dhp-common/src/main/java/eu/dnetlib/dhp/common/action/ReadDatasourceMasterDuplicateFromDB.java

@@ -0,0 +1,81 @@
+
+package eu.dnetlib.dhp.common.action;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.nio.charset.StandardCharsets;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FSDataOutputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.common.DbClient;
+import eu.dnetlib.dhp.common.action.model.MasterDuplicate;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+
+public class ReadDatasourceMasterDuplicateFromDB {
+
+	private static final Logger log = LoggerFactory.getLogger(ReadDatasourceMasterDuplicateFromDB.class);
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static final String QUERY = "SELECT distinct dd.id as masterId, d.officialname as masterName, dd.duplicate as duplicateId "
+		+
+		"FROM dsm_dedup_services dd join dsm_services d on (dd.id = d.id);";
+
+	public static int execute(String dbUrl, String dbUser, String dbPassword, String hdfsPath, String hdfsNameNode)
+		throws IOException {
+		int count = 0;
+		try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
+			Configuration conf = new Configuration();
+			conf.set("fs.defaultFS", hdfsNameNode);
+			FileSystem fileSystem = FileSystem.get(conf);
+			FSDataOutputStream fos = fileSystem.create(new Path(hdfsPath));
+
+			log.info("running query: {}", QUERY);
+			log.info("storing results in: {}", hdfsPath);
+
+			try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8))) {
+				dbClient.processResults(QUERY, rs -> writeMap(datasourceMasterMap(rs), writer));
+				count++;
+			}
+		}
+		return count;
+	}
+
+	private static MasterDuplicate datasourceMasterMap(ResultSet rs) {
+		try {
+			final MasterDuplicate md = new MasterDuplicate();
+
+			final String duplicateId = rs.getString("duplicateId");
+			final String masterId = rs.getString("masterId");
+			final String masterName = rs.getString("masterName");
+
+			md.setDuplicateId(OafMapperUtils.createOpenaireId(10, duplicateId, true));
+			md.setMasterId(OafMapperUtils.createOpenaireId(10, masterId, true));
+			md.setMasterName(masterName);
+
+			return md;
+		} catch (final SQLException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	private static void writeMap(final MasterDuplicate dm, final BufferedWriter writer) {
+		try {
+			writer.write(OBJECT_MAPPER.writeValueAsString(dm));
+			writer.newLine();
+		} catch (final IOException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/action/model/MasterDuplicate.java

@@ -0,0 +1,38 @@
+
+package eu.dnetlib.dhp.common.action.model;
+
+import java.io.Serializable;
+
+/**
+ * @author miriam.baglioni
+ * @Date 21/07/22
+ */
+public class MasterDuplicate implements Serializable {
+	private String duplicateId;
+	private String masterId;
+	private String masterName;
+
+	public String getDuplicateId() {
+		return duplicateId;
+	}
+
+	public void setDuplicateId(String duplicateId) {
+		this.duplicateId = duplicateId;
+	}
+
+	public String getMasterId() {
+		return masterId;
+	}
+
+	public void setMasterId(String masterId) {
+		this.masterId = masterId;
+	}
+
+	public String getMasterName() {
+		return masterName;
+	}
+
+	public void setMasterName(String masterName) {
+		this.masterName = masterName;
+	}
+}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java

@@ -47,8 +47,8 @@ public class CleanContextSparkJob implements Serializable {
 		String inputPath = parser.get("inputPath");
 		log.info("inputPath: {}", inputPath);
 
-		String workingPath = parser.get("workingPath");
-		log.info("workingPath: {}", workingPath);
+		String workingDir = parser.get("workingDir");
+		log.info("workingDir: {}", workingDir);
 
 		String contextId = parser.get("contextId");
 		log.info("contextId: {}", contextId);
@@ -67,12 +67,12 @@ public class CleanContextSparkJob implements Serializable {
 			isSparkSessionManaged,
 			spark -> {
 
-				cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath);
+				cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingDir);
 			});
 	}
 
 	private static <T extends Result> void cleanContext(SparkSession spark, String contextId, String verifyParam,
-		String inputPath, Class<T> entityClazz, String workingPath) {
+		String inputPath, Class<T> entityClazz, String workingDir) {
 		Dataset<T> res = spark
 			.read()
 			.textFile(inputPath)
@@ -106,11 +106,11 @@ public class CleanContextSparkJob implements Serializable {
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
-			.json(workingPath);
+			.json(workingDir);
 
 		spark
 			.read()
-			.textFile(workingPath)
+			.textFile(workingDir)
 			.map(
 				(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
 				Encoders.bean(entityClazz))

