b56708688235252f1d8fddb8c1',	 --Iscte - Instituto Universitário de Lisboa
+             'openorgs____::ab4ac74c35fa5dada770cf08e5110fab',	 -- Universidade Católica Portuguesa
+             'openorgs____::4d4051b56708688235252f1d8fddb8c1',	 -- Iscte - Instituto Universitário de Lisboa
+             'openorgs____::5d55fb216b14691cf68218daf5d78cd9',  -- Munster Technological University
+             'openorgs____::0fccc7640f0cb44d5cd1b06b312a06b9',  -- Cardiff University
+             'openorgs____::8839b55dae0c84d56fd533f52d5d483a'   -- Leibniz Institute of Ecological Urban and Regional Development
         )))  foo;
 
-ANALYZE TABLE TARGET.result COMPUTE STATISTICS;
+--ANALYZE TABLE TARGET.result COMPUTE STATISTICS;

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql

@@ -8,7 +8,7 @@ from ${stats_db_name}.result r
     group by rl.id
 ) rln on rln.id=r.id;
 
-ANALYZE TABLE ${observatory_db_name}.result_cc_licence COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_cc_licence COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_affiliated_country stored as parquet as
 select
@@ -39,7 +39,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, c.code, c.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_affiliated_country COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_affiliated_country COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_affiliated_year stored as parquet as
 select
@@ -70,7 +70,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year;
 
-ANALYZE TABLE ${observatory_db_name}.result_affiliated_year COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_affiliated_year COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_affiliated_year_country stored as parquet as
 select
@@ -101,7 +101,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year, c.code, c.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_affiliated_year_country COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_affiliated_year_country COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_affiliated_datasource stored as parquet as
 select
@@ -134,7 +134,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_affiliated_datasource COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_affiliated_datasource COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_affiliated_datasource_country stored as parquet as
 select
@@ -167,7 +167,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name, c.code, c.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_affiliated_datasource_country COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_affiliated_datasource_country COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_affiliated_organization stored as parquet as
 select
@@ -198,7 +198,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_affiliated_organization COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_affiliated_organization COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_affiliated_organization_country stored as parquet as
 select
@@ -229,7 +229,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name, c.code, c.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_affiliated_organization_country COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_affiliated_organization_country COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_affiliated_funder stored as parquet as
 select
@@ -262,7 +262,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder;
 
-ANALYZE TABLE ${observatory_db_name}.result_affiliated_funder COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_affiliated_funder COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_affiliated_funder_country stored as parquet as
 select
@@ -295,7 +295,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder, c.code, c.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_affiliated_funder_country COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_affiliated_funder_country COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_deposited_country stored as parquet as
 select
@@ -328,7 +328,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, c.code, c.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_deposited_country COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_deposited_country COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_deposited_year stored as parquet as
 select
@@ -361,7 +361,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year;
 
-ANALYZE TABLE ${observatory_db_name}.result_deposited_year COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_deposited_year COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_deposited_year_country stored as parquet as
 select
@@ -394,7 +394,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year, c.code, c.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_deposited_year_country COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_deposited_year_country COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_deposited_datasource stored as parquet as
 select
@@ -427,7 +427,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_deposited_datasource COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_deposited_datasource COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_deposited_datasource_country stored as parquet as
 select
@@ -460,7 +460,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name, c.code, c.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_deposited_datasource_country COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_deposited_datasource_country COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_deposited_organization stored as parquet as
 select
@@ -493,7 +493,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_deposited_organization COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_deposited_organization COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_deposited_organization_country stored as parquet as
 select
@@ -526,7 +526,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name, c.code, c.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_deposited_organization_country COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_deposited_organization_country COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_deposited_funder stored as parquet as
 select
@@ -561,7 +561,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder;
 
-ANALYZE TABLE ${observatory_db_name}.result_deposited_funder COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_deposited_funder COMPUTE STATISTICS;
 
 create table ${observatory_db_name}.result_deposited_funder_country stored as parquet as
 select
@@ -596,4 +596,4 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder, c.code, c.name;
 
-ANALYZE TABLE ${observatory_db_name}.result_deposited_funder_country COMPUTE STATISTICS;
+--ANALYZE TABLE ${observatory_db_name}.result_deposited_funder_country COMPUTE STATISTICS;

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml

@@ -317,15 +317,12 @@
     </action>
 
     <action name="Step16-createIndicatorsTables">
-        <shell xmlns="uri:oozie:shell-action:0.1">
+        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <job-tracker>${jobTracker}</job-tracker>
+            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <name-node>${nameNode}</name-node>
+            <script>scripts/step16-createIndicatorsTables.sql</script>
-            <exec>indicators.sh</exec>
+            <param>stats_db_name=${stats_db_name}</param>
-            <argument>${stats_db_name}</argument>
+            <param>external_stats_db_name=${external_stats_db_name}</param>
-            <argument>${external_stats_db_name}</argument>
+        </hive2>
-            <argument>${wf:appPath()}/scripts/step16-createIndicatorsTables.sql</argument>
-            <file>indicators.sh</file>
-        </shell>
         <ok to="Step16_1-definitions"/>
         <error to="Kill"/>
     </action>
@@ -378,6 +375,7 @@
             <argument>${wf:appPath()}/scripts/step20-createMonitorDB_institutions.sql</argument>
             <argument>${wf:appPath()}/scripts/step20-createMonitorDB_RIs.sql</argument>
             <argument>${wf:appPath()}/scripts/step20-createMonitorDB_RIs_tail.sql</argument>
+            <argument>${wf:appPath()}/scripts/step20-createMonitorDBAll.sql</argument>
             <file>monitor.sh</file>
         </shell>
         <ok to="step21-createObservatoryDB-pre"/>

