Merge branch 'graph_cleaning'

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java

@@ -14,6 +14,7 @@ public class ModelConstants {
 	public static final String DNET_DATA_CITE_RESOURCE = "dnet:dataCite_resource";
 	public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
 	public static final String DNET_COUNTRY_TYPE = "dnet:countries";
+	public static final String DNET_REVIEW_LEVELS = "dnet:review_levels";
 
 	public static final String SYSIMPORT_CROSSWALK_REPOSITORY = "sysimport:crosswalk:repository";
 	public static final String SYSIMPORT_CROSSWALK_ENTITYREGISTRY = "sysimport:crosswalk:entityregistry";

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java

@@ -31,7 +31,7 @@ public class Instance implements Serializable {
 	// typed results
 	private Field<String> processingchargecurrency;
 
-	private Field<String> refereed; // peer-review status
+	private Qualifier refereed; // peer-review status
 
 	public Field<String> getLicense() {
 		return license;
@@ -113,11 +113,11 @@ public class Instance implements Serializable {
 		this.processingchargecurrency = processingchargecurrency;
 	}
 
-	public Field<String> getRefereed() {
+	public Qualifier getRefereed() {
 		return refereed;
 	}
 
-	public void setRefereed(Field<String> refereed) {
+	public void setRefereed(Qualifier refereed) {
 		this.refereed = refereed;
 	}
 

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java

@@ -254,28 +254,25 @@ public class Result extends OafEntity implements Serializable {
 				final StructuredProperty p = baseMainTitle;
 				title = title.stream().filter(t -> t != p).collect(Collectors.toList());
 			}
-//
-//
-//			title.remove(baseMainTitle);
 		}
 
 		StructuredProperty newMainTitle = null;
 		if (r.getTitle() != null) {
 			newMainTitle = getMainTitle(r.getTitle());
-			if (newMainTitle != null) {
+			if (newMainTitle != null && title != null) {
 				final StructuredProperty p = newMainTitle;
 				title = title.stream().filter(t -> t != p).collect(Collectors.toList());
 			}
-
-			// r.getTitle().remove(newMainTitle);
 		}
 
-		if (newMainTitle != null && compareTrust(this, r) < 0)
+		if (newMainTitle != null && compareTrust(this, r) < 0) {
 			baseMainTitle = newMainTitle;
+		}
 
 		title = mergeLists(title, r.getTitle());
-		if (title != null && baseMainTitle != null)
+		if (title != null && baseMainTitle != null) {
 			title.add(baseMainTitle);
+		}
 
 		relevantdate = mergeLists(relevantdate, r.getRelevantdate());
 

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java

@@ -96,12 +96,21 @@ public class ProtoConverter implements Serializable {
 					.stream()
 					.distinct()
 					.collect(Collectors.toCollection(ArrayList::new)) : null);
-		i.setRefereed(mapStringField(ri.getRefereed()));
+		i.setRefereed(mapRefereed(ri.getRefereed()));
 		i.setProcessingchargeamount(mapStringField(ri.getProcessingchargeamount()));
 		i.setProcessingchargecurrency(mapStringField(ri.getProcessingchargecurrency()));
 		return i;
 	}
 
+	private static Qualifier mapRefereed(FieldTypeProtos.StringField refereed) {
+		Qualifier q = new Qualifier();
+		q.setClassid(refereed.getValue());
+		q.setSchemename(refereed.getValue());
+		q.setSchemeid("dnet:review_levels");
+		q.setSchemename("dnet:review_levels");
+		return q;
+	}
+
 	private static List<ExternalReference> convertExternalRefs(OafProtos.Oaf oaf) {
 		ResultProtos.Result r = oaf.getEntity().getResult();
 		if (r.getExternalReferenceCount() > 0) {

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java

@@ -8,6 +8,7 @@ import java.io.File;
 
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -19,6 +20,7 @@ import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
 import eu.dnetlib.message.Message;
 import eu.dnetlib.message.MessageManager;
 
+@Disabled
 public class DnetCollectorWorkerApplicationTests {
 
 	private final ArgumentApplicationParser argumentParser = mock(ArgumentApplicationParser.class);

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

@@ -166,8 +166,10 @@ case object Crossref2Oaf {
 
     val has_review = (json \ "relation" \"has-review" \ "id")
 
-    if(has_review != JNothing)
+    if(has_review != JNothing) {
-      instance.setRefereed(asField("peerReviewed"))
+      instance.setRefereed(
+        createQualifier("0001", "peerReviewed", "dnet:review_levels", "dnet:review_levels"))
+    }
 
 
     instance.setAccessright(getRestrictedQualifier())

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

@@ -0,0 +1,119 @@
+
+package eu.dnetlib.dhp.oa.graph.clean;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.beans.BeanInfo;
+import java.beans.IntrospectionException;
+import java.beans.Introspector;
+import java.beans.PropertyDescriptor;
+import java.lang.reflect.InvocationTargetException;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.TreeMap;
+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.function.MapFunction;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
+import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import scala.Predef;
+
+public class CleanGraphProperties {
+
+	private static final Logger log = LoggerFactory.getLogger(CleanGraphProperties.class);
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static void main(String[] args) throws Exception {
+
+		String jsonConfiguration = IOUtils
+			.toString(
+				CleanGraphProperties.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json"));
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		String inputPath = parser.get("inputPath");
+		log.info("inputPath: {}", inputPath);
+
+		String outputPath = parser.get("outputPath");
+		log.info("outputPath: {}", outputPath);
+
+		String isLookupUrl = parser.get("isLookupUrl");
+		log.info("isLookupUrl: {}", isLookupUrl);
+
+		String graphTableClassName = parser.get("graphTableClassName");
+		log.info("graphTableClassName: {}", graphTableClassName);
+
+		Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
+
+		final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
+		final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService);
+
+		SparkConf conf = new SparkConf();
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				removeOutputDir(spark, outputPath);
+				fixGraphTable(spark, vocs, inputPath, entityClazz, outputPath);
+			});
+	}
+
+	private static <T extends Oaf> void fixGraphTable(
+		SparkSession spark,
+		VocabularyGroup vocs,
+		String inputPath,
+		Class<T> clazz,
+		String outputPath) {
+
+		CleaningRule<T> rule = new CleaningRule<>(vocs);
+
+		readTableFromPath(spark, inputPath, clazz)
+			.map(rule, Encoders.bean(clazz))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.parquet(outputPath);
+	}
+
+	private static <T extends Oaf> Dataset<T> readTableFromPath(
+		SparkSession spark, String inputEntityPath, Class<T> clazz) {
+
+		log.info("Reading Graph table from: {}", inputEntityPath);
+		return spark
+			.read()
+			.textFile(inputEntityPath)
+			.map(
+				(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz),
+				Encoders.bean(clazz));
+	}
+
+	private static void removeOutputDir(SparkSession spark, String path) {
+		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+	}
+
+}

