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

dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java

@@ -1,6 +1,24 @@
 
 package eu.dnetlib.dhp.oa.merge;
 
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static org.apache.spark.sql.functions.col;
+import static org.apache.spark.sql.functions.when;
+
+import java.util.Map;
+import java.util.Optional;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ForkJoinPool;
+import java.util.stream.Collectors;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.api.java.function.ReduceFunction;
+import org.apache.spark.sql.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
@@ -12,25 +30,8 @@ import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
-import org.apache.commons.io.IOUtils;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.api.java.function.ReduceFunction;
-import org.apache.spark.sql.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import scala.Tuple2;
 
-import java.util.Map;
-import java.util.Optional;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ForkJoinPool;
-import java.util.stream.Collectors;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import static org.apache.spark.sql.functions.col;
-import static org.apache.spark.sql.functions.when;
-
 /**
  * Groups the graph content by entity identifier to ensure ID uniqueness
  */

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

@@ -0,0 +1,76 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import java.util.HashSet;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.Set;
+
+import org.apache.commons.lang3.StringUtils;
+
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+
+public class CleaningFunctions {
+
+	public static final String DOI_PREFIX_REGEX = "(^10\\.|\\/10\\.)";
+	public static final String DOI_PREFIX = "10.";
+
+	public static final Set<String> PID_BLACKLIST = new HashSet<>();
+
+	static {
+		PID_BLACKLIST.add("none");
+		PID_BLACKLIST.add("na");
+	}
+
+	public CleaningFunctions() {
+	}
+
+	/**
+	 * Utility method that filter PID values on a per-type basis.
+	 * @param s the PID whose value will be checked.
+	 * @return false if the pid matches the filter criteria, true otherwise.
+	 */
+	public static boolean pidFilter(StructuredProperty s) {
+		final String pidValue = s.getValue();
+		if (Objects.isNull(s.getQualifier()) ||
+			StringUtils.isBlank(pidValue) ||
+			StringUtils.isBlank(pidValue.replaceAll("(?:\\n|\\r|\\t|\\s)", ""))) {
+			return false;
+		}
+		if (CleaningFunctions.PID_BLACKLIST.contains(pidValue)) {
+			return false;
+		}
+		return !PidBlacklistProvider.getBlacklist(s.getQualifier().getClassid()).contains(pidValue);
+	}
+
+	/**
+	 * Utility method that normalises PID values on a per-type basis.
+	 * @param pid the PID whose value will be normalised.
+	 * @return the PID containing the normalised value.
+	 */
+	public static StructuredProperty normalizePidValue(StructuredProperty pid) {
+		pid
+			.setValue(
+				normalizePidValue(
+					pid.getQualifier().getClassid(),
+					pid.getValue()));
+
+		return pid;
+	}
+
+	public static String normalizePidValue(String pidType, String pidValue) {
+		String value = Optional
+			.ofNullable(pidValue)
+			.map(String::trim)
+			.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
+
+		switch (pidType) {
+
+			// TODO add cleaning for more PID types as needed
+			case "doi":
+				return value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX);
+		}
+		return value;
+	}
+
+}

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

@@ -506,6 +506,8 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 								.filter(Objects::nonNull)
 								.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
 								.map(GraphCleaningFunctions::cleanValue)
+								.sorted((s1, s2) -> s2.getValue().length() - s1.getValue().length())
+								.limit(ModelHardLimits.MAX_ABSTRACTS)
 								.collect(Collectors.toList()));
 				}
 				if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {

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

@@ -0,0 +1,294 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import static com.google.common.base.Preconditions.checkArgument;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
+
+import java.io.Serializable;
+import java.nio.charset.StandardCharsets;
+import java.security.MessageDigest;
+import java.util.*;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import org.apache.commons.codec.binary.Hex;
+import org.apache.commons.lang3.StringUtils;
+
+import com.google.common.collect.HashBiMap;
+import com.google.common.collect.Maps;
+
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.*;
+
+/**
+ * Factory class for OpenAIRE identifiers in the Graph
+ */
+public class IdentifierFactory implements Serializable {
+
+	public static final String ID_SEPARATOR = "::";
+	public static final String ID_PREFIX_SEPARATOR = "|";
+
+	public static final int ID_PREFIX_LEN = 12;
+
+	/**
+	 * Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] considered authoritative for that PID_TYPE.
+	 * The id of the record (source_::id) will be rewritten as pidType_::id)
+	 */
+	public static final Map<PidType, HashBiMap<String, String>> PID_AUTHORITY = Maps.newHashMap();
+
+	static {
+		PID_AUTHORITY.put(PidType.doi, HashBiMap.create());
+		PID_AUTHORITY.get(PidType.doi).put(CROSSREF_ID, "Crossref");
+		PID_AUTHORITY.get(PidType.doi).put(DATACITE_ID, "Datacite");
+		PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "ZENODO");
+		PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "Zenodo");
+
+		PID_AUTHORITY.put(PidType.pmc, HashBiMap.create());
+		PID_AUTHORITY.get(PidType.pmc).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
+		PID_AUTHORITY.get(PidType.pmc).put(PUBMED_CENTRAL_ID, "PubMed Central");
+
+		PID_AUTHORITY.put(PidType.pmid, HashBiMap.create());
+		PID_AUTHORITY.get(PidType.pmid).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
+		PID_AUTHORITY.get(PidType.pmid).put(PUBMED_CENTRAL_ID, "PubMed Central");
+
+		PID_AUTHORITY.put(PidType.arXiv, HashBiMap.create());
+		PID_AUTHORITY.get(PidType.arXiv).put(ARXIV_ID, "arXiv.org e-Print Archive");
+
+		PID_AUTHORITY.put(PidType.w3id, HashBiMap.create());
+		PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ROHub");
+	}
+
+	/**
+	 * Declares the associations PID_TYPE -> [DATASOURCE ID, PID SUBSTRING] considered as delegated authority for that
+	 * PID_TYPE. Example, Zenodo is delegated to forge DOIs that contain the 'zenodo' word.
+	 *
+	 * If a record with the same id (same pid) comes from 2 data sources, the one coming from a delegated source wins. E.g. Zenodo records win over those from Datacite.
+	 * See also https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/187 and the class dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
+	 */
+	public static final Map<PidType, Map<String, String>> DELEGATED_PID_AUTHORITY = Maps.newHashMap();
+
+	static {
+		DELEGATED_PID_AUTHORITY.put(PidType.doi, new HashMap<>());
+		DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "zenodo");
+		DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "zenodo");
+		DELEGATED_PID_AUTHORITY.put(PidType.w3id, new HashMap<>());
+		DELEGATED_PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ro-id");
+	}
+
+	/**
+	 * Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] whose records are considered enrichment for the graph.
+	 * Their OpenAIRE ID is built from the declared PID type. Are merged with their corresponding record, identified by
+	 * the same OpenAIRE id.
+	 */
+	public static final Map<PidType, HashBiMap<String, String>> ENRICHMENT_PROVIDER = Maps.newHashMap();
+
+	static {
+		ENRICHMENT_PROVIDER.put(PidType.doi, HashBiMap.create());
+		ENRICHMENT_PROVIDER.get(PidType.doi).put(OPEN_APC_ID, OPEN_APC_NAME);
+	}
+
+	public static Set<String> delegatedAuthorityDatasourceIds() {
+		return DELEGATED_PID_AUTHORITY
+			.values()
+			.stream()
+			.flatMap(m -> m.keySet().stream())
+			.collect(Collectors.toCollection(HashSet::new));
+	}
+
+	public static List<StructuredProperty> getPids(List<StructuredProperty> pid, KeyValue collectedFrom) {
+		return pidFromInstance(pid, collectedFrom, true).distinct().collect(Collectors.toList());
+	}
+
+	public static <T extends Result> String createDOIBoostIdentifier(T entity) {
+		if (entity == null)
+			return null;
+
+		StructuredProperty pid = null;
+		if (entity.getPid() != null) {
+			pid = entity
+				.getPid()
+				.stream()
+				.filter(Objects::nonNull)
+				.filter(s -> s.getQualifier() != null && "doi".equalsIgnoreCase(s.getQualifier().getClassid()))
+				.filter(CleaningFunctions::pidFilter)
+				.findAny()
+				.orElse(null);
+		} else {
+			if (entity.getInstance() != null) {
+				pid = entity
+					.getInstance()
+					.stream()
+					.filter(i -> i.getPid() != null)
+					.flatMap(i -> i.getPid().stream())
+					.filter(CleaningFunctions::pidFilter)
+					.findAny()
+					.orElse(null);
+			}
+		}
+		if (pid != null)
+			return idFromPid(entity, pid, true);
+		return null;
+	}
+
+	/**
+	 * Creates an identifier from the most relevant PID (if available) provided by a known PID authority in the given
+	 * entity T. Returns entity.id when none of the PIDs meet the selection criteria is available.
+	 *
+	 * @param entity the entity providing PIDs and a default ID.
+	 * @param <T> the specific entity type. Currently Organization and Result subclasses are supported.
+	 * @param md5 indicates whether should hash the PID value or not.
+	 * @return an identifier from the most relevant PID, entity.id otherwise
+	 */
+	public static <T extends OafEntity> String createIdentifier(T entity, boolean md5) {
+
+		checkArgument(StringUtils.isNoneBlank(entity.getId()), "missing entity identifier");
+
+		final Map<String, Set<StructuredProperty>> pids = extractPids(entity);
+
+		return pids
+			.values()
+			.stream()
+			.flatMap(Set::stream)
+			.min(new PidComparator<>(entity))
+			.map(
+				min -> Optional
+					.ofNullable(pids.get(min.getQualifier().getClassid()))
+					.map(
+						p -> p
+							.stream()
+							.sorted(new PidValueComparator())
+							.findFirst()
+							.map(s -> idFromPid(entity, s, md5))
+							.orElseGet(entity::getId))
+					.orElseGet(entity::getId))
+			.orElseGet(entity::getId);
+	}
+
+	private static <T extends OafEntity> Map<String, Set<StructuredProperty>> extractPids(T entity) {
+		if (entity instanceof Result) {
+			return Optional
+				.ofNullable(((Result) entity).getInstance())
+				.map(IdentifierFactory::mapPids)
+				.orElse(new HashMap<>());
+		} else {
+			return entity
+				.getPid()
+				.stream()
+				.map(CleaningFunctions::normalizePidValue)
+				.filter(CleaningFunctions::pidFilter)
+				.collect(
+					Collectors
+						.groupingBy(
+							p -> p.getQualifier().getClassid(),
+							Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
+		}
+	}
+
+	private static Map<String, Set<StructuredProperty>> mapPids(List<Instance> instance) {
+		return instance
+			.stream()
+			.map(i -> pidFromInstance(i.getPid(), i.getCollectedfrom(), false))
+			.flatMap(Function.identity())
+			.collect(
+				Collectors
+					.groupingBy(
+						p -> p.getQualifier().getClassid(),
+						Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
+	}
+
+	private static Stream<StructuredProperty> pidFromInstance(List<StructuredProperty> pid, KeyValue collectedFrom,
+		boolean mapHandles) {
+		return Optional
+			.ofNullable(pid)
+			.map(
+				pp -> pp
+					.stream()
+					// filter away PIDs provided by a DS that is not considered an authority for the
+					// given PID Type
+					.filter(p -> shouldFilterPidByCriteria(collectedFrom, p, mapHandles))
+					.map(CleaningFunctions::normalizePidValue)
+					.filter(p -> isNotFromDelegatedAuthority(collectedFrom, p))
+					.filter(CleaningFunctions::pidFilter))
+			.orElse(Stream.empty());
+	}
+
+	private static boolean shouldFilterPidByCriteria(KeyValue collectedFrom, StructuredProperty p, boolean mapHandles) {
+		final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
+
+		if (Objects.isNull(collectedFrom)) {
+			return false;
+		}
+
+		boolean isEnrich = Optional
+			.ofNullable(ENRICHMENT_PROVIDER.get(pType))
+			.map(
+				enrich -> enrich.containsKey(collectedFrom.getKey())
+					|| enrich.containsValue(collectedFrom.getValue()))
+			.orElse(false);
+
+		boolean isAuthority = Optional
+			.ofNullable(PID_AUTHORITY.get(pType))
+			.map(
+				authorities -> authorities.containsKey(collectedFrom.getKey())
+					|| authorities.containsValue(collectedFrom.getValue()))
+			.orElse(false);
+
+		return (mapHandles && pType.equals(PidType.handle)) || isEnrich || isAuthority;
+	}
+
+	private static boolean isNotFromDelegatedAuthority(KeyValue collectedFrom, StructuredProperty p) {
+		final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
+
+		final Map<String, String> da = DELEGATED_PID_AUTHORITY.get(pType);
+		if (Objects.isNull(da)) {
+			return true;
+		}
+		if (!da.containsKey(collectedFrom.getKey())) {
+			return true;
+		}
+		return StringUtils.contains(p.getValue(), da.get(collectedFrom.getKey()));
+	}
+
+	/**
+	 * @see {@link IdentifierFactory#createIdentifier(OafEntity, boolean)}
+	 */
+	public static <T extends OafEntity> String createIdentifier(T entity) {
+
+		return createIdentifier(entity, true);
+	}
+
+	private static <T extends OafEntity> String idFromPid(T entity, StructuredProperty s, boolean md5) {
+		return idFromPid(ModelSupport.getIdPrefix(entity.getClass()), s.getQualifier().getClassid(), s.getValue(), md5);
+	}
+
+	public static String idFromPid(String numericPrefix, String pidType, String pidValue, boolean md5) {
+		return new StringBuilder()
+			.append(numericPrefix)
+			.append(ID_PREFIX_SEPARATOR)
+			.append(createPrefix(pidType))
+			.append(ID_SEPARATOR)
+			.append(md5 ? md5(pidValue) : pidValue)
+			.toString();
+	}
+
+	// create the prefix (length = 12)
+	private static String createPrefix(String pidType) {
+		StringBuilder prefix = new StringBuilder(StringUtils.left(pidType, ID_PREFIX_LEN));
+		while (prefix.length() < ID_PREFIX_LEN) {
+			prefix.append("_");
+		}
+		return prefix.substring(0, ID_PREFIX_LEN);
+	}
+
+	public static String md5(final String s) {
+		try {
+			final MessageDigest md = MessageDigest.getInstance("MD5");
+			md.update(s.getBytes(StandardCharsets.UTF_8));
+			return new String(Hex.encodeHex(md.digest()));
+		} catch (final Exception e) {
+			return null;
+		}
+	}
+
+}