dhp-workflows/dhp-swh/pom.xml

@@ -0,0 +1,110 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>eu.dnetlib.dhp</groupId>
+        <artifactId>dhp-workflows</artifactId>
+        <version>1.2.5-SNAPSHOT</version>
+    </parent>
+    <artifactId>dhp-swh</artifactId>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.apache.spark</groupId>
+            <artifactId>spark-core_${scala.binary.version}</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.spark</groupId>
+            <artifactId>spark-sql_${scala.binary.version}</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-common</artifactId>
+            <version>${project.version}</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>net.sf.saxon</groupId>
+                    <artifactId>Saxon-HE</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+
+        <dependency>
+            <groupId>dom4j</groupId>
+            <artifactId>dom4j</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>xml-apis</groupId>
+            <artifactId>xml-apis</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>jaxen</groupId>
+            <artifactId>jaxen</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.hadoop</groupId>
+            <artifactId>hadoop-distcp</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>eu.dnetlib</groupId>
+            <artifactId>dnet-actionmanager-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>eu.dnetlib</groupId>
+            <artifactId>dnet-actionmanager-common</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>eu.dnetlib</groupId>
+                    <artifactId>dnet-openaireplus-mapping-utils</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>saxonica</groupId>
+                    <artifactId>saxon</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>saxonica</groupId>
+                    <artifactId>saxon-dom</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>jgrapht</groupId>
+                    <artifactId>jgrapht</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>net.sf.ehcache</groupId>
+                    <artifactId>ehcache</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.springframework</groupId>
+                    <artifactId>spring-test</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.apache.*</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>apache</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.httpcomponents</groupId>
+            <artifactId>httpclient</artifactId>
+            <version>4.5.13</version>
+        </dependency>
+        <dependency>
+            <groupId>org.datanucleus</groupId>
+            <artifactId>datanucleus-core</artifactId>
+            <version>3.2.10</version>
+            <scope>compile</scope>
+        </dependency>
+
+    </dependencies>
+</project>

dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/ArchiveRepositoryURLs.java

@@ -0,0 +1,176 @@
+
+package eu.dnetlib.dhp.swh;
+
+import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration;
+
+import java.io.IOException;
+import java.net.URL;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+import java.util.Optional;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.io.SequenceFile;
+import org.apache.hadoop.io.Text;
+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.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
+import eu.dnetlib.dhp.swh.models.LastVisitData;
+import eu.dnetlib.dhp.swh.utils.SWHConnection;
+import eu.dnetlib.dhp.swh.utils.SWHConstants;
+import eu.dnetlib.dhp.swh.utils.SWHUtils;
+
+/**
+ * Sends archive requests to the SWH API for those software repository URLs that are missing from them
+ *
+ *  @author Serafeim Chatzopoulos
+ */
+public class ArchiveRepositoryURLs {
+
+	private static final Logger log = LoggerFactory.getLogger(ArchiveRepositoryURLs.class);
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SWHConnection swhConnection = null;
+
+	public static void main(final String[] args) throws IOException, ParseException {
+		final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					CollectLastVisitRepositoryData.class
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/swh/input_archive_repository_urls.json")));
+		argumentParser.parseArgument(args);
+
+		final String hdfsuri = argumentParser.get("namenode");
+		log.info("hdfsURI: {}", hdfsuri);
+
+		final String inputPath = argumentParser.get("lastVisitsPath");
+		log.info("inputPath: {}", inputPath);
+
+		final String outputPath = argumentParser.get("archiveRequestsPath");
+		log.info("outputPath: {}", outputPath);
+
+		final Integer archiveThresholdInDays = Integer.parseInt(argumentParser.get("archiveThresholdInDays"));
+		log.info("archiveThresholdInDays: {}", archiveThresholdInDays);
+
+		final String apiAccessToken = argumentParser.get("apiAccessToken");
+		log.info("apiAccessToken: {}", apiAccessToken);
+
+		final HttpClientParams clientParams = SWHUtils.getClientParams(argumentParser);
+
+		swhConnection = new SWHConnection(clientParams, apiAccessToken);
+
+		final FileSystem fs = FileSystem.get(getHadoopConfiguration(hdfsuri));
+
+		archive(fs, inputPath, outputPath, archiveThresholdInDays);
+
+	}
+
+	private static void archive(FileSystem fs, String inputPath, String outputPath, Integer archiveThresholdInDays)
+		throws IOException {
+
+		SequenceFile.Reader fr = SWHUtils.getSequenceFileReader(fs, inputPath);
+		SequenceFile.Writer fw = SWHUtils.getSequenceFileWriter(fs, outputPath);
+
+		// Create key and value objects to hold data
+		Text repoUrl = new Text();
+		Text lastVisitData = new Text();
+
+		// Read key-value pairs from the SequenceFile and handle appropriately
+		while (fr.next(repoUrl, lastVisitData)) {
+
+			String response = null;
+			try {
+				response = handleRecord(repoUrl.toString(), lastVisitData.toString(), archiveThresholdInDays);
+			} catch (java.text.ParseException e) {
+				log.error("Could not handle record with repo Url: {}", repoUrl.toString());
+				throw new RuntimeException(e);
+			}
+
+			// response is equal to null when no need for request
+			if (response != null) {
+				SWHUtils.appendToSequenceFile(fw, repoUrl.toString(), response);
+			}
+
+		}
+
+		// Close readers
+		fw.close();
+		fr.close();
+	}
+
+	public static String handleRecord(String repoUrl, String lastVisitData, Integer archiveThresholdInDays)
+		throws IOException, java.text.ParseException {
+
+		log.info("{ Key: {}, Value: {} }", repoUrl, lastVisitData);
+
+		LastVisitData lastVisit = OBJECT_MAPPER.readValue(lastVisitData, LastVisitData.class);
+
+		// a previous attempt for archival has been made, and repository URL was not found
+		// avoid performing the same archive request again
+		if (lastVisit.getStatus() != null &&
+			lastVisit.getStatus().equals(SWHConstants.VISIT_STATUS_NOT_FOUND)) {
+
+			log.info("Avoid request -- previous archive request returned NOT_FOUND");
+			return null;
+		}
+
+		// if we have last visit data
+		if (lastVisit.getSnapshot() != null) {
+
+			String cleanDate = GraphCleaningFunctions.cleanDate(lastVisit.getDate());
+
+			// and the last visit date can be parsed
+			if (cleanDate != null) {
+
+				SimpleDateFormat formatter = new SimpleDateFormat(ModelSupport.DATE_FORMAT);
+				Date lastVisitDate = formatter.parse(cleanDate);
+
+				// OR last visit time < (now() - archiveThresholdInDays)
+				long diffInMillies = Math.abs((new Date()).getTime() - lastVisitDate.getTime());
+				long diffInDays = TimeUnit.DAYS.convert(diffInMillies, TimeUnit.MILLISECONDS);
+				log.info("Date diff from now (in days): {}", diffInDays);
+
+				// do not perform a request, if the last visit date is no older than $archiveThresholdInDays
+				if (archiveThresholdInDays >= diffInDays) {
+					log.info("Avoid request -- no older than {} days", archiveThresholdInDays);
+					return null;
+				}
+			}
+		}
+
+		// ELSE perform an archive request
+		log.info("Perform archive request for: {}", repoUrl);
+
+		// if last visit data are available, re-use version control type,
+		// else use the default one (i.e., git)
+		String visitType = Optional
+			.ofNullable(lastVisit.getType())
+			.orElse(SWHConstants.DEFAULT_VISIT_TYPE);
+
+		URL url = new URL(String.format(SWHConstants.SWH_ARCHIVE_URL, visitType, repoUrl.trim()));
+
+		log.info("Sending archive request: {}", url);
+
+		String response;
+		try {
+			response = swhConnection.call(url.toString());
+		} catch (CollectorException e) {
+			log.error("Error in request: {}", url);
+			response = "{}";
+		}
+
+		return response;
+	}
+
+}

dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/CollectLastVisitRepositoryData.java