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/MasterDuplicateAction.java

@@ -0,0 +1,45 @@
+
+package eu.dnetlib.dhp.oa.graph.clean;
+
+import org.apache.commons.io.IOUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.action.ReadDatasourceMasterDuplicateFromDB;
+
+public class MasterDuplicateAction {
+
+	private static final Logger log = LoggerFactory.getLogger(MasterDuplicateAction.class);
+
+	public static void main(final String[] args) throws Exception {
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					MasterDuplicateAction.class
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/graph/datasourcemaster_parameters.json")));
+
+		parser.parseArgument(args);
+
+		final String dbUrl = parser.get("postgresUrl");
+		log.info("postgresUrl: {}", dbUrl);
+
+		final String dbUser = parser.get("postgresUser");
+		log.info("postgresUser: {}", dbUser);
+
+		final String dbPassword = parser.get("postgresPassword");
+		log.info("postgresPassword: {}", dbPassword);
+
+		final String hdfsPath = parser.get("hdfsPath");
+		log.info("hdfsPath: {}", hdfsPath);
+
+		final String hdfsNameNode = parser.get("hdfsNameNode");
+		log.info("hdfsNameNode: {}", hdfsNameNode);
+
+		int rows = ReadDatasourceMasterDuplicateFromDB.execute(dbUrl, dbUser, dbPassword, hdfsPath, hdfsNameNode);
+
+		log.info("written {} rows", rows);
+	}
+
+}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJob.java

@@ -0,0 +1,197 @@
+
+package eu.dnetlib.dhp.oa.graph.clean.cfhb;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.util.Iterator;
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.api.java.function.MapGroupsFunction;
+import org.apache.spark.sql.*;
+import org.apache.spark.sql.expressions.Aggregator;
+import org.jetbrains.annotations.NotNull;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.common.action.model.MasterDuplicate;
+import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob;
+import eu.dnetlib.dhp.schema.oaf.Instance;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.utils.DHPUtils;
+import scala.Tuple2;
+
+public class CleanCfHbSparkJob {
+
+	private static final Logger log = LoggerFactory.getLogger(CleanCfHbSparkJob.class);
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static void main(String[] args) throws Exception {
+
+		String jsonConfiguration = IOUtils
+			.toString(
+				CleanCountrySparkJob.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/oa/graph/input_clean_cfhb_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 resolvedPath = parser.get("resolvedPath");
+		log.info("resolvedPath: {}", resolvedPath);
+
+		String outputPath = parser.get("outputPath");
+		log.info("outputPath: {}", outputPath);
+
+		String dsMasterDuplicatePath = parser.get("datasourceMasterDuplicate");
+		log.info("datasourceMasterDuplicate: {}", dsMasterDuplicatePath);
+
+		String graphTableClassName = parser.get("graphTableClassName");
+		log.info("graphTableClassName: {}", graphTableClassName);
+
+		Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
+
+		SparkConf conf = new SparkConf();
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
+				HdfsSupport.remove(resolvedPath, spark.sparkContext().hadoopConfiguration());
+				cleanCfHb(
+					spark, inputPath, entityClazz, resolvedPath, dsMasterDuplicatePath, outputPath);
+			});
+	}
+
+	private static <T extends Result> void cleanCfHb(SparkSession spark, String inputPath, Class<T> entityClazz,
+		String resolvedPath, String masterDuplicatePath, String outputPath) {
+
+		// read the master-duplicate tuples
+		Dataset<MasterDuplicate> md = spark
+			.read()
+			.textFile(masterDuplicatePath)
+			.map(as(MasterDuplicate.class), Encoders.bean(MasterDuplicate.class));
+
+		// prepare the resolved CF|HB references with the corresponding EMPTY master ID
+		Dataset<IdCfHbMapping> resolved = spark
+			.read()
+			.textFile(inputPath)
+			.map(as(entityClazz), Encoders.bean(entityClazz))
+			.flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class));
+
+		// set the EMPTY master ID/NAME and save it
+		resolved
+			.joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId")))
+			.map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.json(resolvedPath);
+
+		// read again the resolved CF|HB mapping
+		Dataset<IdCfHbMapping> resolvedDS = spark
+			.read()
+			.textFile(resolvedPath)
+			.map(as(IdCfHbMapping.class), Encoders.bean(IdCfHbMapping.class));
+
+		// read the result table
+		Dataset<T> res = spark
+			.read()
+			.textFile(inputPath)
+			.map(as(entityClazz), Encoders.bean(entityClazz));
+
+		// Join the results with the resolved CF|HB mapping, apply the mapping and save it
+		res
+			.joinWith(resolvedDS, res.col("id").equalTo(resolvedDS.col("resultId")), "left")
+			.groupByKey((MapFunction<Tuple2<T, IdCfHbMapping>, String>) t -> t._1().getId(), Encoders.STRING())
+			.mapGroups(getMapGroupsFunction(), Encoders.bean(entityClazz))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
+			.json(outputPath);
+	}
+
+	private static MapFunction<Tuple2<IdCfHbMapping, MasterDuplicate>, IdCfHbMapping> asIdCfHbMapping() {
+		return t -> {
+			t._1().setMasterId(t._2().getMasterId());
+			t._1().setMasterName(t._2().getMasterName());
+			return t._1();
+		};
+	}
+
+	private static <T extends Result> FlatMapFunction<T, IdCfHbMapping> flattenCfHbFn() {
+		return r -> Stream
+			.concat(
+				r.getCollectedfrom().stream().map(KeyValue::getKey),
+				Stream
+					.concat(
+						r.getInstance().stream().map(Instance::getHostedby).map(KeyValue::getKey),
+						r.getInstance().stream().map(Instance::getCollectedfrom).map(KeyValue::getKey)))
+			.distinct()
+			.map(s -> asIdCfHbMapping(r.getId(), s))
+			.iterator();
+	}
+
+	private static <T extends Result> MapGroupsFunction<String, Tuple2<T, IdCfHbMapping>, T> getMapGroupsFunction() {
+		return new MapGroupsFunction<String, Tuple2<T, IdCfHbMapping>, T>() {
+			@Override
+			public T call(String key, Iterator<Tuple2<T, IdCfHbMapping>> values) {
+				final Tuple2<T, IdCfHbMapping> first = values.next();
+				final T res = first._1();
+
+				updateResult(res, first._2());
+				values.forEachRemaining(t -> updateResult(res, t._2()));
+				return res;
+			}
+
+			private void updateResult(T res, IdCfHbMapping m) {
+				if (Objects.nonNull(m)) {
+					res.getCollectedfrom().forEach(kv -> updateKeyValue(kv, m));
+					res.getInstance().forEach(i -> {
+						updateKeyValue(i.getHostedby(), m);
+						updateKeyValue(i.getCollectedfrom(), m);
+					});
+				}
+			}
+
+			private void updateKeyValue(final KeyValue kv, final IdCfHbMapping a) {
+				if (kv.getKey().equals(a.getCfhb())) {
+					kv.setKey(a.getMasterId());
+					kv.setValue(a.getMasterName());
+				}
+			}
+
+		};
+	}
+
+	private static IdCfHbMapping asIdCfHbMapping(String resultId, String cfHb) {
+		IdCfHbMapping m = new IdCfHbMapping(resultId);
+		m.setCfhb(cfHb);
+		return m;
+	}
+
+	private static <R> MapFunction<String, R> as(Class<R> clazz) {
+		return s -> OBJECT_MAPPER.readValue(s, clazz);
+	}
+}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/IdCfHbMapping.java