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

@@ -0,0 +1,73 @@
+
+package eu.dnetlib.dhp.oa.graph.clean;
+
+import com.google.common.collect.Maps;
+import eu.dnetlib.dhp.schema.oaf.Field;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.spark.api.java.function.MapFunction;
+
+import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
+
+import java.util.Map;
+import java.util.Objects;
+import java.util.function.Function;
+
+public class CleaningRule<T extends Oaf> implements MapFunction<T, T> {
+
+	private VocabularyGroup vocabularies;
+
+	private Map<Class, Function<Object, Object>> mapping = Maps.newHashMap();
+
+
+	public CleaningRule(VocabularyGroup vocabularies) {
+		this.vocabularies = vocabularies;
+
+		mapping.put(Qualifier.class, o -> patchQualifier(o));
+		mapping.put(StructuredProperty.class, o -> patchSp(o));
+		mapping.put(Field.class, o -> patchStringField(o));
+	}
+
+	@Override
+	public T call(T value) throws Exception {
+
+		OafNavigator.apply(value, mapping);
+
+		return value;
+	}
+
+	private Object patchQualifier(Object o) {
+		Qualifier q = (Qualifier) o;
+		if (vocabularies.vocabularyExists(q.getSchemeid())) {
+			return vocabularies.lookup(q.getSchemeid(), q.getClassid());
+		}
+		return o;
+	}
+
+	private Object patchSp(Object o) {
+		StructuredProperty sp = (StructuredProperty) o;
+		if (StringUtils.isBlank(sp.getValue())) {
+			return null;
+		}
+		return o;
+	}
+
+	private Object patchStringField(Object o) {
+		Field f = (Field) o;
+		try {
+			if (StringUtils.isBlank((String) f.getValue())) {
+				return null;
+			}
+		} catch (ClassCastException e) {
+			// ignored on purpose
+		}
+
+		return o;
+	}
+
+	public VocabularyGroup getVocabularies() {
+		return vocabularies;
+	}
+}

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

@@ -0,0 +1,151 @@
+
+package eu.dnetlib.dhp.oa.graph.clean;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.Lists;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import scala.Tuple2;
+
+import java.beans.BeanInfo;
+import java.beans.IntrospectionException;
+import java.beans.Introspector;
+import java.beans.PropertyDescriptor;
+import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
+import java.util.*;
+import java.util.function.Function;
+
+public class OafNavigator {
+
+	public static <E extends Oaf> E apply(E oaf, Map<Class, Function<Object, Object>> mapping) {
+		reflect(oaf, mapping);
+		return oaf;
+	}
+
+	public static void reflect(Object o, Map<Class, Function<Object, Object>> mapping) {
+		visit(o, mapping);
+	}
+
+	public static void visit(final Object thingy, Map<Class, Function<Object, Object>> mapping) {
+
+		try {
+			final Class<?> clazz = thingy.getClass();
+
+			if (!isPrimitive(thingy) && clazz.getPackage().equals(Oaf.class.getPackage())) {
+
+				final BeanInfo beanInfo = Introspector.getBeanInfo(clazz);
+
+				for (final PropertyDescriptor descriptor : beanInfo.getPropertyDescriptors()) {
+					try {
+						final Object value = descriptor.getReadMethod().invoke(thingy);
+
+						if (value != null && !isPrimitive(value)) {
+
+							System.out.println("VISITING " + descriptor.getName() + " " + descriptor.getPropertyType());
+
+							if (Iterable.class.isAssignableFrom(descriptor.getPropertyType())) {
+								for(Object vi : (Iterable) value) {
+
+									visit(vi, mapping);
+								}
+							} else {
+
+								if (mapping.keySet().contains(value.getClass())) {
+									final Object newValue = mapping.get(value.getClass()).apply(value);
+									System.out.println("PATCHING " + descriptor.getName()+ " " + descriptor.getPropertyType());
+									System.out.println("OLD VALUE " + getObjectMapper().writeValueAsString(value));
+									System.out.println("NEW VALUE " + getObjectMapper().writeValueAsString(newValue));
+									descriptor.getWriteMethod().invoke(newValue);
+								}
+
+								visit(value, mapping);
+							}
+						}
+
+					} catch (final IllegalArgumentException e) {
+						// handle this please
+					} catch (final IllegalAccessException e) {
+						// and this also
+					} catch (final InvocationTargetException e) {
+						// and this, too
+					} catch (JsonProcessingException e) {
+						e.printStackTrace();
+					}
+				}
+			}
+		} catch (final IntrospectionException e) {
+			// do something sensible here
+		}
+	}
+
+	private static ObjectMapper getObjectMapper() {
+		final ObjectMapper mapper = new ObjectMapper();
+		return mapper;
+	}
+
+	private static void navigate(Object o, Map<Class, Function<Object, Object>> mapping) {
+		if (Objects.isNull(o) || isPrimitive(o)) {
+			return;
+		} else {
+			try {
+				for (Field field : getAllFields(o.getClass())) {
+					System.out.println(field.getName());
+					field.setAccessible(true);
+					Object value = field.get(o);
+
+					if (Objects.nonNull(value)) {
+						final Class<?> fieldType = field.getType();
+						if ((fieldType.isArray() && !fieldType.getComponentType().isPrimitive())) {
+							Object[] fs = (Object[]) value;
+							for (Object fi : fs) {
+								navigate(fi, mapping);
+							}
+						} if (Iterable.class.isAssignableFrom(fieldType)) {
+							Iterable fs = (Iterable) value;
+							for (Object fi : fs) {
+								navigate(fi, mapping);
+							}
+						} else {
+							if (mapping.keySet().contains(value.getClass())) {
+								System.out.println("PATCHING " + field.getName());
+								field.set(o, mapping.get(value.getClass()).apply(value));
+							}
+						}
+					}
+				}
+
+			} catch (IllegalAccessException | IllegalArgumentException e) {
+				throw new RuntimeException(e);
+			}
+		}
+	}
+
+	private static boolean isPrimitive(Object o) {
+		return o.getClass().isPrimitive()
+			|| o instanceof Class
+			|| o instanceof Integer
+			|| o instanceof Double
+			|| o instanceof Float
+			|| o instanceof Long
+			|| o instanceof Boolean
+			|| o instanceof String
+			|| o instanceof Byte;
+	}
+
+	private static List<Field> getAllFields(Class<?> clazz) {
+		return getAllFields(new LinkedList<>(), clazz);
+	}
+
+	private static List<Field> getAllFields(List<Field> fields, Class<?> clazz) {
+		fields.addAll(Arrays.asList(clazz.getDeclaredFields()));
+
+		final Class<?> superclass = clazz.getSuperclass();
+		if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) {
+			getAllFields(fields, superclass);
+		}
+
+		return fields;
+	}
+
+}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator2.java