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

@@ -1,22 +1,21 @@
+
 package eu.dnetlib.dhp.schema.oaf.utils;
 
-//
-// Source code recreated from a .class file by IntelliJ IDEA
-// (powered by FernFlower decompiler)
-//
-
-
-import eu.dnetlib.dhp.schema.common.EntityType;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
-import eu.dnetlib.dhp.schema.oaf.Oaf;
-import eu.dnetlib.dhp.schema.oaf.OafEntity;
-import eu.dnetlib.dhp.schema.oaf.Result;
-
 import java.util.Comparator;
 import java.util.HashSet;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+// 
+// Source code recreated from a .class file by IntelliJ IDEA
+// (powered by FernFlower decompiler)
+//
+import eu.dnetlib.dhp.schema.common.EntityType;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
 public class MergeComparator implements Comparator<Oaf> {
 	public MergeComparator() {
 	}
@@ -41,14 +40,14 @@ public class MergeComparator implements Comparator<Oaf> {
 		// collectedfrom
 		HashSet<String> lCf = getCollectedFromIds(left);
 		HashSet<String> rCf = getCollectedFromIds(right);
-        if (lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && !rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
+		if (lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")
+			&& !rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
 			return -1;
-        } else if (!lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
+		} else if (!lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")
+			&& rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
 			return 1;
 		}
 
-
-
 		SubEntityType lClass = SubEntityType.fromClass(left.getClass());
 		SubEntityType rClass = SubEntityType.fromClass(right.getClass());
 		return lClass.ordinal() - rClass.ordinal();

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

@@ -1,21 +1,28 @@
 
 package eu.dnetlib.dhp.schema.oaf.utils;
 
+import static com.google.common.base.Preconditions.checkArgument;
+import static org.apache.commons.lang3.ObjectUtils.firstNonNull;
+
+import java.text.ParseException;
+import java.time.ZoneId;
+import java.util.*;
+import java.util.function.BinaryOperator;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.tuple.ImmutablePair;
+import org.apache.commons.lang3.tuple.Pair;
+
+import com.github.sisyphsu.dateparser.DateParserUtils;
+import com.google.common.base.Joiner;
+
 import eu.dnetlib.dhp.schema.common.AccessRightComparator;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang3.tuple.ImmutablePair;
-import org.apache.commons.lang3.tuple.Pair;
-
-import java.text.ParseException;
-import java.util.*;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-
-import static com.google.common.base.Objects.firstNonNull;
-import static com.google.common.base.Preconditions.checkArgument;
 
 public class MergeUtils {
 
@@ -168,8 +175,8 @@ public class MergeUtils {
 		return a || b;
 	}
 
-
+	private static <T, K> List<T> mergeLists(final List<T> left, final List<T> right, int trust,
-    private static <T> List<T> unionDistinctLists(final List<T> left, final List<T> right, int trust) {
+		Function<T, K> keyExtractor, BinaryOperator<T> merger) {
 		if (left == null) {
 			return right;
 		} else if (right == null) {
@@ -179,7 +186,26 @@ public class MergeUtils {
 		List<T> h = trust >= 0 ? left : right;
 		List<T> l = trust >= 0 ? right : left;
 
-        return Stream.concat(h.stream(), l.stream())
+		return new ArrayList<>(Stream
+			.concat(h.stream(), l.stream())
+			.filter(Objects::nonNull)
+			.distinct()
+			.collect(Collectors.toMap(keyExtractor, v -> v, merger))
+			.values());
+	}
+
+	private static <T, K> List<T> unionDistinctLists(final List<T> left, final List<T> right, int trust) {
+		if (left == null) {
+			return right;
+		} else if (right == null) {
+			return left;
+		}
+
+		List<T> h = trust >= 0 ? left : right;
+		List<T> l = trust >= 0 ? right : left;
+
+		return Stream
+			.concat(h.stream(), l.stream())
 			.filter(Objects::nonNull)
 			.distinct()
 			.collect(Collectors.toList());
@@ -192,7 +218,8 @@ public class MergeUtils {
 			return l;
 		}
 
-        return Stream.concat(l.stream(), r.stream())
+		return Stream
+			.concat(l.stream(), r.stream())
 			.filter(StringUtils::isNotBlank)
 			.distinct()
 			.collect(Collectors.toList());
@@ -213,7 +240,8 @@ public class MergeUtils {
 		return new ArrayList<>(values.values());
 	}
 
-    private static List<StructuredProperty> unionTitle(List<StructuredProperty> left, List<StructuredProperty> right, int trust) {
+	private static List<StructuredProperty> unionTitle(List<StructuredProperty> left, List<StructuredProperty> right,
+		int trust) {
 		if (left == null) {
 			return right;
 		} else if (right == null) {
@@ -223,7 +251,8 @@ public class MergeUtils {
 		List<StructuredProperty> h = trust >= 0 ? left : right;
 		List<StructuredProperty> l = trust >= 0 ? right : left;
 
-        return Stream.concat(h.stream(), l.stream())
+		return Stream
+			.concat(h.stream(), l.stream())
 			.filter(Objects::isNull)
 			.distinct()
 			.collect(Collectors.toList());
@@ -263,7 +292,9 @@ public class MergeUtils {
 		// dateofcollection mettere today quando si fa merge
 		merged.setDateofcollection(chooseString(merged.getDateofcollection(), enrich.getDateofcollection(), trust));
 		// setDateoftransformation mettere vuota in dedup, nota per Claudio
-        merged.setDateoftransformation(chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust));
+		merged
+			.setDateoftransformation(
+				chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust));
 		// TODO: was missing in OafEntity.merge
 		merged.setExtraInfo(unionDistinctLists(merged.getExtraInfo(), enrich.getExtraInfo(), trust));
 		// oaiprovenanze da mettere a null quando si genera merge
@@ -273,7 +304,6 @@ public class MergeUtils {
 		return merged;
 	}
 
-
 	public static <T extends Relation> T mergeRelation(T original, T enrich) {
 		int trust = compareTrust(original, enrich);
 		T merge = mergeOafFields(original, enrich, trust);
@@ -309,7 +339,8 @@ public class MergeUtils {
 		final int trust = compareTrust(original, enrich);
 		T merge = mergeOafEntityFields(original, enrich, trust);
 
-        if (merge.getProcessingchargeamount() == null || StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) {
+		if (merge.getProcessingchargeamount() == null
+			|| StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) {
 			merge.setProcessingchargeamount(enrich.getProcessingchargeamount());
 			merge.setProcessingchargecurrency(enrich.getProcessingchargecurrency());
 		}
@@ -350,6 +381,7 @@ public class MergeUtils {
 		// prima prendo l'higher trust, su questo prendo il valore migliore nelle istanze TODO
 		// trust maggiore ma a parita' di trust il piu' specifico (base del vocabolario)
 		// vedi note
+		// cannot use com.google.common.base.Objects.firstNonNull as it throws NPE when both terms are null
 		merge.setResourcetype(firstNonNull(merge.getResourcetype(), enrich.getResourcetype()));
 
 		// ok
@@ -366,12 +398,19 @@ public class MergeUtils {
 		merge.setContext(unionDistinctLists(merge.getContext(), enrich.getContext(), trust));
 
 		// ok
-        merge.setExternalReference(unionDistinctLists(merge.getExternalReference(), enrich.getExternalReference(), trust));
+		merge
+			.setExternalReference(
+				unionDistinctLists(merge.getExternalReference(), enrich.getExternalReference(), trust));
 
 		// instance enrichment or union
 		// review instance equals => add pid to comparision
 		if (!isAnEnrichment(merge) && !isAnEnrichment(enrich))
-            merge.setInstance(unionDistinctLists(merge.getInstance(), enrich.getInstance(), trust));
+			merge
+				.setInstance(
+					mergeLists(
+						merge.getInstance(), enrich.getInstance(), trust,
+						MergeUtils::instanceKeyExtractor,
+						MergeUtils::instanceMerger));
 		else {
 			final List<Instance> enrichmentInstances = isAnEnrichment(merge) ? merge.getInstance()
 				: enrich.getInstance();
@@ -392,6 +431,125 @@ public class MergeUtils {
 		return merge;
 	}
 