@@ -0,0 +1,54 @@
+
+package eu.dnetlib.dhp.oa.graph.clean.cfhb;
+
+import java.io.Serializable;
+
+public class IdCfHbMapping implements Serializable {
+
+	private String resultId;
+
+	private String cfhb;
+
+	private String masterId;
+
+	private String masterName;
+
+	public IdCfHbMapping() {
+	}
+
+	public IdCfHbMapping(String id) {
+		this.resultId = id;
+	}
+
+	public String getResultId() {
+		return resultId;
+	}
+
+	public void setResultId(String resultId) {
+		this.resultId = resultId;
+	}
+
+	public String getCfhb() {
+		return cfhb;
+	}
+
+	public void setCfhb(String cfhb) {
+		this.cfhb = cfhb;
+	}
+
+	public String getMasterId() {
+		return masterId;
+	}
+
+	public void setMasterId(String masterId) {
+		this.masterId = masterId;
+	}
+
+	public String getMasterName() {
+		return masterName;
+	}
+
+	public void setMasterName(String masterName) {
+		this.masterName = masterName;
+	}
+}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java

@@ -58,8 +58,8 @@ public class CleanCountrySparkJob implements Serializable {
 		String inputPath = parser.get("inputPath");
 		log.info("inputPath: {}", inputPath);
 
-		String workingPath = parser.get("workingPath");
-		log.info("workingPath: {}", workingPath);
+		String workingDir = parser.get("workingDir");
+		log.info("workingDir: {}", workingDir);
 
 		String datasourcePath = parser.get("hostedBy");
 		log.info("datasourcePath: {}", datasourcePath);
@@ -85,12 +85,12 @@ public class CleanCountrySparkJob implements Serializable {
 			spark -> {
 
 				cleanCountry(
-					spark, country, verifyParam, inputPath, entityClazz, workingPath, collectedfrom, datasourcePath);
+					spark, country, verifyParam, inputPath, entityClazz, workingDir, collectedfrom, datasourcePath);
 			});
 	}
 
 	private static <T extends Result> void cleanCountry(SparkSession spark, String country, String[] verifyParam,
-		String inputPath, Class<T> entityClazz, String workingPath, String collectedfrom, String datasourcePath) {
+		String inputPath, Class<T> entityClazz, String workingDir, String collectedfrom, String datasourcePath) {
 
 		List<String> hostedBy = spark
 			.read()
@@ -134,11 +134,11 @@ public class CleanCountrySparkJob implements Serializable {
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
-			.json(workingPath);
+			.json(workingDir);
 
 		spark
 			.read()
-			.textFile(workingPath)
+			.textFile(workingDir)
 			.map(
 				(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
 				Encoders.bean(entityClazz))