@@ -0,0 +1,94 @@
+
+package eu.dnetlib.dhp.oa.graph.clean;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+
+import java.lang.reflect.Field;
+import java.util.*;
+import java.util.function.Function;
+
+public class OafNavigator2 {
+
+	public static <E extends Oaf> E apply(E oaf, Map<Class, Function<Object, Object>> mapping) {
+		navigate(oaf, mapping);
+		return oaf;
+	}
+
+	private static void navigate(Object o, Map<Class, Function<Object, Object>> mapping) {
+		if (Objects.isNull(o) || isPrimitive(o)) {
+			return;
+		} else {
+			try {
+				for (Field field : getAllFields(o.getClass())) {
+					System.out.println("VISITING " + field.getName() + " in " + o.getClass());
+					field.setAccessible(true);
+					Object value = field.get(o);
+
+					if (Objects.nonNull(value)) {
+						final Class<?> fieldType = field.getType();
+						if ((fieldType.isArray() && !fieldType.getComponentType().isPrimitive())) {
+							Object[] fs = (Object[]) value;
+							for (Object fi : fs) {
+								navigate(fi, mapping);
+							}
+						} if (Iterable.class.isAssignableFrom(fieldType)) {
+							Iterable fs = (Iterable) value;
+							for (Object fi : fs) {
+								navigate(fi, mapping);
+							}
+						} else {
+							final Function<Object, Object> cleaningFn = mapping.get(value.getClass());
+							if (Objects.nonNull(cleaningFn)) {
+								final Object newValue = cleaningFn.apply(value);
+								if (!Objects.equals(value, newValue)) {
+									System.out.println("PATCHING " + field.getName()+ " " + value.getClass());
+									System.out.println("OLD VALUE " + getObjectMapper().writeValueAsString(value));
+									System.out.println("NEW VALUE " + getObjectMapper().writeValueAsString(newValue));
+									field.set(o, newValue);
+								}
+							}
+						}
+					}
+				}
+
+			} catch (IllegalAccessException | IllegalArgumentException | JsonProcessingException e) {
+				throw new RuntimeException(e);
+			}
+		}
+	}
+
+	private static ObjectMapper getObjectMapper() {
+		final ObjectMapper mapper = new ObjectMapper();
+		return mapper;
+	}
+
+	private static boolean isPrimitive(Object o) {
+		return o.getClass().isPrimitive()
+			|| o instanceof Class
+			|| o instanceof Integer
+			|| o instanceof Double
+			|| o instanceof Float
+			|| o instanceof Long
+			|| o instanceof Boolean
+			|| o instanceof String
+			|| o instanceof Byte;
+	}
+
+	private static List<Field> getAllFields(Class<?> clazz) {
+		return getAllFields(new LinkedList<>(), clazz);
+	}
+
+	private static List<Field> getAllFields(List<Field> fields, Class<?> clazz) {
+		fields.addAll(Arrays.asList(clazz.getDeclaredFields()));
+
+		final Class<?> superclass = clazz.getSuperclass();
+		if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) {
+			getAllFields(fields, superclass);
+		}
+
+		return fields;
+	}
+
+}

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

@@ -39,6 +39,8 @@ import eu.dnetlib.dhp.schema.oaf.Project;
 import eu.dnetlib.dhp.schema.oaf.Publication;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.Software;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import scala.Tuple2;
 
 public class GenerateEntitiesApplication {
@@ -71,7 +73,8 @@ public class GenerateEntitiesApplication {
 		final String isLookupUrl = parser.get("isLookupUrl");
 		log.info("isLookupUrl: {}", isLookupUrl);
 