+	private static String instanceKeyExtractor(Instance i) {
+		return String
+			.join(
+				"::",
+				kvKeyExtractor(i.getHostedby()),
+				kvKeyExtractor(i.getCollectedfrom()),
+				qualifierKeyExtractor(i.getAccessright()),
+				qualifierKeyExtractor(i.getInstancetype()),
+				Optional.ofNullable(i.getUrl()).map(u -> String.join("::", u)).orElse(null),
+				Optional
+					.ofNullable(i.getPid())
+					.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("::")))
+					.orElse(null));
+	}
+
+	private static Instance instanceMerger(Instance i1, Instance i2) {
+		Instance i = new Instance();
+		i.setHostedby(i1.getHostedby());
+		i.setCollectedfrom(i1.getCollectedfrom());
+		i.setAccessright(i1.getAccessright());
+		i.setInstancetype(i1.getInstancetype());
+		i.setPid(mergeLists(i1.getPid(), i2.getPid(), 0, MergeUtils::spKeyExtractor, (sp1, sp2) -> sp1));
+		i
+			.setAlternateIdentifier(
+				mergeLists(
+					i1.getAlternateIdentifier(), i2.getAlternateIdentifier(), 0, MergeUtils::spKeyExtractor,
+					(sp1, sp2) -> sp1));
+
+		i
+			.setRefereed(
+				Collections
+					.min(
+						Stream.of(i1.getRefereed(), i2.getRefereed()).collect(Collectors.toList()),
+						new RefereedComparator()));
+		i
+			.setInstanceTypeMapping(
+				mergeLists(
+					i1.getInstanceTypeMapping(), i2.getInstanceTypeMapping(), 0,
+					MergeUtils::instanceTypeMappingKeyExtractor, (itm1, itm2) -> itm1));
+		i.setFulltext(selectFulltext(i1.getFulltext(), i2.getFulltext()));
+		i.setDateofacceptance(selectOldestDate(i1.getDateofacceptance(), i2.getDateofacceptance()));
+		i.setLicense(firstNonNull(i1.getLicense(), i2.getLicense()));
+		i.setProcessingchargeamount(firstNonNull(i1.getProcessingchargeamount(), i2.getProcessingchargeamount()));
+		i.setProcessingchargecurrency(firstNonNull(i1.getProcessingchargecurrency(), i2.getProcessingchargecurrency()));
+		i
+			.setMeasures(
+				mergeLists(i1.getMeasures(), i2.getMeasures(), 0, MergeUtils::measureKeyExtractor, (m1, m2) -> m1));
+
+		i.setUrl(unionDistinctListOfString(i1.getUrl(), i2.getUrl()));
+
+		return i;
+	}
+
+	private static String measureKeyExtractor(Measure m) {
+		return String
+			.join(
+				"::",
+				m.getId(),
+				m
+					.getUnit()
+					.stream()
+					.map(KeyValue::getKey)
+					.collect(Collectors.joining("::")));
+	}
+
+	private static Field<String> selectOldestDate(Field<String> d1, Field<String> d2) {
+		return Stream
+			.of(d1, d2)
+			.filter(Objects::nonNull)
+			.min(
+				Comparator
+					.comparing(
+						f -> DateParserUtils
+							.parseDate(f.getValue())
+							.toInstant()
+							.atZone(ZoneId.systemDefault())
+							.toLocalDate()))
+			.orElse(d1);
+	}
+
+	private static String selectFulltext(String ft1, String ft2) {
+		if (StringUtils.endsWith(ft1, "pdf")) {
+			return ft1;
+		}
+		if (StringUtils.endsWith(ft2, "pdf")) {
+			return ft2;
+		}
+		return firstNonNull(ft1, ft2);
+	}
+
+	private static String instanceTypeMappingKeyExtractor(InstanceTypeMapping itm) {
+		return String
+			.join(
+				"::",
+				itm.getOriginalType(),
+				itm.getTypeCode(),
+				itm.getTypeLabel(),
+				itm.getVocabularyName());
+	}
+
+	private static String kvKeyExtractor(KeyValue kv) {
+		return Optional.ofNullable(kv).map(KeyValue::getKey).orElse(null);
+	}
+
+	private static String qualifierKeyExtractor(Qualifier q) {
+		return Optional.ofNullable(q).map(Qualifier::getClassid).orElse(null);
+	}
+
+	private static <T> T fieldKeyExtractor(Field<T> f) {
+		return Optional.ofNullable(f).map(Field::getValue).orElse(null);
+	}
+
+	private static String spKeyExtractor(StructuredProperty sp) {
+		return Optional
+			.ofNullable(sp)
+			.map(s -> Joiner.on("::").join(s, qualifierKeyExtractor(s.getQualifier())))
+			.orElse(null);
+	}
+
 	private static <T extends OtherResearchProduct> T mergeORP(T original, T enrich) {
 		int trust = compareTrust(original, enrich);
 		final T merge = mergeResult(original, enrich);
@@ -410,7 +568,9 @@ public class MergeUtils {
 		merge.setDocumentationUrl(unionDistinctLists(merge.getDocumentationUrl(), enrich.getDocumentationUrl(), trust));
 		merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust));
 		merge.setCodeRepositoryUrl(chooseReference(merge.getCodeRepositoryUrl(), enrich.getCodeRepositoryUrl(), trust));
-        merge.setProgrammingLanguage(chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust));
+		merge
+			.setProgrammingLanguage(
+				chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust));
 
 		return merge;
 	}
@@ -423,8 +583,12 @@ public class MergeUtils {
 		merge.setDevice(chooseReference(merge.getDevice(), enrich.getDevice(), trust));
 		merge.setSize(chooseReference(merge.getSize(), enrich.getSize(), trust));
 		merge.setVersion(chooseReference(merge.getVersion(), enrich.getVersion(), trust));
-        merge.setLastmetadataupdate(chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust));
+		merge
-        merge.setMetadataversionnumber(chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust));
+			.setLastmetadataupdate(
+				chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust));
+		merge
+			.setMetadataversionnumber(
+				chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust));
 		merge.setGeolocation(unionDistinctLists(merge.getGeolocation(), enrich.getGeolocation(), trust));
 
 		return merge;
@@ -445,16 +609,27 @@ public class MergeUtils {
 
 		merged.setLegalshortname(chooseReference(merged.getLegalshortname(), enrich.getLegalshortname(), trust));
 		merged.setLegalname(chooseReference(merged.getLegalname(), enrich.getLegalname(), trust));
-        merged.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust));
+		merged
+			.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust));
 		merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust));
 		merged.setLogourl(chooseReference(merged.getLogourl(), enrich.getLogourl(), trust));
 		merged.setEclegalbody(chooseReference(merged.getEclegalbody(), enrich.getEclegalbody(), trust));
 		merged.setEclegalperson(chooseReference(merged.getEclegalperson(), enrich.getEclegalperson(), trust));
 		merged.setEcnonprofit(chooseReference(merged.getEcnonprofit(), enrich.getEcnonprofit(), trust));
-        merged.setEcresearchorganization(chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust));
+		merged
-        merged.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust));
+			.setEcresearchorganization(
-        merged.setEcinternationalorganizationeurinterests(chooseReference(merged.getEcinternationalorganizationeurinterests(), enrich.getEcinternationalorganizationeurinterests(), trust));
+				chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust));
-        merged.setEcinternationalorganization(chooseReference(merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust));
+		merged
+			.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust));
+		merged
+			.setEcinternationalorganizationeurinterests(
+				chooseReference(
+					merged.getEcinternationalorganizationeurinterests(),
+					enrich.getEcinternationalorganizationeurinterests(), trust));
+		merged
+			.setEcinternationalorganization(
+				chooseReference(
+					merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust));
 		merged.setEcenterprise(chooseReference(merged.getEcenterprise(), enrich.getEcenterprise(), trust));
 		merged.setEcsmevalidated(chooseReference(merged.getEcsmevalidated(), enrich.getEcsmevalidated(), trust));
 		merged.setEcnutscode(chooseReference(merged.getEcnutscode(), enrich.getEcnutscode(), trust));
@@ -477,7 +652,9 @@ public class MergeUtils {
 		merged.setKeywords(chooseReference(merged.getKeywords(), enrich.getKeywords(), trust));
 		merged.setDuration(chooseReference(merged.getDuration(), enrich.getDuration(), trust));
 		merged.setEcsc39(chooseReference(merged.getEcsc39(), enrich.getEcsc39(), trust));
-        merged.setOamandatepublications(chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust));
+		merged
+			.setOamandatepublications(
+				chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust));
 		merged.setEcarticle29_3(chooseReference(merged.getEcarticle29_3(), enrich.getEcarticle29_3(), trust));
 		merged.setSubjects(unionDistinctLists(merged.getSubjects(), enrich.getSubjects(), trust));
 		merged.setFundingtree(unionDistinctLists(merged.getFundingtree(), enrich.getFundingtree(), trust));
@@ -502,12 +679,13 @@ public class MergeUtils {
 			merged.setH2020topicdescription(enrich.getH2020topicdescription());
 		}
 
-        merged.setH2020classification(unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust));
+		merged
+			.setH2020classification(
+				unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust));
 
 		return merged;
 	}
 
-
 	/**
 	 * Longest lists list.
 	 *
@@ -679,12 +857,18 @@ public class MergeUtils {
 		merge.setInstanceTypeMapping(firstNonNull(merge.getInstanceTypeMapping(), enrichment.getInstanceTypeMapping()));
 		merge.setHostedby(firstNonNull(merge.getHostedby(), enrichment.getHostedby()));
 		merge.setUrl(unionDistinctLists(merge.getUrl(), enrichment.getUrl(), 0));
-        merge.setDistributionlocation(firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation()));
+		merge
+			.setDistributionlocation(
+				firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation()));
 		merge.setCollectedfrom(firstNonNull(merge.getCollectedfrom(), enrichment.getCollectedfrom()));
 		// pid and alternateId are used for matching
 		merge.setDateofacceptance(firstNonNull(merge.getDateofacceptance(), enrichment.getDateofacceptance()));
-        merge.setProcessingchargeamount(firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount()));
+		merge
-        merge.setProcessingchargecurrency(firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency()));
+			.setProcessingchargeamount(
+				firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount()));
+		merge
+			.setProcessingchargecurrency(
+				firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency()));
 		merge.setRefereed(firstNonNull(merge.getRefereed(), enrichment.getRefereed()));
 		merge.setMeasures(unionDistinctLists(merge.getMeasures(), enrichment.getMeasures(), 0));
 		merge.setFulltext(firstNonNull(merge.getFulltext(), enrichment.getFulltext()));