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java

@@ -54,8 +54,8 @@ public class GetDatasourceFromCountry implements Serializable {
 		String inputPath = parser.get("inputPath");
 		log.info("inputPath: {}", inputPath);
 
-		String workingPath = parser.get("workingPath");
-		log.info("workingPath: {}", workingPath);
+		String workingPath = parser.get("workingDir");
+		log.info("workingDir: {}", workingPath);
 
 		String country = parser.get("country");
 		log.info("country: {}", country);
@@ -70,7 +70,7 @@ public class GetDatasourceFromCountry implements Serializable {
 	}
 
 	private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath,
-		String workingPath) {
+		String workingDir) {
 
 		Dataset<Organization> organization = spark
 			.read()
@@ -100,7 +100,7 @@ public class GetDatasourceFromCountry implements Serializable {
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
-			.json(workingPath);
+			.json(workingDir);
 
 	}
 }

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

@@ -317,13 +317,13 @@
         </switch>
     </decision>
 
-
     <fork name="fork_clean_context">
         <path start="clean_publication_context"/>
         <path start="clean_dataset_context"/>
         <path start="clean_otherresearchproduct_context"/>
         <path start="clean_software_context"/>
     </fork>
+
     <action name="clean_publication_context">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -343,7 +343,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphOutputPath}/publication</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/working/publication</arg>
+            <arg>--workingDir</arg><arg>${workingDir}/working/publication</arg>
             <arg>--contextId</arg><arg>${contextId}</arg>
             <arg>--verifyParam</arg><arg>${verifyParam}</arg>
         </spark>
@@ -370,7 +370,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphOutputPath}/dataset</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/working/dataset</arg>
+            <arg>--workingDir</arg><arg>${workingDir}/working/dataset</arg>
             <arg>--contextId</arg><arg>${contextId}</arg>
             <arg>--verifyParam</arg><arg>${verifyParam}</arg>
         </spark>
@@ -397,7 +397,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/working/otherresearchproduct</arg>
+            <arg>--workingDir</arg><arg>${workingDir}/working/otherresearchproduct</arg>
             <arg>--contextId</arg><arg>${contextId}</arg>
             <arg>--verifyParam</arg><arg>${verifyParam}</arg>
         </spark>
@@ -424,7 +424,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphOutputPath}/software</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/working/software</arg>
+            <arg>--workingDir</arg><arg>${workingDir}/working/software</arg>
             <arg>--contextId</arg><arg>${contextId}</arg>
             <arg>--verifyParam</arg><arg>${verifyParam}</arg>
         </spark>
@@ -434,7 +434,6 @@
 
     <join name="wait_clean_context" to="select_datasourceId_from_country"/>
 
-
     <action name="select_datasourceId_from_country">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -453,20 +452,20 @@
                 --conf spark.sql.shuffle.partitions=7680
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphOutputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--workingDir</arg><arg>${workingDir}/working/hostedby</arg>
             <arg>--country</arg><arg>${country}</arg>
         </spark>
         <ok to="fork_clean_country"/>
         <error to="Kill"/>
     </action>
 
-
     <fork name="fork_clean_country">
         <path start="clean_publication_country"/>
         <path start="clean_dataset_country"/>
         <path start="clean_otherresearchproduct_country"/>
         <path start="clean_software_country"/>
     </fork>
+
     <action name="clean_publication_country">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -486,7 +485,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphOutputPath}/publication</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/working/publication</arg>
+            <arg>--workingDir</arg><arg>${workingDir}/working/publication</arg>
             <arg>--country</arg><arg>${country}</arg>
             <arg>--verifyParam</arg><arg>${verifyCountryParam}</arg>
             <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
@@ -515,7 +514,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphOutputPath}/dataset</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/working/dataset</arg>
+            <arg>--workingDir</arg><arg>${workingDir}/working/dataset</arg>
             <arg>--country</arg><arg>${country}</arg>
             <arg>--verifyParam</arg><arg>${verifyCountryParam}</arg>
             <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
@@ -544,7 +543,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/working/otherresearchproduct</arg>
+            <arg>--workingDir</arg><arg>${workingDir}/working/otherresearchproduct</arg>
             <arg>--country</arg><arg>${country}</arg>
             <arg>--verifyParam</arg><arg>${verifyCountryParam}</arg>
             <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
@@ -573,7 +572,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphOutputPath}/software</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/working/software</arg>
+            <arg>--workingDir</arg><arg>${workingDir}/working/software</arg>
             <arg>--country</arg><arg>${country}</arg>
             <arg>--verifyParam</arg><arg>${verifyCountryParam}</arg>
             <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
@@ -583,7 +582,202 @@
         <error to="Kill"/>
     </action>
 