@@ -0,0 +1,119 @@
+
+package eu.dnetlib.dhp.swh;
+
+import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.net.URL;
+
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.fs.FileStatus;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.SequenceFile;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
+import eu.dnetlib.dhp.swh.utils.SWHConnection;
+import eu.dnetlib.dhp.swh.utils.SWHConstants;
+import eu.dnetlib.dhp.swh.utils.SWHUtils;
+
+/**
+ * Given a file with software repository URLs, this class
+ * collects last visit data from the Software Heritage API.
+ *
+ * @author Serafeim Chatzopoulos
+ */
+public class CollectLastVisitRepositoryData {
+
+	private static final Logger log = LoggerFactory.getLogger(CollectLastVisitRepositoryData.class);
+	private static SWHConnection swhConnection = null;
+
+	public static void main(final String[] args)
+		throws IOException, ParseException {
+		final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					CollectLastVisitRepositoryData.class
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/swh/input_collect_last_visit_repository_data.json")));
+		argumentParser.parseArgument(args);
+
+		log.info("Java Xmx: {}m", Runtime.getRuntime().maxMemory() / (1024 * 1024));
+
+		final String hdfsuri = argumentParser.get("namenode");
+		log.info("hdfsURI: {}", hdfsuri);
+
+		final String inputPath = argumentParser.get("softwareCodeRepositoryURLs");
+		log.info("inputPath: {}", inputPath);
+
+		final String outputPath = argumentParser.get("lastVisitsPath");
+		log.info("outputPath: {}", outputPath);
+
+		final String apiAccessToken = argumentParser.get("apiAccessToken");
+		log.info("apiAccessToken: {}", apiAccessToken);
+
+		final HttpClientParams clientParams = SWHUtils.getClientParams(argumentParser);
+
+		swhConnection = new SWHConnection(clientParams, apiAccessToken);
+
+		final FileSystem fs = FileSystem.get(getHadoopConfiguration(hdfsuri));
+
+		collect(fs, inputPath, outputPath);
+
+		fs.close();
+	}
+
+	private static void collect(FileSystem fs, String inputPath, String outputPath)
+		throws IOException {
+
+		SequenceFile.Writer fw = SWHUtils.getSequenceFileWriter(fs, outputPath);
+
+		// Specify the HDFS directory path you want to read
+		Path directoryPath = new Path(inputPath);
+
+		// List all files in the directory
+		FileStatus[] partStatuses = fs.listStatus(directoryPath);
+
+		for (FileStatus partStatus : partStatuses) {
+
+			// Check if it's a file (not a directory)
+			if (partStatus.isFile()) {
+				handleFile(fs, partStatus.getPath(), fw);
+			}
+
+		}
+
+		fw.close();
+	}
+
+	private static void handleFile(FileSystem fs, Path partInputPath, SequenceFile.Writer fw)
+		throws IOException {
+
+		BufferedReader br = SWHUtils.getFileReader(fs, partInputPath);
+
+		String repoUrl;
+		while ((repoUrl = br.readLine()) != null) {
+
+			URL url = new URL(String.format(SWHConstants.SWH_LATEST_VISIT_URL, repoUrl.trim()));
+
+			String response;
+			try {
+				response = swhConnection.call(url.toString());
+			} catch (CollectorException e) {
+				log.error("Error in request: {}", url);
+				response = "{}";
+			}
+
+			SWHUtils.appendToSequenceFile(fw, repoUrl, response);
+		}
+
+		br.close();
+	}
+
+}

dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/CollectSoftwareRepositoryURLs.java

@@ -0,0 +1,93 @@
+
+package eu.dnetlib.dhp.swh;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+
+import java.util.Optional;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+/**
+ *  Collects unique software repository URLs in the Graph using Hive
+ *
+ * @author Serafeim Chatzopoulos
+ */
+public class CollectSoftwareRepositoryURLs {
+
+	private static final Logger log = LoggerFactory.getLogger(CollectSoftwareRepositoryURLs.class);
+
+	public static <I extends Result> void main(String[] args) throws Exception {
+
+		String jsonConfiguration = IOUtils
+			.toString(
+				CollectSoftwareRepositoryURLs.class
+					.getResourceAsStream("/eu/dnetlib/dhp/swh/input_collect_software_repository_urls.json"));
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+		parser.parseArgument(args);
+
+		final Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String hiveDbName = parser.get("hiveDbName");
+		log.info("hiveDbName: {}", hiveDbName);
+
+		final String outputPath = parser.get("softwareCodeRepositoryURLs");
+		log.info("softwareCodeRepositoryURLs: {}", outputPath);
+
+		final String hiveMetastoreUris = parser.get("hiveMetastoreUris");
+		log.info("hiveMetastoreUris: {}", hiveMetastoreUris);
+
+		final Integer softwareLimit = Integer.parseInt(parser.get("softwareLimit"));
+		log.info("softwareLimit: {}", softwareLimit);
+
+		SparkConf conf = new SparkConf();
+		conf.set("hive.metastore.uris", hiveMetastoreUris);
+
+		runWithSparkHiveSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				doRun(spark, hiveDbName, softwareLimit, outputPath);
+			});
+	}
+
+	private static <I extends Result> void doRun(SparkSession spark, String hiveDbName, Integer limit,
+		String outputPath) {
+
+		String queryTemplate = "SELECT distinct coderepositoryurl.value " +
+			"FROM %s.software " +
+			"WHERE coderepositoryurl.value IS NOT NULL " +
+			"AND datainfo.deletedbyinference = FALSE " +
+			"AND datainfo.invisible = FALSE ";
+
+		if (limit != null) {
+			queryTemplate += String.format("LIMIT %s", limit);
+		}
+
+		String query = String.format(queryTemplate, hiveDbName);
+
+		log.info("Hive query to fetch software code URLs: {}", query);
+
+		Dataset<Row> df = spark.sql(query);
+
+		// write distinct repository URLs
+		df
+			.write()
+			.mode(SaveMode.Overwrite)
+			.csv(outputPath);
+	}
+}

dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/PrepareSWHActionsets.java

@@ -0,0 +1,185 @@
+
+package eu.dnetlib.dhp.swh;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static org.apache.spark.sql.functions.col;
+
+import java.io.Serializable;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Optional;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.GzipCodec;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+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.MapFunction;
+import org.apache.spark.sql.*;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.types.DataTypes;
+import org.apache.spark.sql.types.StructField;
+import org.apache.spark.sql.types.StructType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+import eu.dnetlib.dhp.swh.models.LastVisitData;
+import eu.dnetlib.dhp.swh.utils.SWHConstants;
+import scala.Tuple2;
+
+/**
+ * Creates action sets for Software Heritage data
+ *
+ * @author Serafeim Chatzopoulos
+ */
+public class PrepareSWHActionsets {
+
+	private static final Logger log = LoggerFactory.getLogger(PrepareSWHActionsets.class);
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static <I extends Result> void main(String[] args) throws Exception {
+
+		String jsonConfiguration = IOUtils
+			.toString(
+				PrepareSWHActionsets.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/swh/input_prepare_swh_actionsets.json"));
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+		parser.parseArgument(args);
+
+		final Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String inputPath = parser.get("lastVisitsPath");
+		log.info("inputPath: {}", inputPath);
+
+		final String softwareInputPath = parser.get("softwareInputPath");
+		log.info("softwareInputPath: {}", softwareInputPath);
+
+		final String outputPath = parser.get("actionsetsPath");
+		log.info("outputPath: {}", outputPath);
+
+		SparkConf conf = new SparkConf();
+
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				JavaPairRDD<Text, Text> softwareRDD = prepareActionsets(spark, inputPath, softwareInputPath);
+				softwareRDD
+					.saveAsHadoopFile(
+						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+			});
+	}
+
+	private static Dataset<Row> loadSWHData(SparkSession spark, String inputPath) {
+
+		JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		// read from file and transform to <origin, snapshotId> tuples
+		// Note: snapshot id is the SWH id for us
+		JavaRDD<Row> swhRDD = sc
+			.sequenceFile(inputPath, Text.class, Text.class)
+			.map(t -> t._2().toString())
+			.map(t -> OBJECT_MAPPER.readValue(t, LastVisitData.class))
+			.filter(t -> t.getOrigin() != null && t.getSnapshot() != null) // response from SWH API is empty if repo URL
+																			// was not found
+			.map(item -> RowFactory.create(item.getOrigin(), item.getSnapshot()));
+
+		// convert RDD to 2-column DF
+		List<StructField> fields = Arrays
+			.asList(
+				DataTypes.createStructField("repoUrl", DataTypes.StringType, true),
+				DataTypes.createStructField("swhId", DataTypes.StringType, true));
+		StructType schema = DataTypes.createStructType(fields);
+
+		return spark.createDataFrame(swhRDD, schema);
+	}
+
+	private static Dataset<Row> loadGraphSoftwareData(SparkSession spark, String softwareInputPath) {
+		return spark
+			.read()
+			.textFile(softwareInputPath)
+			.map(
+				(MapFunction<String, Software>) t -> OBJECT_MAPPER.readValue(t, Software.class),
+				Encoders.bean(Software.class))
+			.filter(t -> t.getCodeRepositoryUrl() != null)
+			.select(col("id"), col("codeRepositoryUrl.value").as("repoUrl"));
+	}
+
+	private static <I extends Software> JavaPairRDD<Text, Text> prepareActionsets(SparkSession spark, String inputPath,
+		String softwareInputPath) {
+
+		Dataset<Row> swhDF = loadSWHData(spark, inputPath);
+//		swhDF.show(false);
+
+		Dataset<Row> graphSoftwareDF = loadGraphSoftwareData(spark, softwareInputPath);
+//		graphSoftwareDF.show(5);
+
+		Dataset<Row> joinedDF = graphSoftwareDF.join(swhDF, "repoUrl").select("id", "swhid");
+//		joinedDF.show(false);
+
+		return joinedDF.map((MapFunction<Row, Software>) row -> {
+
+			Software s = new Software();
+
+			// set openaire id
+			s.setId(row.getString(row.fieldIndex("id")));
+
+			// set swh id
+			Qualifier qualifier = OafMapperUtils
+				.qualifier(
+					SWHConstants.SWHID,
+					SWHConstants.SWHID_CLASSNAME,
+					ModelConstants.DNET_PID_TYPES,
+					ModelConstants.DNET_PID_TYPES);
+
+			DataInfo dataInfo = OafMapperUtils
+				.dataInfo(
+					false,
+					null,
+					false,
+					false,
+					ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER,
+					"");
+
+			s
+				.setPid(
+					Arrays
+						.asList(
+							OafMapperUtils
+								.structuredProperty(
+									String.format("swh:1:snp:%s", row.getString(row.fieldIndex("swhid"))),
+									qualifier,
+									dataInfo)));
+
+			// add SWH in the `collectedFrom` field
+			KeyValue kv = new KeyValue();
+			kv.setKey(SWHConstants.SWH_ID);
+			kv.setValue(SWHConstants.SWH_NAME);
+
+			s.setCollectedfrom(Arrays.asList(kv));
+
+			return s;
+		}, Encoders.bean(Software.class))
+			.toJavaRDD()
+			.map(p -> new AtomicAction(Software.class, p))
+			.mapToPair(
+				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
+	}
+}

dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/models/LastVisitData.java

@@ -0,0 +1,71 @@
+
+package eu.dnetlib.dhp.swh.models;
+
+import java.io.Serializable;
+
+import com.cloudera.com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+
+@JsonIgnoreProperties(ignoreUnknown = true)
+public class LastVisitData implements Serializable {
+
+	private String origin;
+	private String type;
+	private String date;
+
+	@JsonProperty("snapshot")
+	private String snapshotId;
+
+	private String status;
+
+	public String getType() {
+		return type;
+	}
+
+	public void setType(String type) {
+		this.type = type;
+	}
+
+	public String getDate() {
+		return date;
+	}
+
+	public void setDate(String date) {
+		this.date = date;
+	}
+
+	public String getSnapshot() {
+		return snapshotId;
+	}
+
+	public void setSnapshot(String snapshotId) {
+		this.snapshotId = snapshotId;
+	}
+
+	public String getStatus() {
+		return status;
+	}
+
+	public void setStatus(String status) {
+		this.status = status;
+	}
+
+	public String getOrigin() {
+		return origin;
+	}
+
+	public void setOrigin(String origin) {
+		this.origin = origin;
+	}
+
+	@Override
+	public String toString() {
+		return "LastVisitData{" +
+			"origin='" + origin + '\'' +
+			", type='" + type + '\'' +
+			", date='" + date + '\'' +
+			", snapshotId='" + snapshotId + '\'' +
+			", status='" + status + '\'' +
+			'}';
+	}
+}

dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/utils/SWHConnection.java

@@ -0,0 +1,40 @@
+
+package eu.dnetlib.dhp.swh.utils;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.http.HttpHeaders;
+
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
+import eu.dnetlib.dhp.common.collection.HttpConnector2;
+
+public class SWHConnection {
+
+	HttpConnector2 conn;
+
+	public SWHConnection(HttpClientParams clientParams, String accessToken) {
+
+		// set custom headers
+		Map<String, String> headers = new HashMap<String, String>() {
+			{
+				put(HttpHeaders.ACCEPT, "application/json");
+				if (accessToken != null) {
+					put(HttpHeaders.AUTHORIZATION, String.format("Bearer %s", accessToken));
+				}
+			}
+		};
+
+		clientParams.setHeaders(headers);
+
+		// create http connector
+		conn = new HttpConnector2(clientParams);
+
+	}
+
+	public String call(String url) throws CollectorException {
+		return conn.getInputSource(url);
+	}
+
+}

dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/utils/SWHConstants.java

@@ -0,0 +1,21 @@
+
+package eu.dnetlib.dhp.swh.utils;
+
+public class SWHConstants {
+	public static final String SWH_LATEST_VISIT_URL = "https://archive.softwareheritage.org/api/1/origin/%s/visit/latest/";
+
+	public static final String SWH_ARCHIVE_URL = "https://archive.softwareheritage.org/api/1/origin/save/%s/url/%s/";
+
+	public static final String DEFAULT_VISIT_TYPE = "git";
+
+	public static final String VISIT_STATUS_NOT_FOUND = "not_found";
+
+	public static final String SWHID = "swhid";
+
+	public static final String SWHID_CLASSNAME = "Software Hash Identifier";
+
+	public static final String SWH_ID = "10|openaire____::dbfd07503aaa1ed31beed7dec942f3f4";
+
+	public static final String SWH_NAME = "Software Heritage";
+
+}

dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/utils/SWHUtils.java

@@ -0,0 +1,95 @@
+
+package eu.dnetlib.dhp.swh.utils;
+
+import static eu.dnetlib.dhp.common.Constants.*;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
+import java.util.Optional;
+
+import org.apache.hadoop.fs.FSDataInputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.SequenceFile;
+import org.apache.hadoop.io.Text;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
+
+public class SWHUtils {
+
+	private static final Logger log = LoggerFactory.getLogger(SWHUtils.class);
+
+	public static HttpClientParams getClientParams(ArgumentApplicationParser argumentParser) {
+
+		final HttpClientParams clientParams = new HttpClientParams();
+		clientParams
+			.setMaxNumberOfRetry(
+				Optional
+					.ofNullable(argumentParser.get(MAX_NUMBER_OF_RETRY))
+					.map(Integer::parseInt)
+					.orElse(HttpClientParams._maxNumberOfRetry));
+		log.info("maxNumberOfRetry is {}", clientParams.getMaxNumberOfRetry());
+
+		clientParams
+			.setRequestDelay(
+				Optional
+					.ofNullable(argumentParser.get(REQUEST_DELAY))
+					.map(Integer::parseInt)
+					.orElse(HttpClientParams._requestDelay));
+		log.info("requestDelay is {}", clientParams.getRequestDelay());
+
+		clientParams
+			.setRetryDelay(
+				Optional
+					.ofNullable(argumentParser.get(RETRY_DELAY))
+					.map(Integer::parseInt)
+					.orElse(HttpClientParams._retryDelay));
+		log.info("retryDelay is {}", clientParams.getRetryDelay());
+
+		clientParams
+			.setRequestMethod(
+				Optional
+					.ofNullable(argumentParser.get(REQUEST_METHOD))
+					.orElse(HttpClientParams._requestMethod));
+		log.info("requestMethod is {}", clientParams.getRequestMethod());
+
+		return clientParams;
+	}
+
+	public static BufferedReader getFileReader(FileSystem fs, Path inputPath) throws IOException {
+		FSDataInputStream inputStream = fs.open(inputPath);
+		return new BufferedReader(
+			new InputStreamReader(inputStream, StandardCharsets.UTF_8));
+	}
+
+	public static SequenceFile.Writer getSequenceFileWriter(FileSystem fs, String outputPath) throws IOException {
+		return SequenceFile
+			.createWriter(
+				fs.getConf(),
+				SequenceFile.Writer.file(new Path(outputPath)),
+				SequenceFile.Writer.keyClass(Text.class),
+				SequenceFile.Writer.valueClass(Text.class));
+	}
+
+	public static SequenceFile.Reader getSequenceFileReader(FileSystem fs, String inputPath) throws IOException {
+		Path filePath = new Path(inputPath);
+		SequenceFile.Reader.Option fileOption = SequenceFile.Reader.file(filePath);
+
+		return new SequenceFile.Reader(fs.getConf(), fileOption);
+	}
+
+	public static void appendToSequenceFile(SequenceFile.Writer fw, String keyStr, String valueStr) throws IOException {
+		Text key = new Text();
+		key.set(keyStr);
+
+		Text value = new Text();
+		value.set(valueStr);
+
+		fw.append(key, value);
+	}
+}

dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/input_archive_repository_urls.json

@@ -0,0 +1,56 @@
+[
+  {
+    "paramName": "n",
+    "paramLongName": "namenode",
+    "paramDescription": "the Name Node URI",
+    "paramRequired": true
+  },
+  {
+    "paramName": "lv",
+    "paramLongName": "lastVisitsPath",
+    "paramDescription": "the URL where to store last visits data",
+    "paramRequired": true
+  },
+  {
+    "paramName": "arp",
+    "paramLongName": "archiveRequestsPath",
+    "paramDescription": "the URL where to store the responses of the archive requests",
+    "paramRequired": true
+  },
+  {
+    "paramName": "mnr",
+    "paramLongName": "maxNumberOfRetry",
+    "paramDescription": "the maximum number of admitted connection retries",
+    "paramRequired": false
+  },
+  {
+    "paramName": "rqd",
+    "paramLongName": "requestDelay",
+    "paramDescription": "the delay (ms) between requests",
+    "paramRequired": false
+  },
+  {
+    "paramName": "rtd",
+    "paramLongName": "retryDelay",
+    "paramDescription": "the delay (ms) between retries",
+    "paramRequired": false
+  },
+  {
+    "paramName": "rm",
+    "paramLongName": "requestMethod",
+    "paramDescription": "the method of the requests to perform",
+    "paramRequired": false
+  },
+  {
+    "paramName": "atid",
+    "paramLongName": "archiveThresholdInDays",
+    "paramDescription": "the thershold (in days) required to issue an archive request",
+    "paramRequired": false
+  },
+  {
+    "paramName": "aat",
+    "paramLongName": "apiAccessToken",
+    "paramDescription": "the API access token of the SWH API",
+    "paramRequired": false
+  }
+]

dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/input_collect_last_visit_repository_data.json