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

@@ -0,0 +1,27 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+public class ModelHardLimits {
+
+	private ModelHardLimits() {
+	}
+
+	public static final String LAYOUT = "index";
+	public static final String INTERPRETATION = "openaire";
+	public static final String SEPARATOR = "-";
+
+	public static final int MAX_EXTERNAL_ENTITIES = 50;
+	public static final int MAX_AUTHORS = 200;
+	public static final int MAX_AUTHOR_FULLNAME_LENGTH = 1000;
+	public static final int MAX_TITLE_LENGTH = 5000;
+	public static final int MAX_TITLES = 10;
+	public static final int MAX_ABSTRACTS = 10;
+	public static final int MAX_ABSTRACT_LENGTH = 150000;
+	public static final int MAX_RELATED_ABSTRACT_LENGTH = 500;
+	public static final int MAX_INSTANCES = 10;
+
+	public static String getCollectionName(String format) {
+		return format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION;
+	}
+
+}

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

@@ -0,0 +1,38 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import java.util.Comparator;
+
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+
+public class OrganizationPidComparator implements Comparator<StructuredProperty> {
+
+	@Override
+	public int compare(StructuredProperty left, StructuredProperty right) {
+
+		PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
+		PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
+
+		if (lClass.equals(PidType.openorgs))
+			return -1;
+		if (rClass.equals(PidType.openorgs))
+			return 1;
+
+		if (lClass.equals(PidType.GRID))
+			return -1;
+		if (rClass.equals(PidType.GRID))
+			return 1;
+
+		if (lClass.equals(PidType.mag_id))
+			return -1;
+		if (rClass.equals(PidType.mag_id))
+			return 1;
+
+		if (lClass.equals(PidType.urn))
+			return -1;
+		if (rClass.equals(PidType.urn))
+			return 1;
+
+		return 0;
+	}
+}

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

@@ -0,0 +1,8 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import java.util.HashMap;
+import java.util.HashSet;
+
+public class PidBlacklist extends HashMap<String, HashSet<String>> {
+}

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

@@ -0,0 +1,40 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Optional;
+import java.util.Set;
+
+import org.apache.commons.io.IOUtils;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+public class PidBlacklistProvider {
+
+	private static final PidBlacklist blacklist;
+
+	static {
+		try {
+			String json = IOUtils.toString(IdentifierFactory.class.getResourceAsStream("pid_blacklist.json"));
+			blacklist = new ObjectMapper().readValue(json, PidBlacklist.class);
+
+		} catch (IOException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	public static PidBlacklist getBlacklist() {
+		return blacklist;
+	}
+
+	public static Set<String> getBlacklist(String pidType) {
+		return Optional
+			.ofNullable(getBlacklist().get(pidType))
+			.orElse(new HashSet<>());
+	}
+
+	private PidBlacklistProvider() {
+	}
+
+}

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

@@ -0,0 +1,48 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import java.util.Comparator;
+
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Organization;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+
+public class PidComparator<T extends OafEntity> implements Comparator<StructuredProperty> {
+
+	private final T entity;
+
+	public PidComparator(T entity) {
+		this.entity = entity;
+	}
+
+	@Override
+	public int compare(StructuredProperty left, StructuredProperty right) {
+
+		if (left == null && right == null)
+			return 0;
+		if (left == null)
+			return 1;
+		if (right == null)
+			return -1;
+
+		if (ModelSupport.isSubClass(entity, Result.class)) {
+			return compareResultPids(left, right);
+		}
+		if (ModelSupport.isSubClass(entity, Organization.class)) {
+			return compareOrganizationtPids(left, right);
+		}
+
+		// Else (but unlikely), lexicographical ordering will do.
+		return left.getQualifier().getClassid().compareTo(right.getQualifier().getClassid());
+	}
+
+	private int compareResultPids(StructuredProperty left, StructuredProperty right) {
+		return new ResultPidComparator().compare(left, right);
+	}
+
+	private int compareOrganizationtPids(StructuredProperty left, StructuredProperty right) {
+		return new OrganizationPidComparator().compare(left, right);
+	}
+}

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

@@ -0,0 +1,79 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import org.apache.commons.lang3.EnumUtils;
+
+public enum PidType {
+
+	/**
+	 * The DOI syntax shall be made up of a DOI prefix and a DOI suffix separated by a forward slash.
+	 *
+	 * There is no defined limit on the length of the DOI name, or of the DOI prefix or DOI suffix.
+	 *
+	 * The DOI name is case-insensitive and can incorporate any printable characters from the legal graphic characters
+	 * of Unicode. Further constraints on character use (e.g. use of language-specific alphanumeric characters) can be
+	 * defined for an application by the ISO 26324 Registration Authority.
+	 *
+	 *
+	 * DOI prefix: The DOI prefix shall be composed of a directory indicator followed by a registrant code.
+	 * These two components shall be separated by a full stop (period). The directory indicator shall be "10" and
+	 * distinguishes the entire set of character strings (prefix and suffix) as digital object identifiers within the
+	 * resolution system.
+	 *
+	 * Registrant code: The second element of the DOI prefix shall be the registrant code. The registrant code is a
+	 * unique string assigned to a registrant.
+	 *
+	 * DOI suffix: The DOI suffix shall consist of a character string of any length chosen by the registrant.
+	 * Each suffix shall be unique to the prefix element that precedes it. The unique suffix can be a sequential number,
+	 * or it might incorporate an identifier generated from or based on another system used by the registrant
+	 * (e.g. ISAN, ISBN, ISRC, ISSN, ISTC, ISNI; in such cases, a preferred construction for such a suffix can be
+	 * specified, as in Example 1).
+	 *
+	 * Source: https://www.doi.org/doi_handbook/2_Numbering.html#2.2
+	 */
+	doi,
+
+	/**
+	 * PubMed Unique Identifier (PMID)
+	 *
+	 * This field is a 1-to-8 digit accession number with no leading zeros. It is present on all records and is the
+	 * accession number for managing and disseminating records. PMIDs are not reused after records are deleted.
+	 *
+	 * Beginning in February 2012 PMIDs include extensions following a decimal point to account for article versions
+	 * (e.g., 21804956.2). All citations are considered version 1 until replaced.  The extended PMID is not displayed
+	 * on the MEDLINE format.
+	 *
+	 * View the citation in abstract format in PubMed to access additional versions when available (see the article in
+	 * the Jan-Feb 2012 NLM Technical Bulletin).
+	 *
+	 * Source: https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmid
+	 */
+	pmid,
+
+	/**
+	 * This field contains the unique identifier for the cited article in PubMed Central. The identifier begins with the
+	 * prefix PMC.
+	 *
+	 * Source: https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmc
+	 */
+	pmc, handle, arXiv, nct, pdb, w3id,
+
+	// Organization
+	openorgs, ROR, GRID, PIC, ISNI, Wikidata, FundRef, corda, corda_h2020, mag_id, urn,
+
+	// Used by dedup
+	undefined, original;
+
+	public static boolean isValid(String type) {
+		return EnumUtils.isValidEnum(PidType.class, type);
+	}
+
+	public static PidType tryValueOf(String s) {
+		try {
+			return PidType.valueOf(s);
+		} catch (Exception e) {
+			return PidType.original;
+		}
+	}
+
+}

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

@@ -0,0 +1,33 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import java.util.Comparator;
+import java.util.Optional;
+
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+
+public class PidValueComparator implements Comparator<StructuredProperty> {
+
+	@Override
+	public int compare(StructuredProperty left, StructuredProperty right) {
+
+		if (left == null && right == null)
+			return 0;
+		if (left == null)
+			return 1;
+		if (right == null)
+			return -1;
+
+		StructuredProperty l = CleaningFunctions.normalizePidValue(left);
+		StructuredProperty r = CleaningFunctions.normalizePidValue(right);
+
+		return Optional
+			.ofNullable(l.getValue())
+			.map(
+				lv -> Optional
+					.ofNullable(r.getValue())
+					.map(rv -> lv.compareTo(rv))
+					.orElse(-1))
+			.orElse(1);
+	}
+}

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

@@ -0,0 +1,39 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import java.util.Comparator;
+
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+
+/**
+ * Comparator for sorting the values from the dnet:review_levels vocabulary, implements the following ordering
+ *
+ * peerReviewed (0001) > nonPeerReviewed (0002) > UNKNOWN (0000)
+ */
+public class RefereedComparator implements Comparator<Qualifier> {
+
+	@Override
+	public int compare(Qualifier left, Qualifier right) {
+
+		String lClass = left.getClassid();
+		String rClass = right.getClassid();
+
+		if ("0001".equals(lClass))
+			return -1;
+		if ("0001".equals(rClass))
+			return 1;
+
+		if ("0002".equals(lClass))
+			return -1;
+		if ("0002".equals(rClass))
+			return 1;
+
+		if ("0000".equals(lClass))
+			return -1;
+		if ("0000".equals(rClass))
+			return 1;
+
+		return 0;
+	}
+}

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

@@ -0,0 +1,53 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import java.util.Comparator;
+
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+
+public class ResultPidComparator implements Comparator<StructuredProperty> {
+
+	@Override
+	public int compare(StructuredProperty left, StructuredProperty right) {
+
+		PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
+		PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
+
+		if (lClass.equals(PidType.doi))
+			return -1;
+		if (rClass.equals(PidType.doi))
+			return 1;
+
+		if (lClass.equals(PidType.pmid))
+			return -1;
+		if (rClass.equals(PidType.pmid))
+			return 1;
+
+		if (lClass.equals(PidType.pmc))
+			return -1;
+		if (rClass.equals(PidType.pmc))
+			return 1;
+
+		if (lClass.equals(PidType.handle))
+			return -1;
+		if (rClass.equals(PidType.handle))
+			return 1;
+
+		if (lClass.equals(PidType.arXiv))
+			return -1;
+		if (rClass.equals(PidType.arXiv))
+			return 1;
+
+		if (lClass.equals(PidType.nct))
+			return -1;
+		if (rClass.equals(PidType.nct))
+			return 1;
+
+		if (lClass.equals(PidType.pdb))
+			return -1;
+		if (rClass.equals(PidType.pdb))
+			return 1;
+
+		return 0;
+	}
+}

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

@@ -0,0 +1,77 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
+
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.Optional;
+import java.util.stream.Collectors;
+
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+public class ResultTypeComparator implements Comparator<Result> {
+
+	@Override
+	public int compare(Result left, Result right) {
+
+		if (left == null && right == null)
+			return 0;
+		if (left == null)
+			return 1;
+		if (right == null)
+			return -1;
+
+		HashSet<String> lCf = getCollectedFromIds(left);
+		HashSet<String> rCf = getCollectedFromIds(right);
+
+		if (lCf.contains(CROSSREF_ID) && !rCf.contains(CROSSREF_ID)) {
+			return -1;
+		}
+		if (!lCf.contains(CROSSREF_ID) && rCf.contains(CROSSREF_ID)) {
+			return 1;
+		}
+
+		String lClass = left.getResulttype().getClassid();
+		String rClass = right.getResulttype().getClassid();
+
+		if (lClass.equals(rClass))
+			return 0;
+
+		if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
+			return -1;
+		if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
+			return 1;
+
+		if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
+			return -1;
+		if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
+			return 1;
+
+		if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
+			return -1;
+		if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
+			return 1;
+
+		if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
+			return -1;
+		if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
+			return 1;
+
+		// Else (but unlikely), lexicographical ordering will do.
+		return lClass.compareTo(rClass);
+	}
+
+	protected HashSet<String> getCollectedFromIds(Result left) {
+		return Optional
+			.ofNullable(left.getCollectedfrom())
+			.map(
+				cf -> cf
+					.stream()
+					.map(KeyValue::getKey)
+					.collect(Collectors.toCollection(HashSet::new)))
+			.orElse(new HashSet<>());
+	}
+}