-		final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupUrl);
+		final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
+		final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService);
 
 		final SparkConf conf = new SparkConf();
 		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
@@ -139,9 +142,11 @@ public class GenerateEntitiesApplication {
 		switch (type.toLowerCase()) {
 			case "oaf-store-claim":
 			case "oaf-store-cleaned":
+			case "oaf-store-claim":
 				return new OafToOafMapper(vocs, false).processMdRecord(s);
 			case "odf-store-claim":
 			case "odf-store-cleaned":
+			case "odf-store-claim":
 				return new OdfToOafMapper(vocs, false).processMdRecord(s);
 			case "oaf-store-intersection":
 				return new OafToOafMapper(vocs, true).processMdRecord(s);

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

@@ -71,6 +71,7 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.schema.oaf.Software;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 
 public class MigrateDbEntitiesApplication extends AbstractMigrationApplication implements Closeable {
 
@@ -151,7 +152,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
 		super(hdfsPath);
 		this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
 		this.lastUpdateTimestamp = new Date().getTime();
-		this.vocs = VocabularyGroup.loadVocsFromIS(isLookupUrl);
+		this.vocs = VocabularyGroup.loadVocsFromIS(ISLookupClientFactory.getLookUpService(isLookupUrl));
 	}
 
 	public void execute(final String sqlFile, final Function<ResultSet, List<Oaf>> producer)

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

@@ -133,7 +133,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 		instance
 			.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
 		instance.setLicense(field(doc.valueOf("//oaf:license"), info));
-		instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
+		instance.setRefereed(prepareQualifier(doc, "//oaf:refereed", DNET_REVIEW_LEVELS));
 		instance
 			.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
 		instance

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

@@ -4,19 +4,7 @@ package eu.dnetlib.dhp.oa.graph.raw;
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_DATE;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_RESOURCE;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_PARTS;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PART_OF;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_SUPPLEMENTED_BY;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_SUPPLEMENT_TO;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.PART;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.SUPPLEMENT;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -129,7 +117,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 		instance
 			.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
 		instance.setLicense(field(doc.valueOf("//oaf:license"), info));
-		instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
+		instance.setRefereed(prepareQualifier(doc, "//oaf:refereed", DNET_REVIEW_LEVELS));
 		instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
 		instance
 			.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));

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

@@ -60,6 +60,10 @@ public class OafMapperUtils {
 			.collect(Collectors.toList());
 	}
 
+	public static Qualifier unknown(final String schemeid, final String schemename) {
+		return qualifier("UNKNOWN", "Unknown", schemeid, schemename);
+	}
+
 	public static Qualifier qualifier(
 		final String classid,
 		final String classname,

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

@@ -4,14 +4,29 @@ package eu.dnetlib.dhp.oa.graph.raw.common;
 import java.io.Serializable;
 import java.util.HashMap;
 import java.util.Map;
+import java.util.Optional;
+
+import org.apache.commons.lang3.StringUtils;
+
+import com.google.common.collect.Maps;
+
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
 
 public class Vocabulary implements Serializable {
 
 	private final String id;
 	private final String name;
 
+	/**
+	 * Code to Term mappings for this Vocabulary.
+	 */
 	private final Map<String, VocabularyTerm> terms = new HashMap<>();
 
+	/**
+	 * Synonym to Code mappings for this Vocabulary.
+	 */
+	private final Map<String, String> synonyms = Maps.newHashMap();
+
 	public Vocabulary(final String id, final String name) {
 		this.id = id;
 		this.name = name;
@@ -30,7 +45,7 @@ public class Vocabulary implements Serializable {
 	}
 
 	public VocabularyTerm getTerm(final String id) {
-		return terms.get(id.toLowerCase());
+		return Optional.ofNullable(id).map(s -> s.toLowerCase()).map(s -> terms.get(s)).orElse(null);
 	}
 
 	protected void addTerm(final String id, final String name) {
@@ -40,4 +55,32 @@ public class Vocabulary implements Serializable {
 	protected boolean termExists(final String id) {
 		return terms.containsKey(id.toLowerCase());
 	}
+
+	protected void addSynonym(final String syn, final String termCode) {
+		synonyms.put(syn, termCode.toLowerCase());
+	}
+
+	public VocabularyTerm getTermBySynonym(final String syn) {
+		return getTerm(synonyms.get(syn));
+	}
+
+	public Qualifier getTermAsQualifier(final String termId) {
+		if (StringUtils.isBlank(termId)) {
+			return OafMapperUtils.unknown(getId(), getName());
+		} else if (termExists(termId)) {
+			final VocabularyTerm t = getTerm(termId);
+			return OafMapperUtils.qualifier(t.getId(), t.getName(), getId(), getName());
+		} else {
+			return OafMapperUtils.qualifier(termId, termId, getId(), getName());
+		}
+	}
+
+	public Qualifier getSynonymAsQualifier(final String syn) {
+		return Optional
+			.ofNullable(getTermBySynonym(syn))
+			.map(term -> getTermAsQualifier(term.getId()))
+			.orElse(null);
+		// .orElse(OafMapperUtils.unknown(getId(), getName()));
+	}
+
 }

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

@@ -1,33 +1,39 @@
 
 package eu.dnetlib.dhp.oa.graph.raw.common;
 
-import java.io.IOException;
 import java.io.Serializable;
-import java.util.HashMap;
+import java.util.*;
-import java.util.Map;
+import java.util.function.Supplier;
+import java.util.stream.Collectors;
 
-import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 
-import eu.dnetlib.dhp.oa.graph.raw.GenerateEntitiesApplication;
 import eu.dnetlib.dhp.schema.oaf.Qualifier;
-import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 
 public class VocabularyGroup implements Serializable {
 