-    <join name="wait_clean_country" to="End"/>
+    <join name="wait_clean_country" to="should_patch_datasource_ids"/>
+
+    <decision name="should_patch_datasource_ids">
+        <switch>
+            <case to="get_ds_master_duplicate">${wf:conf('shouldClean') eq true}</case>
+            <default to="End"/>
+        </switch>
+    </decision>
+
+    <action name="get_ds_master_duplicate">
+        <java>
+            <main-class>eu.dnetlib.dhp.oa.graph.clean.MasterDuplicateAction</main-class>
+            <arg>--postgresUrl</arg><arg>${postgresURL}</arg>
+            <arg>--postgresUser</arg><arg>${postgresUser}</arg>
+            <arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
+            <arg>--hdfsPath</arg><arg>${workingDir}/masterduplicate</arg>
+            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
+        </java>
+        <ok to="fork_patch_cfhb"/>
+        <error to="Kill"/>
+    </action>
+
+    <fork name="fork_patch_cfhb">
+        <path start="patch_publication_cfhb"/>
+        <path start="patch_dataset_cfhb"/>
+        <path start="patch_otherresearchproduct_cfhb"/>
+        <path start="patch_software_cfhb"/>
+    </fork>
+
+    <action name="patch_publication_cfhb">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>patch publication cfhb</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob</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}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${graphOutputPath}/publication</arg>
+            <arg>--resolvedPath</arg><arg>${workingDir}/cfHbResolved/publication</arg>
+            <arg>--outputPath</arg><arg>${workingPath}/cfHbPatched/publication</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
+            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
+        </spark>
+        <ok to="wait_clean_cfhb"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="patch_dataset_cfhb">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>patch dataset cfhb</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob</class>
+            <jar>dhp-graph-mapper-${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>${graphOutputPath}/dataset</arg>
+            <arg>--resolvedPath</arg><arg>${workingDir}/cfHbResolved/dataset</arg>
+            <arg>--outputPath</arg><arg>${workingPath}/cfHbPatched/dataset</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
+            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
+        </spark>
+        <ok to="wait_clean_cfhb"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="patch_otherresearchproduct_cfhb">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>patch otherresearchproduct cfhb</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob</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}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
+            <arg>--resolvedPath</arg><arg>${workingDir}/cfHbResolved/otherresearchproduct</arg>
+            <arg>--outputPath</arg><arg>${workingPath}/cfHbPatched/otherresearchproduct</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
+            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
+        </spark>
+        <ok to="wait_clean_cfhb"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="patch_software_cfhb">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>patch software cfhb</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob</class>
+            <jar>dhp-graph-mapper-${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>${graphOutputPath}/software</arg>
+            <arg>--resolvedPath</arg><arg>${workingDir}/cfHbResolved/software</arg>
+            <arg>--outputPath</arg><arg>${workingPath}/cfHbPatched/software</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
+            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
+        </spark>
+        <ok to="wait_clean_cfhb"/>
+        <error to="Kill"/>
+    </action>
+
+    <join name="wait_clean_cfhb" to="fork_copy_cfhb_patched_results"/>
+
+    <fork name="fork_copy_cfhb_patched_results">
+        <path start="copy_cfhb_patched_publication"/>
+        <path start="copy_cfhb_patched_dataset"/>
+        <path start="copy_cfhb_patched_otherresearchproduct"/>
+        <path start="copy_cfhb_patched_software"/>
+    </fork>
+
+    <action name="copy_cfhb_patched_publication">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <prepare>
+                <delete path="${graphOutputPath}/publication"/>
+            </prepare>
+            <arg>${workingDir}/cfHbPatched/publication</arg>
+            <arg>${graphOutputPath}/publication</arg>
+        </distcp>
+        <ok to="copy_wait"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="copy_cfhb_patched_dataset">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <prepare>
+                <delete path="${graphOutputPath}/dataset"/>
+            </prepare>
+            <arg>${workingDir}/cfHbPatched/dataset</arg>
+            <arg>${graphOutputPath}/dataset</arg>
+        </distcp>
+        <ok to="copy_wait"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="copy_cfhb_patched_otherresearchproduct">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <prepare>
+                <delete path="${graphOutputPath}/otherresearchproduct"/>
+            </prepare>
+            <arg>${workingDir}/cfHbPatched/otherresearchproduct</arg>
+            <arg>${graphOutputPath}/otherresearchproduct</arg>
+        </distcp>
+        <ok to="copy_wait"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="copy_cfhb_patched_software">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <prepare>
+                <delete path="${graphOutputPath}/software"/>
+            </prepare>
+            <arg>${workingDir}/cfHbPatched/software</arg>
+            <arg>${graphOutputPath}/software</arg>
+        </distcp>
+        <ok to="copy_wait"/>
+        <error to="Kill"/>
+    </action>
+
+    <join name="copy_wait" to="End"/>
 
     <end name="End"/>
+
 </workflow-app>

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/datasourcemaster_parameters.json