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/BlackListProviderTest.java

@@ -0,0 +1,21 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import java.util.Set;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+
+class BlackListProviderTest {
+
+	@Test
+	void blackListTest() {
+
+		Assertions.assertNotNull(PidBlacklistProvider.getBlacklist());
+		Assertions.assertNotNull(PidBlacklistProvider.getBlacklist().get("doi"));
+		Assertions.assertTrue(PidBlacklistProvider.getBlacklist().get("doi").size() > 0);
+		final Set<String> xxx = PidBlacklistProvider.getBlacklist("xxx");
+		Assertions.assertNotNull(xxx);
+		Assertions.assertEquals(0, xxx.size());
+	}
+}

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java

@@ -0,0 +1,87 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
+import java.io.IOException;
+
+import org.apache.commons.io.IOUtils;
+import org.junit.jupiter.api.Test;
+
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.schema.oaf.Publication;
+
+class IdentifierFactoryTest {
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
+		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+
+	@Test
+	void testCreateIdentifierForPublication() throws IOException {
+
+		verifyIdentifier(
+			"publication_doi1.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
+
+		verifyIdentifier(
+			"publication_doi2.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
+
+		verifyIdentifier(
+			"publication_doi3.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
+
+		verifyIdentifier(
+			"publication_doi4.json", "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66", true);
+
+		verifyIdentifier(
+			"publication_doi5.json", "50|doi_________::3bef95c0ca26dd55451fc8839ea69d27", true);
+
+		verifyIdentifier(
+			"publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", true);
+
+		verifyIdentifier(
+			"publication_pmc2.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
+
+		verifyIdentifier(
+			"publication_openapc.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
+
+		final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
+		verifyIdentifier("publication_3.json", defaultID, true);
+		verifyIdentifier("publication_4.json", defaultID, true);
+		verifyIdentifier("publication_5.json", defaultID, true);
+
+	}
+
+	@Test
+	void testCreateIdentifierForPublicationNoHash() throws IOException {
+
+		verifyIdentifier("publication_doi1.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
+		verifyIdentifier("publication_doi2.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
+		verifyIdentifier("publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
+		verifyIdentifier(
+			"publication_urn1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
+
+		final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
+		verifyIdentifier("publication_3.json", defaultID, false);
+		verifyIdentifier("publication_4.json", defaultID, false);
+		verifyIdentifier("publication_5.json", defaultID, false);
+	}
+
+	@Test
+	void testCreateIdentifierForROHub() throws IOException {
+		verifyIdentifier(
+			"orp-rohub.json", "50|w3id________::afc7592914ae190a50570db90f55f9c2", true);
+	}
+
+	protected void verifyIdentifier(String filename, String expectedID, boolean md5) throws IOException {
+		final String json = IOUtils.toString(getClass().getResourceAsStream(filename));
+		final Publication pub = OBJECT_MAPPER.readValue(json, Publication.class);
+
+		String id = IdentifierFactory.createIdentifier(pub, md5);
+		System.out.println(id);
+		assertNotNull(id);
+		assertEquals(expectedID, id);
+	}
+
+}

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java

@@ -5,28 +5,47 @@ import static org.junit.jupiter.api.Assertions.*;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
 import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
 import java.util.HashSet;
 import java.util.List;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.common.ModelSupport;
+import org.apache.commons.beanutils.BeanUtils;
 import org.apache.commons.io.IOUtils;
 import org.junit.jupiter.api.Test;
 
 import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.Lists;
 
 import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Dataset;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.dhp.schema.oaf.Publication;
-import eu.dnetlib.dhp.schema.oaf.Result;
 
 public class MergeUtilsTest {
 
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
 		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
 
+	@Test
+	void testMergePubs_new() throws IOException {
+		Publication pt = read("publication_test.json", Publication.class);
+		Publication p1 = read("publication_test.json", Publication.class);
+
+		assertEquals(1, pt.getCollectedfrom().size());
+		assertEquals(ModelConstants.CROSSREF_ID, pt.getCollectedfrom().get(0).getKey());
+
+		Instance i = new Instance();
+		i.setUrl(Lists.newArrayList("https://..."));
+		p1.getInstance().add(i);
+
+		Publication ptp1 = MergeUtils.mergePublication(pt, p1);
+
+		assertNotNull(ptp1.getInstance());
+		assertEquals(2, ptp1.getInstance().size());
+
+	}
+
 	@Test
 	void testMergePubs() throws IOException {
 		Publication p1 = read("publication_1.json", Publication.class);

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java

@@ -178,8 +178,8 @@ class OafMapperUtilsTest {
 
 		assertEquals(
 			ModelConstants.DATASET_RESULTTYPE_CLASSID,
-			MergeUtils
+			((Result) MergeUtils
-				.mergeResult(p2, d1)
+				.merge(p2, d1))
 					.getResulttype()
 					.getClassid());
 	}

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json

@@ -0,0 +1,12 @@
+{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0000/ra.v2i3.114::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.91019644836e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.0"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"4.65008652949e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0000/ra.v2i3.114"}]}]}
+{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0001/(aj).v3i6.458::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.91019644836e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.0"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"4.01810569717e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0001/(aj).v3i6.458"}]}]}
+{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0001/1587::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.91019644836e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.0"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.39172290649e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0001/1587"}]}]}
+{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0001/462::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"6.33235333753e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.36"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.00285265116e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0001/462"}]}]}
+{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0001/731::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.91019644836e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.0"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"4.01810569717e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0001/731"}]}]}
+{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0001/ijllis.v9i4.2066.g2482::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.91019644836e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.0"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"8.48190886761e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0001/ijllis.v9i4.2066.g2482"}]}]}
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dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_3.json

@@ -0,0 +1 @@
+{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"scp-number"},"value":"79953761260"}]}

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_4.json

@@ -0,0 +1 @@
+{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[]}

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_5.json

@@ -0,0 +1 @@
+{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f"}

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi1.json

@@ -0,0 +1,33 @@
+{
+  "id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
+  "instance": [
+    {
+      "collectedfrom": {
+        "key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2",
+        "value": "Crossref"
+      },
+      "pid": [
+        {
+          "qualifier": {"classid": "doi"},
+          "value": "10.1016/j.cmet.2010.03.013"
+        }
+      ]
+    },
+    {
+      "pid": [
+        {
+          "qualifier": {"classid": "urn"},
+          "value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
+        },
+        {
+          "qualifier": {"classid": "scp-number"},
+          "value": "79953761260"
+        },
+        {
+          "qualifier": {"classid": "pmc"},
+          "value": "21459329"
+        }
+      ]
+    }
+  ]
+}

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi2.json

@@ -0,0 +1,37 @@
+{
+  "id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
+  "instance": [
+    {
+      "collectedfrom": {
+        "key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2",
+        "value": "Crossref"
+      },
+      "pid": [
+        {
+          "qualifier": {"classid": "doi"},
+          "value": "10.1016/j.cmet.2010.03.013"
+        }
+      ]
+    },
+    {
+      "collectedfrom": {
+        "key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
+        "value": "Europe PubMed Central"
+      },
+      "pid": [
+        {
+          "qualifier": {"classid": "urn"},
+          "value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
+        },
+        {
+          "qualifier": {"classid": "scp-number"},
+          "value": "79953761260"
+        },
+        {
+          "qualifier": {"classid": "pmc"},
+          "value": "21459329"
+        }
+      ]
+    }
+  ]
+}

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json

@@ -0,0 +1,37 @@
+{
+  "id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
+  "instance": [
+    {
+      "collectedfrom": {
+        "key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
+        "value": "Zenodo"
+      },
+      "pid": [
+        {
+          "qualifier": {"classid": "doi"},
+          "value": "10.1016/j.cmet.2010.03.013"
+        }
+      ]
+    },
+    {
+      "collectedfrom": {
+        "key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
+        "value": "Europe PubMed Central"
+      },
+      "pid": [
+        {
+          "qualifier": {"classid": "urn"},
+          "value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
+        },
+        {
+          "qualifier": {"classid": "scp-number"},
+          "value": "79953761260"
+        },
+        {
+          "qualifier": {"classid": "pmc"},
+          "value": "21459329"
+        }
+      ]
+    }
+  ]
+}

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi4.json

@@ -0,0 +1,37 @@
+{
+  "id": "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66",
+  "instance": [
+    {
+      "collectedfrom": {
+        "key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
+        "value": "Zenodo"
+      },
+      "pid": [
+        {
+          "qualifier": {"classid": "doi"},
+          "value": "10.1016/j.cmet.2010.03.013"
+        },
+        {
+          "qualifier": {"classid": "handle"},
+          "value": "11012/83840"
+        }
+      ]
+    },
+    {
+      "collectedfrom": {
+        "key": "10|opendoar____::2852",
+        "value": "Digital library of Brno University of Technology"
+      },
+      "pid": [
+        {
+          "qualifier": {"classid": "pmc"},
+          "value": "21459329"
+        },
+        {
+          "qualifier": {"classid": "handle"},
+          "value": "11012/83840"
+        }
+      ]
+    }
+  ]
+}

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi5.json

@@ -0,0 +1,37 @@
+{
+  "id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
+  "instance": [
+    {
+      "collectedfrom": {
+        "key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
+        "value": "Zenodo"
+      },
+      "pid": [
+        {
+          "qualifier": {"classid": "doi"},
+          "value": "10.5281/zenodo.5121485"
+        }
+      ]
+    },
+    {
+      "collectedfrom": {
+        "key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
+        "value": "Europe PubMed Central"
+      },
+      "pid": [
+        {
+          "qualifier": {"classid": "urn"},
+          "value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
+        },
+        {
+          "qualifier": {"classid": "scp-number"},
+          "value": "79953761260"
+        },
+        {
+          "qualifier": {"classid": "pmc"},
+          "value": "21459329"
+        }
+      ]
+    }
+  ]
+}

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_irish_tender_1.json

@@ -0,0 +1,3 @@
+{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", "resulttype" : { "classid" : "publication" }, "pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}], "collectedfrom" : [ { "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value" : "Crossref"} ], "isGreen": null, "openAccessColor":  "gold", "isInDiamondJournal": null, "publiclyFunded": null}
+{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g", "resulttype" : { "classid" : "publication" }, "isGreen": true, "openAccessColor":  "gold", "isInDiamondJournal": true, "publiclyFunded": false }
+{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1h", "resulttype" : { "classid" : "publication" }, "isGreen": false, "openAccessColor":  null, "isInDiamondJournal": true, "publiclyFunded": false }

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_irish_tender_2.json

@@ -0,0 +1,3 @@
+{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", "resulttype" : { "classid" : "publication" }, "pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}], "collectedfrom" : [ { "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value" : "Crossref"} ], "isGreen": null, "openAccessColor":  "gold", "isInDiamondJournal": null, "publiclyFunded": null}
+{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g", "resulttype" : { "classid" : "publication" }, "isGreen": true, "openAccessColor":  "bronze", "isInDiamondJournal": true, "publiclyFunded": false }
+{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1h", "resulttype" : { "classid" : "publication" }, "isGreen": false, "openAccessColor":  null, "isInDiamondJournal": true, "publiclyFunded": false }