-	public static VocabularyGroup loadVocsFromIS(final String isLookupUrl) throws IOException, ISLookUpException {
+	public static final String VOCABULARIES_XQUERY = "for $x in collection(' /db/DRIVER/VocabularyDSResources/VocabularyDSResourceType') \n"
-		final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl);
+		+
+		"let $vocid := $x//VOCABULARY_NAME/@code\n" +
+		"let $vocname := $x//VOCABULARY_NAME/text()\n" +
+		"for $term in ($x//TERM)\n" +
+		"return concat($vocid,' @=@ ',$vocname,' @=@ ',$term/@code,' @=@ ',$term/@english_name)";
 
-		final String xquery = IOUtils
+	public static final String VOCABULARY_SYNONYMS_XQUERY = "for $x in collection('/db/DRIVER/VocabularyDSResources/VocabularyDSResourceType')\n"
-			.toString(
+		+
-				GenerateEntitiesApplication.class
+		"let $vocid := $x//VOCABULARY_NAME/@code\n" +
-					.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery"));
+		"let $vocname := $x//VOCABULARY_NAME/text()\n" +
+		"for $term in ($x//TERM)\n" +
+		"for $syn in ($term//SYNONYM/@term)\n" +
+		"return concat($vocid,' @=@ ',$term/@code,' @=@ ', $syn)\n";
+
+	public static VocabularyGroup loadVocsFromIS(ISLookUpService isLookUpService) throws ISLookUpException {
 
 		final VocabularyGroup vocs = new VocabularyGroup();
 
-		for (final String s : isLookUpService.quickSearchProfile(xquery)) {
+		for (final String s : isLookUpService.quickSearchProfile(VOCABULARIES_XQUERY)) {
 			final String[] arr = s.split("@=@");
 			if (arr.length == 4) {
 				final String vocId = arr[0].trim();
@@ -40,6 +46,19 @@ public class VocabularyGroup implements Serializable {
 				}
 
 				vocs.addTerm(vocId, termId, termName);
+				vocs.addSynonyms(vocId, termId, termId);
+			}
+		}
+
+		for (final String s : isLookUpService.quickSearchProfile(VOCABULARY_SYNONYMS_XQUERY)) {
+			final String[] arr = s.split("@=@");
+			if (arr.length == 3) {
+				final String vocId = arr[0].trim();
+				final String termId = arr[1].trim();
+				final String syn = arr[2].trim();
+
+				vocs.addSynonyms(vocId, termId, syn);
+				vocs.addSynonyms(vocId, termId, termId);
 			}
 		}
 
@@ -66,16 +85,37 @@ public class VocabularyGroup implements Serializable {
 		}
 	}
 
-	public Qualifier getTermAsQualifier(final String vocId, final String id) {
+	public Set<String> getTerms(String vocId) {
-		if (StringUtils.isBlank(id)) {
+		if (!vocabularyExists(vocId)) {
-			return OafMapperUtils.qualifier("UNKNOWN", "UNKNOWN", vocId, vocId);
+			return new HashSet<>();
-		} else if (termExists(vocId, id)) {
-			final Vocabulary v = vocs.get(vocId.toLowerCase());
-			final VocabularyTerm t = v.getTerm(id);
-			return OafMapperUtils.qualifier(t.getId(), t.getName(), v.getId(), v.getName());
-		} else {
-			return OafMapperUtils.qualifier(id, id, vocId, vocId);
 		}
+		return vocs
+			.get(vocId.toLowerCase())
+			.getTerms()
+			.values()
+			.stream()
+			.map(t -> t.getId())
+			.collect(Collectors.toCollection(HashSet::new));
+	}
+
+	public Qualifier lookup(String vocId, String id) {
+		return Optional
+			.ofNullable(getSynonymAsQualifier(vocId, id))
+			.orElse(getTermAsQualifier(vocId, id));
+	}
+
+	public Qualifier getTermAsQualifier(final String vocId, final String id) {
+		if (vocabularyExists(vocId)) {
+			return vocs.get(vocId.toLowerCase()).getTermAsQualifier(id);
+		}
+		return OafMapperUtils.qualifier(id, id, "", "");
+	}
+
+	public Qualifier getSynonymAsQualifier(final String vocId, final String syn) {
+		if (StringUtils.isBlank(vocId)) {
+			return OafMapperUtils.unknown("", "");
+		}
+		return vocs.get(vocId.toLowerCase()).getSynonymAsQualifier(syn);
 	}
 
 	public boolean termExists(final String vocId, final String id) {
@@ -86,4 +126,16 @@ public class VocabularyGroup implements Serializable {
 		return vocs.containsKey(vocId.toLowerCase());
 	}
 
+	private void addSynonyms(final String vocId, final String termId, final String syn) {
+		String id = Optional
+			.ofNullable(vocId)
+			.map(s -> s.toLowerCase())
+			.orElseThrow(
+				() -> new IllegalArgumentException(String.format("empty vocabulary id for [term:%s, synonym:%s]")));
+		Optional
+			.ofNullable(vocs.get(id))
+			.orElseThrow(() -> new IllegalArgumentException("missing vocabulary id: " + vocId))
+			.addSynonym(syn, termId);
+	}
+
 }