@@ -0,0 +1,32 @@
+[
+  {
+    "paramName": "pu",
+    "paramLongName": "postgresUrl",
+    "paramDescription": "the jdbc url to the postgres",
+    "paramRequired": true
+  },
+  {
+    "paramName": "uid",
+    "paramLongName": "postgresUser",
+    "paramDescription": "the postgres user",
+    "paramRequired": true
+  },
+  {
+    "paramName": "pwd",
+    "paramLongName": "postgresPassword",
+    "paramDescription": "the postgres password=",
+    "paramRequired": true
+  },
+  {
+    "paramName": "p",
+    "paramLongName": "hdfsPath",
+    "paramDescription": "the target path on HDFS",
+    "paramRequired": true
+  },
+  {
+    "paramName": "nn",
+    "paramLongName": "hdfsNameNode",
+    "paramDescription": "the HDFS nameNode",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_cfhb_parameters.json

@@ -0,0 +1,38 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "in",
+    "paramLongName": "inputPath",
+    "paramDescription": "the path to the graph data dump to read",
+    "paramRequired": true
+  },
+  {
+    "paramName": "rp",
+    "paramLongName": "resolvedPath",
+    "paramDescription": "the path to store the resolved records",
+    "paramRequired": true
+  },
+  {
+    "paramName": "out",
+    "paramLongName": "outputPath",
+    "paramDescription": "the path to store the output graph",
+    "paramRequired": true
+  },
+  {
+    "paramName": "class",
+    "paramLongName": "graphTableClassName",
+    "paramDescription": "class name moelling the graph table",
+    "paramRequired": true
+  },
+  {
+    "paramName": "md",
+    "paramLongName": "datasourceMasterDuplicate",
+    "paramDescription": "path to the file on HDFS holding the datasource id tuples [master, duplicate]",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json

@@ -12,8 +12,8 @@
     "paramRequired": true
   },
   {
-    "paramName": "wp",
-    "paramLongName": "workingPath",
+    "paramName": "wd",
+    "paramLongName": "workingDir",
     "paramDescription": "the path to store the output graph",
     "paramRequired": true
   },

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json

@@ -12,8 +12,8 @@
     "paramRequired": true
   },
   {
-    "paramName": "wp",
-    "paramLongName": "workingPath",
+    "paramName": "wd",
+    "paramLongName": "workingDir",
     "paramDescription": "the path to store the output graph",
     "paramRequired": true
   },

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json

@@ -12,8 +12,8 @@
     "paramRequired": true
   },
   {
-    "paramName": "wp",
-    "paramLongName": "workingPath",
+    "paramName": "wd",
+    "paramLongName": "workingDir",
     "paramDescription": "the path to store the output graph",
     "paramRequired": true
   },