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_openapc.json

@@ -0,0 +1,31 @@
+{
+  "id": "50|openapc_____::000023f9cb6e3a247c764daec4273cbc",
+  "resuttype": {
+    "classid": "publication"
+  },
+  "instance": [
+    {
+      "collectedfrom": {
+        "key": "10|apc_________::e2b1600b229fc30663c8a1f662debddf",
+        "value": "OpenAPC Global Initiative"
+      },
+      "pid": [
+        {
+          "qualifier": {"classid": "doi"},
+          "value": "10.1016/j.cmet.2010.03.013"
+        },
+        {
+          "qualifier": {"classid": "pmc"},
+          "value": "21459329"
+        },
+        {
+          "qualifier": {"classid": "pmid"},
+          "value": "25811027"
+        }
+      ],
+      "url":["https://doi.org/10.1155/2015/439379"]
+    }
+  ]
+}
+
+

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc1.json

@@ -0,0 +1,17 @@
+{
+  "id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
+  "pid": [
+    {
+      "qualifier": {"classid": "urn"},
+      "value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
+    },
+    {
+      "qualifier": {"classid": "scp-number"},
+      "value": "79953761260"
+    },
+    {
+      "qualifier": {"classid": "pmc"},
+      "value": "21459329"
+    }
+  ]
+}

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json

@@ -0,0 +1,21 @@
+{
+  "id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
+  "instance": [
+    {
+      "collectedfrom": {
+        "key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
+        "value": "Europe PubMed Central"
+      },
+      "pid": [
+        {
+          "qualifier": {"classid": "doi"},
+          "value": "10.1016/j.cmet.2010.03.013"
+        },
+        {
+          "qualifier":{"classid":"pmc"},
+          "value":"21459329"
+        }
+      ]
+    }
+  ]
+}

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_test.json

@@ -0,0 +1,428 @@
+{
+  "author": [
+    {
+      "affiliation": null,
+      "fullname": "Deymier, Ghislaine",
+      "name": "Ghislaine",
+      "pid": [],
+      "rank": 1,
+      "surname": "Deymier"
+    },
+    {
+      "affiliation": null,
+      "fullname": "Gaschet, Frédéric",
+      "name": "Frédéric",
+      "pid": [],
+      "rank": 2,
+      "surname": "Gaschet"
+    },
+    {
+      "affiliation": null,
+      "fullname": "Pouyanne, Guillaume",
+      "name": "Guillaume",
+      "pid": [],
+      "rank": 3,
+      "surname": "Pouyanne"
+    }
+  ],
+  "bestaccessright": {
+    "classid": "OPEN",
+    "classname": "Open Access",
+    "schemeid": "dnet:access_modes",
+    "schemename": "dnet:access_modes"
+  },
+  "collectedfrom": [
+    {
+      "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2",
+      "value" : "Crossref"
+    }
+  ],
+  "context": [],
+  "contributor": [],
+  "country": [],
+  "coverage": [],
+  "dataInfo": {
+    "deletedbyinference": false,
+    "inferred": false,
+    "invisible": false,
+    "provenanceaction": {
+      "classid": "sysimport:crosswalk:repository",
+      "classname": "Harvested",
+      "schemeid": "dnet:provenanceActions",
+      "schemename": "dnet:provenanceActions"
+    },
+    "trust": "0.9"
+  },
+  "dateofacceptance": {
+    "dataInfo": {
+      "deletedbyinference": false,
+      "inferred": false,
+      "invisible": false,
+      "provenanceaction": {
+        "classid": "sysimport:crosswalk:repository",
+        "classname": "Harvested",
+        "schemeid": "dnet:provenanceActions",
+        "schemename": "dnet:provenanceActions"
+      },
+      "trust": "0.9"
+    },
+    "value": "2013-11-30"
+  },
+  "dateofcollection": "2024-02-28T00:22:13+0000",
+  "dateoftransformation": "2024-03-06T08:43:13.253Z",
+  "description": [
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:repository",
+          "classname": "Harvested",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "value": "For analyzing the reciprocal interaction between urban sprawl and car use, research has first focused on the link between urban density and mobility. By looking for a reduction in energy consumption, cities have favoured a compact planning development. Then reflection has broadened from the simple density to the wider, multi-dimensional concept of urban form. This controversy has led to a renewal of analysis in term of the costs of urban growth, notably by comparing the costs of \"compact\" and \"sprawled\" development. The idea is to compare the mobility costs of different urban forms. However, most often because of a lack of data, such studies are scarce. This paper suggests an innovative method to compute mobility costs at an infra-urban scale : The Spatialized Travel Account (STA). It is based on the CERTU's travel account methodology at a metropolitan scale. It puts forward an accurate estimate of the mobility costs for each transport mode (individual and public) and for each type of payer (households, firms, local authorities...). In order to test the relationships between mobility costs and urban form, we link the computed costs to morphological characteristics of infra-urban zones, taking in account sociodemographic characteristics of households."
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:repository",
+          "classname": "Harvested",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "value": "L'interaction réciproque entre étalement urbain et usage de l'automobile a conduit la recherche à se focaliser sur le lien entre les densités urbaines et la mobilité. En cherchant à réduire leur consommation d'énergie pour les transports, et donc leurs émissions de Gaz à Effet de Serre, les villes ont alors cherché à planifier la \" ville compacte \", privilégiant notamment la reconstruction de la ville sur elle-même et la densification. Par la suite, la réflexion s'est élargie de la simple densité à la notion de forme urbaine et à toutes ses dimensions. Cette controverse devait conduire à un renouveau des analyses en termes de coûts de la croissance urbaine : le débat reste vif, encore aujourd'hui, sur les coûts comparés de la ville étalée et de la ville compacte. Plus largement, il s'agit d'explorer les coûts des différentes formes urbaines en termes de mobilité. Malgré cela, généralement pour des raisons de disponibilité de données, les études sur le sujet restent extrêmement rares. Cet article propose un outil novateur pour mesurer les coûts de la mobilité à l'échelle intraurbaine : le Compte Déplacements Territorialisé (CDT). Il s'inspire de la méthode développée par le CERTU pour l'établissement des Comptes Déplacements Voyageurs à l'échelle métropolitaine. Le CDT propose, pour chacune des zones de l'agglomération, une estimation précise de l'ensemble des coûts liés aux déplacements de personnes, ventilés par mode de transport (individuels et collectifs) et par type de financeurs (ménages, entreprises, collectivités territoriales, etc.). Nous proposons une application de cette méthode à la controverse sur le lien entre forme urbaine et coûts de la mobilité. Les coûts sont reliés aux caractéristiques morphologiques des zones (en termes de densité et de diversité, notamment), en prenant soin de contrôler les facteurs socio-économiques qui influent traditionnellement sur les comportements de mobilité (taille du ménage, revenu, etc.)."
+    }
+  ],
+  "eoscifguidelines": [],
+  "externalReference": [],
+  "extraInfo": [],
+  "format": [
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:repository",
+          "classname": "Harvested",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "value": "application/pdf"
+    }
+  ],
+  "fulltext": [],
+  "id": "50|06cdd3ff4700::4826ac62a11a957fe332e2c291dcfcca",
+  "instance": [
+    {
+      "accessright": {
+        "classid": "OPEN",
+        "classname": "Open Access",
+        "schemeid": "dnet:access_modes",
+        "schemename": "dnet:access_modes"
+      },
+      "alternateIdentifier": [
+        {
+          "dataInfo": {
+            "deletedbyinference": false,
+            "inferred": false,
+            "invisible": false,
+            "provenanceaction": {
+              "classid": "sysimport:crosswalk:repository",
+              "classname": "Harvested",
+              "schemeid": "dnet:provenanceActions",
+              "schemename": "dnet:provenanceActions"
+            },
+            "trust": "0.9"
+          },
+          "qualifier": {
+            "classid": "doi",
+            "classname": "Digital Object Identifier",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "10.46298/cst.12132"
+        }
+      ],
+      "collectedfrom": {
+        "key": "10|openaire____::6824b298c96ba906a3e6a70593affbf5",
+        "value": "Episciences"
+      },
+      "dateofacceptance": {
+        "dataInfo": {
+          "deletedbyinference": false,
+          "inferred": false,
+          "invisible": false,
+          "provenanceaction": {
+            "classid": "sysimport:crosswalk:repository",
+            "classname": "Harvested",
+            "schemeid": "dnet:provenanceActions",
+            "schemename": "dnet:provenanceActions"
+          },
+          "trust": "0.9"
+        },
+        "value": "2013-11-30"
+      },
+      "hostedby": {
+        "key": "10|openaire____::6824b298c96ba906a3e6a70593affbf5",
+        "value": "Episciences"
+      },
+      "instanceTypeMapping": [
+        {
+          "originalType": "http://purl.org/coar/resource_type/c_6501",
+          "typeCode": "http://purl.org/coar/resource_type/c_6501",
+          "typeLabel": "journal article",
+          "vocabularyName": "openaire::coar_resource_types_3_1"
+        },
+        {
+          "originalType": "http://purl.org/coar/resource_type/c_6501",
+          "typeCode": "Article",
+          "typeLabel": "Article",
+          "vocabularyName": "openaire::user_resource_types"
+        }
+      ],
+      "instancetype": {
+        "classid": "0001",
+        "classname": "Article",
+        "schemeid": "dnet:publication_resource",
+        "schemename": "dnet:publication_resource"
+      },
+      "license": {
+        "dataInfo": {
+          "deletedbyinference": false,
+          "inferred": false,
+          "invisible": false,
+          "provenanceaction": {
+            "classid": "sysimport:crosswalk:repository",
+            "classname": "Harvested",
+            "schemeid": "dnet:provenanceActions",
+            "schemename": "dnet:provenanceActions"
+          },
+          "trust": "0.9"
+        },
+        "value": "CC BY NC SA"
+      },
+      "pid": [],
+      "refereed": {
+        "classid": "0002",
+        "classname": "nonPeerReviewed",
+        "schemeid": "dnet:review_levels",
+        "schemename": "dnet:review_levels"
+      },
+      "url": [
+        "https://doi.org/10.46298/cst.12132",
+        "https://cst.episciences.org/12132"
+      ]
+    }
+  ],
+  "language": {
+    "classid": "fra/fre",
+    "classname": "French",
+    "schemeid": "dnet:languages",
+    "schemename": "dnet:languages"
+  },
+  "lastupdatetimestamp": 1710636106633,
+  "metaResourceType": {
+    "classid": "Research Literature",
+    "classname": "Research Literature",
+    "schemeid": "openaire::meta_resource_types",
+    "schemename": "openaire::meta_resource_types"
+  },
+  "originalId": [
+    "oai:episciences.org:cst:12132",
+    "50|06cdd3ff4700::4826ac62a11a957fe332e2c291dcfcca"
+  ],
+  "pid": [],
+  "publisher": {
+    "dataInfo": {
+      "deletedbyinference": false,
+      "inferred": false,
+      "invisible": false,
+      "provenanceaction": {
+        "classid": "sysimport:crosswalk:repository",
+        "classname": "Harvested",
+        "schemeid": "dnet:provenanceActions",
+        "schemename": "dnet:provenanceActions"
+      },
+      "trust": "0.9"
+    },
+    "value": "episciences.org"
+  },
+  "relevantdate": [
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:repository",
+          "classname": "Harvested",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "Accepted",
+        "classname": "Accepted",
+        "schemeid": "dnet:dataCite_date",
+        "schemename": "dnet:dataCite_date"
+      },
+      "value": "2024-02-11"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:repository",
+          "classname": "Harvested",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "issued",
+        "classname": "issued",
+        "schemeid": "dnet:dataCite_date",
+        "schemename": "dnet:dataCite_date"
+      },
+      "value": "2013-11-30"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:repository",
+          "classname": "Harvested",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "available",
+        "classname": "available",
+        "schemeid": "dnet:dataCite_date",
+        "schemename": "dnet:dataCite_date"
+      },
+      "value": "2013-11-30"
+    }
+  ],
+  "resourcetype": {
+    "classid": "journal article",
+    "classname": "journal article",
+    "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,
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:repository",
+          "classname": "Harvested",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "keyword",
+        "classname": "keyword",
+        "schemeid": "dnet:subject_classification_typologies",
+        "schemename": "dnet:subject_classification_typologies"
+      },
+      "value": "JEL: H - Public Economics/H.H7 - State and Local Government • Intergovernmental Relations/H.H7.H72 - State and Local Budget and Expenditures"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:repository",
+          "classname": "Harvested",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "keyword",
+        "classname": "keyword",
+        "schemeid": "dnet:subject_classification_typologies",
+        "schemename": "dnet:subject_classification_typologies"
+      },
+      "value": "Local public finance"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:repository",
+          "classname": "Harvested",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "keyword",
+        "classname": "keyword",
+        "schemeid": "dnet:subject_classification_typologies",
+        "schemename": "dnet:subject_classification_typologies"
+      },
+      "value": "JEL: R - Urban, Rural, Regional, Real Estate, and Transportation Economics/R.R5 - Regional Government Analysis/R.R5.R51 - Finance in Urban and Rural Economies"
+    }
+  ],
+  "title": [
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:repository",
+          "classname": "Harvested",
+          "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": "Urban form and the costs of daily mobility. The spatialized travel account tool and its application to the Bordeaux metropolitan area"
+    }
+  ]
+}