@@ -0,0 +1,50 @@
+[
+  {
+    "paramName": "n",
+    "paramLongName": "namenode",
+    "paramDescription": "the Name Node URI",
+    "paramRequired": true
+  },
+  {
+    "paramName": "scr",
+    "paramLongName": "softwareCodeRepositoryURLs",
+    "paramDescription": "the URL from where to read software repository URLs",
+    "paramRequired": true
+  },
+  {
+    "paramName": "lv",
+    "paramLongName": "lastVisitsPath",
+    "paramDescription": "the URL where to store last visits data",
+    "paramRequired": true
+  },
+  {
+    "paramName": "mnr",
+    "paramLongName": "maxNumberOfRetry",
+    "paramDescription": "the maximum number of admitted connection retries",
+    "paramRequired": false
+  },
+  {
+    "paramName": "rqd",
+    "paramLongName": "requestDelay",
+    "paramDescription": "the delay (ms) between requests",
+    "paramRequired": false
+  },
+  {
+    "paramName": "rtd",
+    "paramLongName": "retryDelay",
+    "paramDescription": "the delay (ms) between retries",
+    "paramRequired": false
+  },
+  {
+    "paramName": "rm",
+    "paramLongName": "requestMethod",
+    "paramDescription": "the method of the requests to perform",
+    "paramRequired": false
+  },
+  {
+    "paramName": "aat",
+    "paramLongName": "apiAccessToken",
+    "paramDescription": "the API access token of the SWH API",
+    "paramRequired": false
+  }
+]

dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/input_collect_software_repository_urls.json

@@ -0,0 +1,32 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "scr",
+    "paramLongName": "softwareCodeRepositoryURLs",
+    "paramDescription": "the URL where to store software repository URLs",
+    "paramRequired": true
+  },
+  {
+    "paramName": "db",
+    "paramLongName": "hiveDbName",
+    "paramDescription": "the target hive database name",
+    "paramRequired": true
+  },
+  {
+    "paramName": "hmu",
+    "paramLongName": "hiveMetastoreUris",
+    "paramDescription": "the hive metastore uris",
+    "paramRequired": true
+  },
+  {
+    "paramName": "slim",
+    "paramLongName": "softwareLimit",
+    "paramDescription": "limit on the number of software repo URL to fetch",
+    "paramRequired": false
+  }
+]

dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/input_prepare_swh_actionsets.json

@@ -0,0 +1,26 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "lv",
+    "paramLongName": "lastVisitsPath",
+    "paramDescription": "the URL where to store last visits data",
+    "paramRequired": true
+  },
+  {
+    "paramName": "ap",
+    "paramLongName": "actionsetsPath",
+    "paramDescription": "the URL path where to store actionsets",
+    "paramRequired": true
+  },
+  {
+    "paramName": "sip",
+    "paramLongName": "softwareInputPath",
+    "paramDescription": "the URL path of the software in the graph",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/job.properties

@@ -0,0 +1,19 @@
+# hive
+hiveDbName=openaire_prod_20230914
+
+# input/output files
+softwareCodeRepositoryURLs=${workingDir}/1_code_repo_urls.csv
+lastVisitsPath=${workingDir}/2_last_visits.seq
+archiveRequestsPath=${workingDir}/3_archive_requests.seq
+actionsetsPath=${workingDir}/4_actionsets
+graphPath=/tmp/prod_provision/graph/18_graph_blacklisted
+
+apiAccessToken=eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJhMTMxYTQ1My1hM2IyLTQwMTUtODQ2Ny05MzAyZjk3MTFkOGEifQ.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.XHj1VIZu1dZ4Ej32-oU84mFmaox9cLNjXosNxwZM0Xs
+
+maxNumberOfRetry=2
+retryDelay=1
+requestDelay=100
+
+softwareLimit=500
+
+resume=collect-software-repository-urls

dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/oozie_app/config-default.xml

@@ -0,0 +1,54 @@
+<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>
+    <property>
+        <name>hiveMetastoreUris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>spark2YarnHistoryServerAddress</name>
+        <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
+    </property>
+    <property>
+        <name>spark2EventLogDir</name>
+        <value>/user/spark/spark2ApplicationHistory</value>
+    </property>
+    <property>
+        <name>spark2ExtraListeners</name>
+        <value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
+    </property>
+    <property>
+        <name>spark2SqlQueryExecutionListeners</name>
+        <value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
+    </property>
+    <property>
+        <name>oozieActionShareLibForSpark2</name>
+        <value>spark2</value>
+    </property>
+    <property>
+        <name>resourceManager</name>
+        <value>http://iis-cdh5-test-m2.ocean.icm.edu.pl:8088/cluster</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>sparkSqlWarehouseDir</name>
+        <value>/user/hive/warehouse</value>
+    </property>
+</configuration>

dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/oozie_app/workflow.xml

@@ -0,0 +1,183 @@
+<workflow-app name="Software-Heritage-Integration-Workflow" xmlns="uri:oozie:workflow:0.5">
+
+    <!-- Custom parameters   -->
+    <parameters>
+        <property>
+            <name>hiveDbName</name>
+            <description>The name of the Hive DB to be used</description>
+        </property>
+        <property>
+            <name>softwareCodeRepositoryURLs</name>
+            <description>The path in the HDFS to save the software repository URLs</description>
+        </property>
+        <property>
+            <name>lastVisitsPath</name>
+            <description>The path in the HDFS to save the responses of the last visit requests</description>
+        </property>
+        <property>
+            <name>archiveRequestsPath</name>
+            <description>The path in the HDFS to save the responses of the archive requests</description>
+        </property>
+        <property>
+            <name>actionsetsPath</name>
+            <description>The path in the HDFS to save the action sets</description>
+        </property>
+        <property>
+            <name>graphPath</name>
+            <description>The path in the HDFS to the base folder of the graph</description>
+        </property>
+        <property>
+            <name>maxNumberOfRetry</name>
+            <description>Max number of retries for failed API calls</description>
+        </property>
+        <property>
+            <name>retryDelay</name>
+            <description>Retry delay for failed requests (in sec)</description>
+        </property>
+        <property>
+            <name>requestDelay</name>
+            <description>Delay between API requests (in ms)</description>
+        </property>
+        <property>
+            <name>apiAccessToken</name>
+            <description>The API Key of the SWH API</description>
+        </property>
+        <property>
+            <name>softwareLimit</name>
+            <description>Limit on the number of repo URLs to use (Optional); for debug purposes</description>
+        </property>
+        <property>
+            <name>resumeFrom</name>
+            <description>Variable that indicates the step to start from</description>
+        </property>
+    </parameters>
+
+    <!-- Global variables  -->
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+            <property>
+                <name>actionsetsPath</name>
+                <value>${actionsetsPath}</value>
+            </property>
+            <property>
+                <name>apiAccessToken</name>
+                <value>${apiAccessToken}</value>
+            </property>
+        </configuration>
+    </global>
+
+    <start to="startFrom"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <decision name="startFrom">
+        <switch>
+            <case to="collect-software-repository-urls">${wf:conf('resumeFrom') eq 'collect-software-repository-urls'}</case>
+            <case to="create-swh-actionsets">${wf:conf('resumeFrom') eq 'create-swh-actionsets'}</case>
+            <default to="collect-software-repository-urls"/>
+        </switch>
+    </decision>
+
+    <action name="collect-software-repository-urls">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Collect software repository URLs</name>
+            <class>eu.dnetlib.dhp.swh.CollectSoftwareRepositoryURLs</class>
+            <jar>dhp-swh-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --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}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+
+            <arg>--softwareCodeRepositoryURLs</arg><arg>${softwareCodeRepositoryURLs}</arg>
+            <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
+            <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
+            <arg>--softwareLimit</arg><arg>${softwareLimit}</arg>
+        </spark>
+        <ok to="collect-repository-last-visit-data"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="collect-repository-last-visit-data">
+        <java>
+            <main-class>eu.dnetlib.dhp.swh.CollectLastVisitRepositoryData</main-class>
+
+            <arg>--namenode</arg><arg>${nameNode}</arg>
+            <arg>--softwareCodeRepositoryURLs</arg><arg>${softwareCodeRepositoryURLs}</arg>
+            <arg>--lastVisitsPath</arg><arg>${lastVisitsPath}</arg>
+
+            <arg>--maxNumberOfRetry</arg><arg>${maxNumberOfRetry}</arg>
+            <arg>--requestDelay</arg><arg>${requestDelay}</arg>
+            <arg>--retryDelay</arg><arg>${retryDelay}</arg>
+            <arg>--requestMethod</arg><arg>GET</arg>
+            <arg>--apiAccessToken</arg><arg>${apiAccessToken}</arg>
+
+        </java>
+        <ok to="archive-repository-urls"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="archive-repository-urls">
+        <java>
+            <main-class>eu.dnetlib.dhp.swh.ArchiveRepositoryURLs</main-class>
+
+            <arg>--namenode</arg><arg>${nameNode}</arg>
+            <arg>--lastVisitsPath</arg><arg>${lastVisitsPath}</arg>
+            <arg>--archiveRequestsPath</arg><arg>${archiveRequestsPath}</arg>
+            <arg>--archiveThresholdInDays</arg><arg>365</arg>
+
+            <arg>--maxNumberOfRetry</arg><arg>${maxNumberOfRetry}</arg>
+            <arg>--requestDelay</arg><arg>${requestDelay}</arg>
+            <arg>--retryDelay</arg><arg>${retryDelay}</arg>
+            <arg>--requestMethod</arg><arg>POST</arg>
+            <arg>--apiAccessToken</arg><arg>${apiAccessToken}</arg>
+
+        </java>
+        <ok to="create-swh-actionsets"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="create-swh-actionsets">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Create actionsets for SWH data</name>
+            <class>eu.dnetlib.dhp.swh.PrepareSWHActionsets</class>
+            <jar>dhp-swh-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --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}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+
+            <arg>--lastVisitsPath</arg><arg>${lastVisitsPath}</arg>
+            <arg>--actionsetsPath</arg><arg>${actionsetsPath}</arg>
+            <arg>--softwareInputPath</arg><arg>${graphPath}/software</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+
+</workflow-app>

dhp-workflows/dhp-swh/src/test/java/eu/dnetlib/dhp/swh/ArchiveRepositoryURLsTest.java

@@ -0,0 +1,38 @@
+
+package eu.dnetlib.dhp.swh;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.text.ParseException;
+import java.util.Arrays;
+
+import org.apache.hadoop.fs.FileSystem;
+import org.junit.jupiter.api.Test;
+
+import eu.dnetlib.dhp.swh.utils.SWHUtils;
+
+public class ArchiveRepositoryURLsTest {
+
+	@Test
+	void testArchive() throws IOException, ParseException {
+		String inputPath = getClass()
+			.getResource("/eu/dnetlib/dhp/swh/lastVisitDataToArchive.csv")
+			.getPath();
+
+		File file = new File(inputPath);
+		FileReader fr = new FileReader(file);
+		BufferedReader br = new BufferedReader(fr); // creates a buffering character input stream
+
+		String line;
+		while ((line = br.readLine()) != null) {
+			String[] tokens = line.split("\t");
+
+			String response = ArchiveRepositoryURLs.handleRecord(tokens[0], tokens[1], 365);
+			System.out.println(tokens[0] + "\t" + response);
+			System.out.println();
+		}
+		fr.close();
+	}
+}

dhp-workflows/dhp-swh/src/test/java/eu/dnetlib/dhp/swh/PrepareSWHActionsetsTest.java