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java

@@ -0,0 +1,213 @@
+
+package eu.dnetlib.dhp.oa.graph.clean.cfhb;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.spark.SparkConf;
+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.SparkSession;
+import org.junit.jupiter.api.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.schema.oaf.Dataset;
+import eu.dnetlib.dhp.schema.oaf.Publication;
+
+public class CleanCfHbSparkJobTest {
+
+	private static final Logger log = LoggerFactory.getLogger(CleanCfHbSparkJobTest.class);
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path testBaseTmpPath;
+
+	private static String resolvedPath;
+
+	private static String graphInputPath;
+
+	private static String graphOutputPath;
+
+	private static String dsMasterDuplicatePath;
+
+	@BeforeAll
+	public static void beforeAll() throws IOException, URISyntaxException {
+
+		testBaseTmpPath = Files.createTempDirectory(CleanCfHbSparkJobTest.class.getSimpleName());
+		log.info("using test base path {}", testBaseTmpPath);
+
+		final File entitiesSources = Paths
+			.get(CleanCfHbSparkJobTest.class.getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities").toURI())
+			.toFile();
+
+		FileUtils
+			.copyDirectory(
+				entitiesSources,
+				testBaseTmpPath.resolve("input").resolve("entities").toFile());
+
+		FileUtils
+			.copyFileToDirectory(
+				Paths
+					.get(
+						CleanCfHbSparkJobTest.class
+							.getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/masterduplicate.json")
+							.toURI())
+					.toFile(),
+				testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toFile());
+
+		graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString();
+		resolvedPath = testBaseTmpPath.resolve("workingDir").resolve("cfHbResolved").toString();
+		graphOutputPath = testBaseTmpPath.resolve("workingDir").resolve("cfHbPatched").toString();
+		dsMasterDuplicatePath = testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toString();
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(CleanCfHbSparkJobTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("spark.ui.enabled", "false");
+
+		spark = SparkSession
+			.builder()
+			.appName(CleanCfHbSparkJobTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(testBaseTmpPath.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void testCleanCfHbSparkJob() throws Exception {
+		final String outputPath = graphOutputPath + "/dataset";
+		final String inputPath = graphInputPath + "/dataset";
+
+		org.apache.spark.sql.Dataset<Dataset> records = read(spark, inputPath, Dataset.class);
+		Dataset d = records
+			.filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'")
+			.first();
+		assertEquals("10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", d.getCollectedfrom().get(0).getKey());
+		assertEquals("Bacterial Protein Interaction Database - DUP", d.getCollectedfrom().get(0).getValue());
+		assertEquals(
+			"10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", d.getInstance().get(0).getCollectedfrom().getKey());
+		assertEquals(
+			"Bacterial Protein Interaction Database - DUP", d.getInstance().get(0).getCollectedfrom().getValue());
+
+		d = records
+			.filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3adc37a'")
+			.first();
+		assertEquals("10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", d.getCollectedfrom().get(0).getKey());
+		assertEquals("FILUR DATA - DUP", d.getCollectedfrom().get(0).getValue());
+		assertEquals(
+			"10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", d.getInstance().get(0).getCollectedfrom().getKey());
+		assertEquals("FILUR DATA - DUP", d.getInstance().get(0).getCollectedfrom().getValue());
+		assertEquals(
+			"10|re3data_____::6ffd7bc058f762912dc494cd9c175341", d.getInstance().get(0).getHostedby().getKey());
+		assertEquals("depositar - DUP", d.getInstance().get(0).getHostedby().getValue());
+
+		d = records
+			.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'")
+			.first();
+		assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey());
+		assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue());
+		assertEquals(
+			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey());
+		assertEquals(
+			"DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue());
+		assertEquals(
+			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey());
+		assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue());
+
+		CleanCfHbSparkJob
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--inputPath", inputPath,
+					"--outputPath", outputPath,
+					"--resolvedPath", resolvedPath + "/dataset",
+					"--graphTableClassName", Dataset.class.getCanonicalName(),
+					"--datasourceMasterDuplicate", dsMasterDuplicatePath
+				});
+
+		assertTrue(Files.exists(Paths.get(graphOutputPath, "dataset")));
+
+		records = read(spark, outputPath, Dataset.class);
+
+		assertEquals(3, records.count());
+
+		d = records
+			.filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'")
+			.first();
+		assertEquals("10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", d.getCollectedfrom().get(0).getKey());
+		assertEquals("Bacterial Protein Interaction Database", d.getCollectedfrom().get(0).getValue());
+		assertEquals(
+			"10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", d.getInstance().get(0).getCollectedfrom().getKey());
+		assertEquals("Bacterial Protein Interaction Database", d.getInstance().get(0).getCollectedfrom().getValue());
+
+		d = records
+			.filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3adc37a'")
+			.first();
+		assertEquals("10|re3data_____::fc1db64b3964826913b1e9eafe830490", d.getCollectedfrom().get(0).getKey());
+		assertEquals("FULIR Data", d.getCollectedfrom().get(0).getValue());
+		assertEquals(
+			"10|re3data_____::fc1db64b3964826913b1e9eafe830490", d.getInstance().get(0).getCollectedfrom().getKey());
+		assertEquals("FULIR Data", d.getInstance().get(0).getCollectedfrom().getValue());
+		assertEquals(
+			"10|fairsharing_::3f647cadf56541fb9513cb63ec370187", d.getInstance().get(0).getHostedby().getKey());
+		assertEquals("depositar", d.getInstance().get(0).getHostedby().getValue());
+
+		d = records
+			.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'")
+			.first();
+		assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey());
+		assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue());
+		assertEquals(
+			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey());
+		assertEquals(
+			"DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue());
+		assertEquals(
+			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey());
+		assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue());
+
+		d = records
+			.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'")
+			.first();
+		assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey());
+		assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue());
+		assertEquals(
+			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey());
+		assertEquals(
+			"DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue());
+		assertEquals(
+			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey());
+		assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue());
+	}
+
+	private <R> org.apache.spark.sql.Dataset<R> read(SparkSession spark, String path, Class<R> clazz) {
+		return spark
+			.read()
+			.textFile(path)
+			.map(as(clazz), Encoders.bean(clazz));
+	}
+
+	private static <R> MapFunction<String, R> as(Class<R> clazz) {
+		return s -> OBJECT_MAPPER.readValue(s, clazz);
+	}
+}

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java

@@ -1002,7 +1002,8 @@ class MappersTest {
 
 	@Test
 	void testEOSCFuture_ROHub() throws IOException {
-		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("photic-zone-transformed.xml")));
+		final String xml = IOUtils
+			.toString(Objects.requireNonNull(getClass().getResourceAsStream("photic-zone-transformed.xml")));
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
 		final OtherResearchProduct rocrate = (OtherResearchProduct) list.get(0);
 		assertNotNull(rocrate.getEoscifguidelines());

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/cfhb/masterduplicate.json

@@ -0,0 +1,4 @@
+{ "duplicateId" :  "10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", "masterId" : "10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", "masterName" : "Bacterial Protein Interaction Database" }
+{ "duplicateId" :  "10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", "masterId" : "10|re3data_____::fc1db64b3964826913b1e9eafe830490", "masterName" : "FULIR Data" }
+{ "duplicateId" :  "10|re3data_____::6ffd7bc058f762912dc494cd9c175341", "masterId" : "10|fairsharing_::3f647cadf56541fb9513cb63ec370187", "masterName" : "depositar" }
+{ "duplicateId" :  "10|scindeksserb::07022f78a8cc6d1171092454ecdbb47c", "masterId" : "10|doajarticles::07022f78a8cc6d1171092454ecdbb47c", "masterName" : "Artefact" }