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_urn1.json

@@ -0,0 +1,23 @@
+{
+  "id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
+  "pid": [
+    {
+      "qualifier": {
+        "classid": "urn"
+      },
+      "value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
+    },
+    {
+      "qualifier": {
+        "classid": "scp-number"
+      },
+      "value": "79953761260"
+    },
+    {
+      "qualifier": {
+        "classid": "pmcid"
+      },
+      "value": "21459329"
+    }
+  ]
+}

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java

@@ -1,14 +1,14 @@
 
 package eu.dnetlib.dhp.actionmanager.promote;
 
+import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
+
+import java.util.function.BiFunction;
+
 import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
 import eu.dnetlib.dhp.schema.oaf.Oaf;
 import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
 
-import java.util.function.BiFunction;
-
-import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
-
 /** OAF model merging support. */
 public class MergeAndGet {
 

dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java

@@ -8,6 +8,7 @@ import static org.mockito.Mockito.*;
 
 import java.util.function.BiFunction;
 
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Nested;
 import org.junit.jupiter.api.Test;
 
@@ -85,6 +86,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
+		@Disabled
 		void shouldBehaveProperlyForRelationAndRelation() {
 			// given
 			Relation a = mock(Relation.class);
@@ -96,7 +98,9 @@ public class MergeAndGetTest {
 			// then
 			Oaf x = fn.get().apply(a, b);
 			assertTrue(Relation.class.isAssignableFrom(x.getClass()));
-			verify(a).mergeFrom(b);
+
+			// TODO should be reimplemented
+			// verify(a).mergeFrom(b);
 			assertEquals(a, x);
 		}
 
@@ -145,6 +149,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
+		@Disabled
 		void shouldBehaveProperlyForOafEntityAndOafEntity() {
 			// given
 			OafEntity a = mock(OafEntity.class);
@@ -156,7 +161,9 @@ public class MergeAndGetTest {
 			// then
 			Oaf x = fn.get().apply(a, b);
 			assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
-			verify(a).mergeFrom(b);
+
+			// TODO should be reimplemented
+			// verify(a).mergeFrom(b);
 			assertEquals(a, x);
 		}
 	}

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

@@ -64,6 +64,12 @@ public class PrepareAffiliationRelations implements Serializable {
 		final String pubmedInputPath = parser.get("pubmedInputPath");
 		log.info("pubmedInputPath: {}", pubmedInputPath);
 
+		final String openapcInputPath = parser.get("openapcInputPath");
+		log.info("openapcInputPath: {}", openapcInputPath);
+
+		final String dataciteInputPath = parser.get("dataciteInputPath");
+		log.info("dataciteInputPath: {}", dataciteInputPath);
+
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
@@ -85,8 +91,20 @@ public class PrepareAffiliationRelations implements Serializable {
 				JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
 					spark, pubmedInputPath, collectedFromPubmed);
 
+				List<KeyValue> collectedFromOpenAPC = OafMapperUtils
+					.listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC");
+				JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelations(
+					spark, openapcInputPath, collectedFromOpenAPC);
+
+				List<KeyValue> collectedFromDatacite = OafMapperUtils
+						.listKeyValues(ModelConstants.DATACITE_ID, "Datacite");
+				JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
+						spark, dataciteInputPath, collectedFromDatacite);
+
 				crossrefRelations
 					.union(pubmedRelations)
+					.union(openAPCRelations)
+					.union(dataciteRelations)
 					.saveAsHadoopFile(
 						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/score/deserializers/BipProjectModel.java

@@ -38,7 +38,6 @@ public class BipProjectModel {
 		return projectId;
 	}
 
-
 	// each project bip measure has exactly one value, hence one key-value pair
 	private Measure createMeasure(String measureId, String measureValue) {
 

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

@@ -75,6 +75,7 @@ public class GetFOSSparkJob implements Serializable {
 		fosData.map((MapFunction<Row, FOSDataModel>) r -> {
 			FOSDataModel fosDataModel = new FOSDataModel();
 			fosDataModel.setDoi(r.getString(0).toLowerCase());
+			fosDataModel.setOaid(r.getString(1).toLowerCase());
 			fosDataModel.setLevel1(r.getString(2));
 			fosDataModel.setLevel2(r.getString(3));
 			fosDataModel.setLevel3(r.getString(4));

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

@@ -16,12 +16,14 @@ 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.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import eu.dnetlib.dhp.schema.oaf.Subject;
@@ -52,28 +54,46 @@ public class PrepareFOSSparkJob implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
+		final Boolean distributeDOI = Optional
+			.ofNullable(parser.get("distributeDoi"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+
 		SparkConf conf = new SparkConf();
 		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
 			spark -> {
+				if (distributeDOI)
 					distributeFOSdois(
 						spark,
 						sourcePath,
 
 						outputPath);
+				else
+					distributeFOSoaid(spark, sourcePath, outputPath);
 			});
 	}
 
-	private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) {
+	private static void distributeFOSoaid(SparkSession spark, String sourcePath, String outputPath) {
 		Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class);
 
 		fosDataset
-			.groupByKey((MapFunction<FOSDataModel, String>) v -> v.getDoi().toLowerCase(), Encoders.STRING())
+			.groupByKey((MapFunction<FOSDataModel, String>) v -> v.getOaid().toLowerCase(), Encoders.STRING())
 			.mapGroups((MapGroupsFunction<String, FOSDataModel, Result>) (k, it) -> {
+				return getResult(ModelSupport.getIdPrefix(Result.class) + "|" + k, it);
+			}, Encoders.bean(Result.class))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
+			.json(outputPath + "/fos");
+	}
+
+	@NotNull
+	private static Result getResult(String k, Iterator<FOSDataModel> it) {
 		Result r = new Result();
 		FOSDataModel first = it.next();
-				r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
+		r.setId(k);
 
 		HashSet<String> level1 = new HashSet<>();
 		HashSet<String> level2 = new HashSet<>();
@@ -107,7 +127,17 @@ public class PrepareFOSSparkJob implements Serializable {
 								ModelConstants.DNET_PROVENANCE_ACTIONS),
 						null));
 		return r;
-			}, Encoders.bean(Result.class))
+	}
+
+	private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) {
+		Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class);
+
+		fosDataset
+			.groupByKey((MapFunction<FOSDataModel, String>) v -> v.getDoi().toLowerCase(), Encoders.STRING())
+			.mapGroups(
+				(MapGroupsFunction<String, FOSDataModel, Result>) (k,
+					it) -> getResult(DHPUtils.generateUnresolvedIdentifier(k, DOI), it),
+				Encoders.bean(Result.class))
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")

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

@@ -0,0 +1,92 @@
+
+package eu.dnetlib.dhp.actionmanager.fosnodoi;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.*;
+
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.GzipCodec;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaPairRDD;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.utils.*;
+import scala.Tuple2;
+
+public class CreateActionSetSparkJob implements Serializable {
+
+	private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static void main(final String[] args) throws IOException, ParseException {
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					Objects
+						.requireNonNull(
+							CreateActionSetSparkJob.class
+								.getResourceAsStream(
+									"/eu/dnetlib/dhp/actionmanager/fosnodoi/as_parameters.json"))));
+
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String inputPath = parser.get("sourcePath");
+		log.info("inputPath {}", inputPath);
+
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}", outputPath);
+
+		SparkConf conf = new SparkConf();
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> createActionSet(spark, inputPath, outputPath));
+
+	}
+
+	private static void createActionSet(SparkSession spark, String inputPath, String outputPath) {
+		spark
+			.read()
+			.textFile(inputPath)
+			.map(
+				(MapFunction<String, Result>) value -> OBJECT_MAPPER.readValue(value, Result.class),
+				Encoders.bean(Result.class))
+			.toJavaRDD()
+			.map(p -> new AtomicAction(p.getClass(), p))
+			.mapToPair(
+				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+			.saveAsHadoopFile(
+				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+	}
+
+}

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

@@ -22,12 +22,14 @@ import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.*;
 import eu.dnetlib.dhp.utils.DHPUtils;
@@ -37,16 +39,12 @@ public class CreateActionSetSparkJob implements Serializable {
 	public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
 	public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
 
-	// DOI-to-DOI citations
-	public static final String COCI = "COCI";
-
-	// PMID-to-PMID citations
-	public static final String POCI = "POCI";
-
 	private static final String DOI_PREFIX = "50|doi_________::";
 
 	private static final String PMID_PREFIX = "50|pmid________::";
+	private static final String ARXIV_PREFIX = "50|arXiv_______::";
 
+	private static final String PMCID_PREFIX = "50|pmcid_______::";
 	private static final String TRUST = "0.91";
 
 	private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
@@ -79,38 +77,30 @@ public class CreateActionSetSparkJob implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath {}", outputPath);
 
-		final boolean shouldDuplicateRels = Optional
-			.ofNullable(parser.get("shouldDuplicateRels"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.FALSE);
-
 		SparkConf conf = new SparkConf();
 		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
-			spark -> extractContent(spark, inputPath, outputPath, shouldDuplicateRels));
+			spark -> extractContent(spark, inputPath, outputPath));
 