@@ -0,0 +1,97 @@
+
+package eu.dnetlib.dhp.swh;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+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.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+
+public class PrepareSWHActionsetsTest {
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+
+	private static final Logger log = LoggerFactory
+		.getLogger(PrepareSWHActionsetsTest.class);
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files.createTempDirectory(PrepareSWHActionsetsTest.class.getSimpleName());
+
+		log.info("Using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(PrepareSWHActionsetsTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(PrepareSWHActionsetsTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void testRun() throws Exception {
+
+		String lastVisitsPath = getClass()
+			.getResource("/eu/dnetlib/dhp/swh/last_visits_data.seq")
+			.getPath();
+
+		String outputPath = workingDir.toString() + "/actionSet";
+
+		String softwareInputPath = getClass()
+			.getResource("/eu/dnetlib/dhp/swh/software.json.gz")
+			.getPath();
+
+		PrepareSWHActionsets
+			.main(
+				new String[] {
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-lastVisitsPath", lastVisitsPath,
+					"-softwareInputPath", softwareInputPath,
+					"-actionsetsPath", outputPath
+				});
+
+	}
+}

dhp-workflows/dhp-swh/src/test/java/eu/dnetlib/dhp/swh/SWHConnectionTest.java

@@ -0,0 +1,58 @@
+
+package eu.dnetlib.dhp.swh;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
+import eu.dnetlib.dhp.swh.utils.SWHConnection;
+import eu.dnetlib.dhp.swh.utils.SWHConstants;
+
+//import org.apache.hadoop.hdfs.MiniDFSCluster;
+
+public class SWHConnectionTest {
+	private static final Logger log = LoggerFactory.getLogger(SWHConnectionTest.class);
+
+	@Test
+	void testGetCall() throws IOException {
+
+		HttpClientParams clientParams = new HttpClientParams();
+		clientParams.setRequestMethod("GET");
+
+		SWHConnection swhConnection = new SWHConnection(clientParams, null);
+
+		String repoUrl = "https://github.com/stanford-futuredata/FAST";
+		URL url = new URL(String.format(SWHConstants.SWH_LATEST_VISIT_URL, repoUrl));
+		String response = null;
+		try {
+			response = swhConnection.call(url.toString());
+		} catch (CollectorException e) {
+			System.out.println("Error in request: " + url);
+		}
+		System.out.println(response);
+	}
+
+	@Test
+	void testPostCall() throws MalformedURLException {
+		HttpClientParams clientParams = new HttpClientParams();
+		clientParams.setRequestMethod("POST");
+
+		SWHConnection swhConnection = new SWHConnection(clientParams, null);
+
+		String repoUrl = "https://github.com/stanford-futuredata/FAST";
+		URL url = new URL(String.format(SWHConstants.SWH_ARCHIVE_URL, SWHConstants.DEFAULT_VISIT_TYPE, repoUrl));
+		String response = null;
+		try {
+			response = swhConnection.call(url.toString());
+		} catch (CollectorException e) {
+			System.out.println("Error in request: " + url);
+		}
+		System.out.println(response);
+	}
+}

dhp-workflows/dhp-swh/src/test/resources/eu/dnetlib/dhp/swh/lastVisitDataToArchive.csv

@@ -0,0 +1,7 @@
+https://bitbucket.org/samskillman/yt-stokes	{"origin":"https://bitbucket.org/samskillman/yt-stokes","visit":43,"date":"2021-09-13T21:59:27.125171+00:00","status":"failed","snapshot":null,"type":"hg","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://bitbucket.org/samskillman/yt-stokes/get/","snapshot_url":null}
+https://github.com/bioinsilico/BIPSPI	{"origin":"https://github.com/bioinsilico/BIPSPI","visit":1,"date":"2020-03-18T14:50:21.541822+00:00","status":"full","snapshot":"c6c69d2cd73ce89811448da5f031611df6f63bdb","type":"git","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://github.com/bioinsilico/BIPSPI/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/c6c69d2cd73ce89811448da5f031611df6f63bdb/"}
+https://github.com/mloop/kdiff-type1-error-rate/blob/master/analysis/simulation.R	{}
+https://github.com/schwanbeck/YSMR	{"origin":"https://github.com/schwanbeck/YSMR","visit":6,"date":"2023-08-02T15:25:02.650676+00:00","status":"full","snapshot":"a9d1c5f0bca2def198b89f65bc9f7da3be8439ed","type":"git","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://github.com/schwanbeck/YSMR/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/a9d1c5f0bca2def198b89f65bc9f7da3be8439ed/"}
+https://github.com/lvclark/TASSELGBS_combine	{"origin":"https://github.com/lvclark/TASSELGBS_combine","visit":1,"date":"2020-04-12T20:44:09.405589+00:00","status":"full","snapshot":"ffa6fefd3f5becefbea9fe0e6d5d93859c95c071","type":"git","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://github.com/lvclark/TASSELGBS_combine/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/ffa6fefd3f5becefbea9fe0e6d5d93859c95c071/"}
+https://github.com/PRIDE-Toolsuite/inspector-example-files	{"origin":"https://github.com/PRIDE-Toolsuite/inspector-example-files","visit":12,"date":"2021-01-25T08:54:13.394674+00:00","status":"full","snapshot":"0b56eb0ad07cf778df6dabefc4b73636e0ae8b37","type":"git","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://github.com/PRIDE-Toolsuite/inspector-example-files/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/0b56eb0ad07cf778df6dabefc4b73636e0ae8b37/"}
+https://bitbucket.org/matwey/chelyabinsk	{"origin":"https://bitbucket.org/matwey/chelyabinsk","visit":6,"date":"2021-09-24T19:32:43.322909+00:00","status":"full","snapshot":"215913858c3ee0e61e1aaea18241c5ee006da1b0","type":"hg","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://bitbucket.org/matwey/chelyabinsk/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/215913858c3ee0e61e1aaea18241c5ee006da1b0/"}

dhp-workflows/pom.xml

@@ -38,6 +38,7 @@
         <module>dhp-broker-events</module>
         <module>dhp-doiboost</module>
         <module>dhp-impact-indicators</module>
+        <module>dhp-swh</module>
     </modules>
 
     <pluginRepositories>

pom.xml

@@ -112,6 +112,16 @@
 			<url>https://maven.d4science.org/nexus/content/repositories/dnet-deps</url>
 			<layout>default</layout>
 		</repository>
+		<repository>
+			<id>maven-restlet</id>
+			<name>Restlet repository</name>
+			<url>https://maven.restlet.talend.com</url>
+		</repository>
+		<repository>
+			<id>conjars</id>
+			<name>conjars</name>
+			<url>https://conjars.wensel.net/repo/</url>
+		</repository>
 	</repositories>
 
 	<dependencies>
@@ -878,7 +888,7 @@
 		<mockito-core.version>3.3.3</mockito-core.version>
 		<mongodb.driver.version>3.4.2</mongodb.driver.version>
 		<vtd.version>[2.12,3.0)</vtd.version>
-		<dhp-schemas.version>[3.17.1]</dhp-schemas.version>
+		<dhp-schemas.version>[3.17.2]</dhp-schemas.version>
 		<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
 		<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
 		<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>