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/EOSCFuture_Test.java

@@ -1,13 +1,14 @@
+
 package eu.dnetlib.dhp.oa.provision;
 
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
-import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
-import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory;
-import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
-import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
-import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
+import java.io.IOException;
+import java.io.StringReader;
+
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+
 import org.apache.commons.io.IOUtils;
 import org.apache.solr.client.solrj.util.ClientUtils;
 import org.apache.solr.common.SolrInputDocument;
@@ -18,71 +19,73 @@ import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import java.io.IOException;
-import java.io.StringReader;
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
 
-import static org.junit.jupiter.api.Assertions.assertNotNull;
+import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
+import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
+import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory;
+import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
+import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
+import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
 
 public class EOSCFuture_Test {
 
-    public static ObjectMapper OBJECT_MAPPER = new ObjectMapper()
-            .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+	public static ObjectMapper OBJECT_MAPPER = new ObjectMapper()
+		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
 
-    public static final String VERSION = "2021-04-15T10:05:53Z";
-    public static final String DSID = "b9ee796a-c49f-4473-a708-e7d67b84c16d_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl";
+	public static final String VERSION = "2021-04-15T10:05:53Z";
+	public static final String DSID = "b9ee796a-c49f-4473-a708-e7d67b84c16d_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl";
 
-    private ContextMapper contextMapper;
+	private ContextMapper contextMapper;
 
-    @BeforeEach
-    public void setUp() {
-        contextMapper = new ContextMapper();
-    }
+	@BeforeEach
+	public void setUp() {
+		contextMapper = new ContextMapper();
+	}
 
+	@Test
+	public void testEOSC_ROHub() throws IOException, DocumentException, TransformerException {
 
-    @Test
-    public void testEOSC_ROHub() throws IOException, DocumentException, TransformerException {
+		final ContextMapper contextMapper = new ContextMapper();
 
-        final ContextMapper contextMapper = new ContextMapper();
+		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
+			XmlConverterJob.schemaLocation);
 
-        final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
-                XmlConverterJob.schemaLocation);
+		final OtherResearchProduct p = OBJECT_MAPPER
+			.readValue(
+				IOUtils.toString(getClass().getResourceAsStream("eosc-future/photic-zone.json")),
+				OtherResearchProduct.class);
 
-        final OtherResearchProduct p = OBJECT_MAPPER
-                .readValue(IOUtils.toString(getClass().getResourceAsStream("eosc-future/photic-zone.json")), OtherResearchProduct.class);
+		final String xml = xmlRecordFactory.build(new JoinedEntity<>(p));
 
-        final String xml = xmlRecordFactory.build(new JoinedEntity<>(p));
+		assertNotNull(xml);
 
-        assertNotNull(xml);
+		final Document doc = new SAXReader().read(new StringReader(xml));
 
-        final Document doc = new SAXReader().read(new StringReader(xml));
+		assertNotNull(doc);
+		System.out.println(doc.asXML());
 
-        assertNotNull(doc);
-        System.out.println(doc.asXML());
+		testRecordTransformation(xml);
+	}
 
+	private void testRecordTransformation(final String record) throws IOException, TransformerException {
+		final String fields = IOUtils.toString(getClass().getResourceAsStream("fields.xml"));
+		final String xslt = IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"));
 
-        testRecordTransformation(xml);
-    }
+		final String transformer = XmlIndexingJob.getLayoutTransformer("DMF", fields, xslt);
 
+		final Transformer tr = SaxonTransformerFactory.newInstance(transformer);
 
-        private void testRecordTransformation(final String record) throws IOException, TransformerException {
-            final String fields = IOUtils.toString(getClass().getResourceAsStream("fields.xml"));
-            final String xslt = IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"));
+		final String indexRecordXML = XmlIndexingJob.toIndexRecord(tr, record);
 
-            final String transformer = XmlIndexingJob.getLayoutTransformer("DMF", fields, xslt);
+		final SolrInputDocument solrDoc = new StreamingInputDocumentFactory(VERSION, DSID)
+			.parseDocument(indexRecordXML);
 
-            final Transformer tr = SaxonTransformerFactory.newInstance(transformer);
+		final String xmlDoc = ClientUtils.toXML(solrDoc);
 
-            final String indexRecordXML = XmlIndexingJob.toIndexRecord(tr, record);
-
-            final SolrInputDocument solrDoc = new StreamingInputDocumentFactory(VERSION, DSID)
-                    .parseDocument(indexRecordXML);
-
-            final String xmlDoc = ClientUtils.toXML(solrDoc);
-
-            Assertions.assertNotNull(xmlDoc);
-            System.out.println(xmlDoc);
-        }
+		Assertions.assertNotNull(xmlDoc);
+		System.out.println(xmlDoc);
+	}
 
 }