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/config-default.xml

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

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

@@ -0,0 +1,289 @@
+<workflow-app name="clean graph" xmlns="uri:oozie:workflow:0.5">
+
+    <parameters>
+        <property>
+            <name>graphInputPath</name>
+            <description>the input path to read graph content</description>
+        </property>
+        <property>
+            <name>graphOutputPath</name>
+            <description>the target path to store cleaned graph</description>
+        </property>
+        <property>
+            <name>isLookupUrl</name>
+            <description>the address of the lookUp service</description>
+        </property>
+
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
+        <property>
+            <name>spark2YarnHistoryServerAddress</name>
+            <description>spark 2.* yarn history server address</description>
+        </property>
+        <property>
+            <name>spark2EventLogDir</name>
+            <description>spark 2.* event log dir location</description>
+        </property>
+    </parameters>
+
+	<start to="fork_clean_graph"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <fork name="fork_clean_graph">
+        <path start="clean_publication"/>
+        <path start="clean_dataset"/>
+        <path start="clean_otherresearchproduct"/>
+        <path start="clean_software"/>
+        <path start="clean_datasource"/>
+        <path start="clean_organization"/>
+        <path start="clean_project"/>
+        <path start="clean_relation"/>
+    </fork>
+
+    <action name="clean_publication">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Clean publications</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.network.timeout=${sparkNetworkTimeout}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${graphInputPath}/publication</arg>
+            <arg>--outputPath</arg><arg>${graphOutputPath}/publication</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+        </spark>
+        <ok to="wait_clean"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="clean_dataset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Clean datasets</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.network.timeout=${sparkNetworkTimeout}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${graphInputPath}/dataset</arg>
+            <arg>--outputPath</arg><arg>${graphOutputPath}/dataset</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+        </spark>
+        <ok to="wait_clean"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="clean_otherresearchproduct">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Clean otherresearchproducts</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.network.timeout=${sparkNetworkTimeout}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${graphInputPath}/otherresearchproduct</arg>
+            <arg>--outputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+        </spark>
+        <ok to="wait_clean"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="clean_software">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Clean softwares</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.network.timeout=${sparkNetworkTimeout}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${graphInputPath}/software</arg>
+            <arg>--outputPath</arg><arg>${graphOutputPath}/software</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+        </spark>
+        <ok to="wait_clean"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="clean_datasource">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Clean datasources</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.network.timeout=${sparkNetworkTimeout}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${graphInputPath}/datasource</arg>
+            <arg>--outputPath</arg><arg>${graphOutputPath}/datasource</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+        </spark>
+        <ok to="wait_clean"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="clean_organization">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Clean organizations</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.network.timeout=${sparkNetworkTimeout}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${graphInputPath}/organization</arg>
+            <arg>--outputPath</arg><arg>${graphOutputPath}/organization</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+        </spark>
+        <ok to="wait_clean"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="clean_project">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Clean projects</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.network.timeout=${sparkNetworkTimeout}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${graphInputPath}/project</arg>
+            <arg>--outputPath</arg><arg>${graphOutputPath}/project</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+        </spark>
+        <ok to="wait_clean"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="clean_relation">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Clean relations</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.network.timeout=${sparkNetworkTimeout}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${graphInputPath}/relation</arg>
+            <arg>--outputPath</arg><arg>${graphOutputPath}/relation</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+        </spark>
+        <ok to="wait_clean"/>
+        <error to="Kill"/>
+    </action>
+
+    <join name="wait_clean" to="End"/>
+
+    <end name="End"/>
+</workflow-app>

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

@@ -0,0 +1,32 @@
+[
+  {
+    "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": "out",
+    "paramLongName": "outputPath",
+    "paramDescription": "the path to store the output graph",
+    "paramRequired": true
+  },
+  {
+    "paramName": "isu",
+    "paramLongName": "isLookupUrl",
+    "paramDescription": "url to the ISLookup Service",
+    "paramRequired": true
+  },
+  {
+    "paramName": "class",
+    "paramLongName": "graphTableClassName",
+    "paramDescription": "class name moelling the graph table",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies_synonyms.xquery

@@ -0,0 +1,6 @@
+for $x in collection('/db/DRIVER/VocabularyDSResources/VocabularyDSResourceType')
+let $vocid := $x//VOCABULARY_NAME/@code
+let $vocname := $x//VOCABULARY_NAME/text()
+	for $term in ($x//TERM)
+		for $syn in ($term//SYNONYM/@term)
+			return concat($vocid,' @=@ ',$term/@code,' @=@ ', $syn)

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

@@ -0,0 +1,112 @@
+
+package eu.dnetlib.dhp.oa.graph.clean;
+
+import static org.junit.jupiter.api.Assertions.*;
+import static org.mockito.Mockito.lenient;
+
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import org.apache.commons.io.IOUtils;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.platform.commons.util.StringUtils;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
+import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyTerm;
+import eu.dnetlib.dhp.schema.oaf.Publication;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+
+@ExtendWith(MockitoExtension.class)
+public class CleaningRuleTest {
+
+	public static final ObjectMapper MAPPER = new ObjectMapper();
+
+	@Mock
+	private ISLookUpService isLookUpService;
+
+	private VocabularyGroup vocabularies;
+
+	private CleaningRule<Publication> cleaningRule;
+
+	@BeforeEach
+	public void setUp() throws ISLookUpException, IOException {
+		lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs());
+		lenient()
+			.when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY))
+			.thenReturn(synonyms());
+
+		vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService);
+		cleaningRule = new CleaningRule(vocabularies);
+	}
+
+	@Test
+	public void testCleaning() throws Exception {
+
+		assertNotNull(cleaningRule.getVocabularies());
+
+		String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json"));
+		Publication p_in = MAPPER.readValue(json, Publication.class);
+
+		Publication p_out = cleaningRule.call(p_in);
+
+		assertNotNull(p_out);
+
+		assertEquals("eng", p_out.getLanguage().getClassid());
+		assertEquals("English", p_out.getLanguage().getClassname());
+
+		assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid());
+		assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname());
+
+		assertEquals("CLOSED", p_out.getInstance().get(0).getAccessright().getClassid());
+		assertEquals("Closed Access", p_out.getInstance().get(0).getAccessright().getClassname());
+
+		Set<String> pidTerms = vocabularies.getTerms("dnet:pid_types");
+		assertTrue(
+			p_out
+				.getPid()
+				.stream()
+				.map(p -> p.getQualifier())
+				.allMatch(q -> pidTerms.contains(q.getClassid())));
+
+		// TODO add more assertions to verity the cleaned values
+		System.out.println(MAPPER.writeValueAsString(p_out));
+
+		assertTrue(
+			p_out
+				.getPid()
+				.stream()
+				.allMatch(sp -> StringUtils.isNotBlank(sp.getValue())));
+	}
+
+	private Stream<Qualifier> getAuthorPidTypes(Publication pub) {
+		return pub
+			.getAuthor()
+			.stream()
+			.map(a -> a.getPid())
+			.flatMap(p -> p.stream())
+			.map(s -> s.getQualifier());
+	}
+
+	private List<String> vocs() throws IOException {
+		return IOUtils
+			.readLines(CleaningRuleTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt"));
+	}
+
+	private List<String> synonyms() throws IOException {
+		return IOUtils
+			.readLines(CleaningRuleTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"));
+	}
+}

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

@@ -0,0 +1,757 @@
+{
+  "author": [
+    {
+      "affiliation": [
+      ],
+      "fullname": "Brien, Tom",
+      "name": "Tom",
+      "pid": [
+        {
+          "dataInfo": {
+            "deletedbyinference": false,
+            "inferenceprovenance": "",
+            "inferred": false,
+            "invisible": false,
+            "provenanceaction": {
+              "classid": "sysimport:crosswalk:datasetarchive",
+              "classname": "sysimport:crosswalk:datasetarchive",
+              "schemeid": "dnet:provenanceActions",
+              "schemename": "dnet:provenanceActions"
+            },
+            "trust": "0.9"
+          },
+          "qualifier": {
+            "classid": "ORCID12",
+            "classname": "ORCID12",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "0000-0001-9613-6639"
+        }
+      ],
+      "rank": 1,
+      "surname": "Brien"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Ade, Peter",
+      "name": "Peter",
+      "pid": [
+        {
+          "dataInfo": {
+            "deletedbyinference": false,
+            "inferenceprovenance": "",
+            "inferred": false,
+            "invisible": false,
+            "provenanceaction": {
+              "classid": "sysimport:crosswalk:datasetarchive",
+              "classname": "sysimport:crosswalk:datasetarchive",
+              "schemeid": "dnet:provenanceActions",
+              "schemename": "dnet:provenanceActions"
+            },
+            "trust": "0.9"
+          },
+          "qualifier": {
+            "classid": "xyz",
+            "classname": "XYZ",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "qwerty"
+        }
+      ],
+      "rank": 2,
+      "surname": "Ade"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Barry, Peter S.",
+      "name": "Peter S.",
+      "pid": [
+      ],
+      "rank": 3,
+      "surname": "Barry"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Dunscombe, Chris J.",
+      "name": "Chris J.",
+      "pid": [
+      ],
+      "rank": 4,
+      "surname": "Dunscombe"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Leadley, David R.",
+      "name": "David R.",
+      "pid": [
+      ],
+      "rank": 5,
+      "surname": "Leadley"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Morozov, Dmitry V.",
+      "name": "Dmitry V.",
+      "pid": [
+      ],
+      "rank": 6,
+      "surname": "Morozov"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Myronov, Maksym",
+      "name": "Maksym",
+      "pid": [
+      ],
+      "rank": 7,
+      "surname": "Myronov"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Parker, Evan",
+      "name": "Evan",
+      "pid": [
+      ],
+      "rank": 8,
+      "surname": "Parker"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Prest, Martin J.",
+      "name": "Martin J.",
+      "pid": [
+      ],
+      "rank": 9,
+      "surname": "Prest"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Prunnila, Mika",
+      "name": "Mika",
+      "pid": [
+      ],
+      "rank": 10,
+      "surname": "Prunnila"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Sudiwala, Rashmi V.",
+      "name": "Rashmi V.",
+      "pid": [
+      ],
+      "rank": 11,
+      "surname": "Sudiwala"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Whall, Terry E.",
+      "name": "Terry E.",
+      "pid": [
+      ],
+      "rank": 12,
+      "surname": "Whall"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Mauskopf",
+      "name": "",
+      "pid": [
+      ],
+      "rank": 13,
+      "surname": ""
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": " P. D. ",
+      "name": "",
+      "pid": [
+      ],
+      "rank": 14,
+      "surname": ""
+    }
+  ],
+  "bestaccessright": {
+    "classid": "CLOSED",
+    "classname": "Closed Access",
+    "schemeid": "dnet:access_modes",
+    "schemename": "dnet:access_modes"
+  },
+  "collectedfrom": [
+    {
+      "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
+      "value": "VIRTA"
+    }
+  ],
+  "context": [
+  ],
+  "contributor": [
+  ],
+  "country": [
+  ],
+  "coverage": [
+  ],
+  "dataInfo": {
+    "deletedbyinference": false,
+    "inferenceprovenance": "",
+    "inferred": false,
+    "invisible": false,
+    "provenanceaction": {
+      "classid": "sysimport:crosswalk:datasetarchive",
+      "classname": "sysimport:crosswalk:datasetarchive",
+      "schemeid": "dnet:provenanceActions",
+      "schemename": "dnet:provenanceActions"
+    },
+    "trust": "0.9"
+  },
+  "dateofacceptance": {
+    "dataInfo": {
+      "deletedbyinference": false,
+      "inferenceprovenance": "",
+      "inferred": false,
+      "invisible": false,
+      "provenanceaction": {
+        "classid": "sysimport:crosswalk:datasetarchive",
+        "classname": "sysimport:crosswalk:datasetarchive",
+        "schemeid": "dnet:provenanceActions",
+        "schemename": "dnet:provenanceActions"
+      },
+      "trust": "0.9"
+    },
+    "value": "2016-01-01"
+  },
+  "dateofcollection": "",
+  "dateoftransformation": "2020-04-22T12:34:08.009Z",
+  "description": [
+  ],
+  "externalReference": [
+  ],
+  "extraInfo": [
+  ],
+  "format": [
+  ],
+  "fulltext": [
+  ],
+  "id": "50|CSC_________::2250a70c903c6ac6e4c01438259e9375",
+  "instance": [
+    {
+      "accessright": {
+        "classid": "CLOSED",
+        "classname": "CLOSED",
+        "schemeid": "dnet:access_modes",
+        "schemename": "dnet:access_modes"
+      },
+      "collectedfrom": {
+        "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
+        "value": "VIRTA"
+      },
+      "dateofacceptance": {
+        "dataInfo": {
+          "deletedbyinference": false,
+          "inferenceprovenance": "",
+          "inferred": false,
+          "invisible": false,
+          "provenanceaction": {
+            "classid": "sysimport:crosswalk:datasetarchive",
+            "classname": "sysimport:crosswalk:datasetarchive",
+            "schemeid": "dnet:provenanceActions",
+            "schemename": "dnet:provenanceActions"
+          },
+          "trust": "0.9"
+        },
+        "value": "2016-01-01"
+      },
+      "distributionlocation": "",
+      "hostedby": {
+        "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
+        "value": "VIRTA"
+      },
+      "instancetype": {
+        "classid": "Comentario",
+        "classname": "Comentario",
+        "schemeid": "dnet:publication_resource",
+        "schemename": "dnet:publication_resource"
+      },
+      "url": [
+        "http://juuli.fi/Record/0275158616",
+        "http://dx.doi.org/10.1007/s109090161569x"
+      ]
+    }
+  ],
+  "journal": {
+    "dataInfo": {
+      "deletedbyinference": false,
+      "inferenceprovenance": "",
+      "inferred": false,
+      "invisible": false,
+      "provenanceaction": {
+        "classid": "sysimport:crosswalk:datasetarchive",
+        "classname": "sysimport:crosswalk:datasetarchive",
+        "schemeid": "dnet:provenanceActions",
+        "schemename": "dnet:provenanceActions"
+      },
+      "trust": "0.9"
+    },
+    "edition": "",
+    "ep": " 7",
+    "iss": "9 March",
+    "issnLinking": "",
+    "issnOnline": "",
+    "issnPrinted": "0022-2291",
+    "name": "Journal of Low Temperature Physics - Early Acces",
+    "sp": "1 ",
+    "vol": ""
+  },
+  "language": {
+    "classid": "en",
+    "classname": "en",
+    "schemeid": "dnet:languages",
+    "schemename": "dnet:languages"
+  },
+  "lastupdatetimestamp": 1591283286319,
+  "oaiprovenance": {
+    "originDescription": {
+      "altered": true,
+      "baseURL": "https%3A%2F%2Fvirta-jtp.csc.fi%2Fapi%2Fcerif",
+      "datestamp": "2019-07-30",
+      "harvestDate": "2020-04-22T11:04:38.685Z",
+      "identifier": "oai:virta-jtp.csc.fi:Publications/0275158616",
+      "metadataNamespace": ""
+    }
+  },
+  "originalId": [
+    "CSC_________::2250a70c903c6ac6e4c01438259e9375"
+  ],
+  "pid": [
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "doi",
+        "classname": "doi",
+        "schemeid": "dnet:pid_types",
+        "schemename": "dnet:pid_types"
+      },
+      "value": "10.1007/s109090161569x"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "doi",
+        "classname": "doi",
+        "schemeid": "dnet:pid_types",
+        "schemename": "dnet:pid_types"
+      },
+      "value": "10.1007/s109090161569x"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "doi",
+        "classname": "doi",
+        "schemeid": "dnet:pid_types",
+        "schemename": "dnet:pid_types"
+      },
+      "value": ""
+    }
+  ],
+  "relevantdate": [
+  ],
+  "resourcetype": {
+    "classid": "0001",
+    "classname": "0001",
+    "schemeid": "dnet:dataCite_resource",
+    "schemename": "dnet:dataCite_resource"
+  },
+  "resulttype": {
+    "classid": "publication",
+    "classname": "publication",
+    "schemeid": "dnet:result_typologies",
+    "schemename": "dnet:result_typologies"
+  },
+  "source": [
+  ],
+  "subject": [
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "ta213"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "infrared detectors"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "lens antennas"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "silicon"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "slot antennas"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "strained silicon"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "cold electron bolometers"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "doped silicon"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "measure noise"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "noise equivalent power"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "optical characterisation"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "optical response"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "photon noise"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "value": "silicon absorbers"
+    }
+  ],
+  "title": [
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "main title",
+        "classname": "main title",
+        "schemeid": "dnet:dataCite_title",
+        "schemename": "dnet:dataCite_title"
+      },
+      "value": "Optical response of strained- and unstrained-silicon cold-electron bolometers"
+    }
+  ]
+}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java

@@ -1168,10 +1168,10 @@ public class XmlRecordFactory implements Serializable {
 									.asXmlElement(
 										"distributionlocation", instance.getDistributionlocation()));
 					}
-					if (instance.getRefereed() != null && isNotBlank(instance.getRefereed().getValue())) {
+					if (instance.getRefereed() != null && !instance.getRefereed().isBlank()) {
 						fields
 							.add(
-								XmlSerializationUtils.asXmlElement("refereed", instance.getRefereed().getValue()));
+								XmlSerializationUtils.mapQualifier("refereed", instance.getRefereed()));
 					}
 					if (instance.getProcessingchargeamount() != null
 						&& isNotBlank(instance.getProcessingchargeamount().getValue())) {