 	}
 
-	private static void extractContent(SparkSession spark, String inputPath, String outputPath,
+	private static void extractContent(SparkSession spark, String inputPath, String outputPath) {
-		boolean shouldDuplicateRels) {
 
-		getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, COCI)
+		getTextTextJavaPairRDD(spark, inputPath)
-			.union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, POCI))
 			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
 	}
 
-	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath,
+	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath) {
-		boolean shouldDuplicateRels, String prefix) {
 		return spark
 			.read()
-			.textFile(inputPath + "/" + prefix + "/" + prefix + "_JSON/*")
+			.textFile(inputPath)
 			.map(
 				(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
 				Encoders.bean(COCI.class))
 			.flatMap(
 				(FlatMapFunction<COCI, Relation>) value -> createRelation(
-					value, shouldDuplicateRels, prefix)
+					value)
 						.iterator(),
 				Encoders.bean(Relation.class))
 			.filter((FilterFunction<Relation>) Objects::nonNull)
@@ -121,34 +111,68 @@ public class CreateActionSetSparkJob implements Serializable {
 					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
 	}
 
-	private static List<Relation> createRelation(COCI value, boolean duplicate, String p) {
+	private static List<Relation> createRelation(COCI value) throws JsonProcessingException {
 
 		List<Relation> relationList = new ArrayList<>();
-		String prefix;
+
 		String citing;
 		String cited;
 
-		switch (p) {
+		switch (value.getCiting_pid()) {
-			case COCI:
+			case "doi":
-				prefix = DOI_PREFIX;
+				citing = DOI_PREFIX
-				citing = prefix
 					+ IdentifierFactory
 						.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting()));
-				cited = prefix
+				break;
+			case "pmid":
+				citing = PMID_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCiting()));
+				break;
+			case "arxiv":
+				citing = ARXIV_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCiting()));
+				break;
+			case "pmcid":
+				citing = PMCID_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCiting()));
+				break;
+			case "isbn":
+			case "issn":
+				return relationList;
+
+			default:
+				throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
+		}
+
+		switch (value.getCited_pid()) {
+			case "doi":
+				cited = DOI_PREFIX
 					+ IdentifierFactory
 						.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCited()));
 				break;
-			case POCI:
+			case "pmid":
-				prefix = PMID_PREFIX;
+				cited = PMID_PREFIX
-				citing = prefix
-					+ IdentifierFactory
-						.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCiting()));
-				cited = prefix
 					+ IdentifierFactory
 						.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCited()));
 				break;
+			case "arxiv":
+				cited = ARXIV_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCited()));
+				break;
+			case "pmcid":
+				cited = PMCID_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCited()));
+				break;
+			case "isbn":
+			case "issn":
+				return relationList;
 			default:
-				throw new IllegalStateException("Invalid prefix: " + p);
+				throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
 		}
 
 		if (!citing.equals(cited)) {
@@ -157,15 +181,6 @@ public class CreateActionSetSparkJob implements Serializable {
 					getRelation(
 						citing,
 						cited, ModelConstants.CITES));
-
-			if (duplicate && value.getCiting().endsWith(".refs")) {
-				citing = prefix + IdentifierFactory
-					.md5(
-						CleaningFunctions
-							.normalizePidValue(
-								"doi", value.getCiting().substring(0, value.getCiting().indexOf(".refs"))));
-				relationList.add(getRelation(citing, cited, ModelConstants.CITES));
-			}
 		}
 
 		return relationList;

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

@@ -12,10 +12,7 @@ import java.util.zip.ZipInputStream;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FSDataInputStream;
+import org.apache.hadoop.fs.*;
-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;
 
@@ -37,17 +34,17 @@ public class GetOpenCitationsRefs implements Serializable {
 
 		parser.parseArgument(args);
 
-		final String[] inputFile = parser.get("inputFile").split(";");
+//		final String[] inputFile = parser.get("inputFile").split(";");
-		log.info("inputFile {}", Arrays.asList(inputFile));
+//		log.info("inputFile {}", Arrays.asList(inputFile));
 
-		final String workingPath = parser.get("workingPath");
+		final String inputPath = parser.get("inputPath");
-		log.info("workingPath {}", workingPath);
+		log.info("inputPath {}", inputPath);
 
 		final String hdfsNameNode = parser.get("hdfsNameNode");
 		log.info("hdfsNameNode {}", hdfsNameNode);
 
-		final String prefix = parser.get("prefix");
+		final String outputPath = parser.get("outputPath");
-		log.info("prefix {}", prefix);
+		log.info("outputPath {}", outputPath);
 
 		Configuration conf = new Configuration();
 		conf.set("fs.defaultFS", hdfsNameNode);
@@ -56,20 +53,20 @@ public class GetOpenCitationsRefs implements Serializable {
 
 		GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
 
-		for (String file : inputFile) {
+		ocr.doExtract(inputPath, outputPath, fileSystem);
-			ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem, prefix);
-		}
 
 	}
 
-	private void doExtract(String inputFile, String workingPath, FileSystem fileSystem, String prefix)
+	private void doExtract(String inputPath, String outputPath, FileSystem fileSystem)
 		throws IOException {
 
-		final Path path = new Path(inputFile);
+		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
-
+			.listFiles(
-		FSDataInputStream oc_zip = fileSystem.open(path);
+				new Path(inputPath), true);
-
+		while (fileStatusListIterator.hasNext()) {
-		// int count = 1;
+			LocatedFileStatus fileStatus = fileStatusListIterator.next();
+			// do stuff with the file like ...
+			FSDataInputStream oc_zip = fileSystem.open(fileStatus.getPath());
 			try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
 				ZipEntry entry = null;
 				while ((entry = zis.getNextEntry()) != null) {
@@ -81,7 +78,7 @@ public class GetOpenCitationsRefs implements Serializable {
 						// count++;
 						try (
 							FSDataOutputStream out = fileSystem
-							.create(new Path(workingPath + "/" + prefix + "/" + fileName + ".gz"));
+								.create(new Path(outputPath + "/" + fileName + ".gz"));
 							GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
 
 							IOUtils.copy(zis, gzipOs);
@@ -92,6 +89,7 @@ public class GetOpenCitationsRefs implements Serializable {
 				}
 
 			}
+		}
 
 	}
 

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

@@ -0,0 +1,171 @@
+
+package eu.dnetlib.dhp.actionmanager.opencitations;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.Arrays;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.stream.Collectors;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FSDataInputStream;
+import org.apache.hadoop.fs.FSDataOutputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.function.ForeachFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import scala.Tuple2;
+
+/**
+ * @author miriam.baglioni
+ * @Date 29/02/24
+ */
+public class MapOCIdsInPids implements Serializable {
+
+	private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
+	private static final String DELIMITER = ",";
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static void main(final String[] args) throws IOException, ParseException {
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					Objects
+						.requireNonNull(
+							MapOCIdsInPids.class
+								.getResourceAsStream(
+									"/eu/dnetlib/dhp/actionmanager/opencitations/remap_parameters.json"))));
+
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String inputPath = parser.get("inputPath");
+		log.info("inputPath {}", inputPath);
+
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}", outputPath);
+
+		final String nameNode = parser.get("nameNode");
+		log.info("nameNode {}", nameNode);
+
+		unzipCorrespondenceFile(inputPath, nameNode);
+		SparkConf conf = new SparkConf();
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> mapIdentifiers(spark, inputPath, outputPath));
+
+	}
+
+	private static void unzipCorrespondenceFile(String inputPath, String hdfsNameNode) throws IOException {
+		Configuration conf = new Configuration();
+		conf.set("fs.defaultFS", hdfsNameNode);
+
+		final Path path = new Path(inputPath + "/correspondence/omid.zip");
+		FileSystem fileSystem = FileSystem.get(conf);
+
+		FSDataInputStream project_zip = fileSystem.open(path);
+
+		try (ZipInputStream zis = new ZipInputStream(project_zip)) {
+			ZipEntry entry = null;
+			while ((entry = zis.getNextEntry()) != null) {
+
+				if (!entry.isDirectory()) {
+					String fileName = entry.getName();
+					byte buffer[] = new byte[1024];
+					int count;
+
+					try (
+						FSDataOutputStream out = fileSystem
+							.create(new Path(inputPath + "/correspondence/omid.csv"))) {
+
+						while ((count = zis.read(buffer, 0, buffer.length)) != -1)
+							out.write(buffer, 0, count);
+
+					}
+
+				}
+
+			}
+
+		}
+
+	}
+
+	private static void mapIdentifiers(SparkSession spark, String inputPath, String outputPath) {
+		Dataset<COCI> coci = spark
+			.read()
+			.textFile(inputPath + "/JSON")
+			.map(
+				(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
+				Encoders.bean(COCI.class));
+
+		Dataset<Tuple2<String, String>> correspondenceData = spark
+			.read()
+			.format("csv")
+			.option("sep", DELIMITER)
+			.option("inferSchema", "true")
+			.option("header", "true")
+			.option("quotes", "\"")
+			.load(inputPath + "/correspondence/omid.csv")
+			.repartition(5000)
+			.flatMap((FlatMapFunction<Row, Tuple2<String, String>>) r -> {
+				String ocIdentifier = r.getAs("omid");
+				String[] correspondentIdentifiers = ((String) r.getAs("id")).split(" ");
+				return Arrays
+					.stream(correspondentIdentifiers)
+					.map(ci -> new Tuple2<String, String>(ocIdentifier, ci))
+					.collect(Collectors.toList())
+					.iterator();
+			}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
+
+		Dataset<COCI> mappedCitingDataset = coci
+			.joinWith(correspondenceData, coci.col("citing").equalTo(correspondenceData.col("_1")))
+			.map((MapFunction<Tuple2<COCI, Tuple2<String, String>>, COCI>) t2 -> {
+				String correspondent = t2._2()._2();
+				t2._1().setCiting_pid(correspondent.substring(0, correspondent.indexOf(":")));
+				t2._1().setCiting(correspondent.substring(correspondent.indexOf(":") + 1));
+				return t2._1();
+			}, Encoders.bean(COCI.class));
+
+		mappedCitingDataset
+			.joinWith(correspondenceData, mappedCitingDataset.col("cited").equalTo(correspondenceData.col("_1")))
+			.map((MapFunction<Tuple2<COCI, Tuple2<String, String>>, COCI>) t2 -> {
+				String correspondent = t2._2()._2();
+				t2._1().setCited_pid(correspondent.substring(0, correspondent.indexOf(":")));
+				t2._1().setCited(correspondent.substring(correspondent.indexOf(":") + 1));
+				return t2._1();
+			}, Encoders.bean(COCI.class))
+			.write()
+			.mode(SaveMode.Append)
+			.option("compression", "gzip")
+			.json(outputPath);
+
+	}
+
+}

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

@@ -12,11 +12,9 @@ import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.*;
-import org.apache.hadoop.fs.LocatedFileStatus;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.fs.RemoteIterator;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.*;
 import org.slf4j.Logger;
@@ -42,19 +40,21 @@ public class ReadCOCI implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
-		final String[] inputFile = parser.get("inputFile").split(";");
+		final String hdfsNameNode = parser.get("hdfsNameNode");
-		log.info("inputFile {}", Arrays.asList(inputFile));
+		log.info("hdfsNameNode {}", hdfsNameNode);
+
 		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingPath = parser.get("inputPath");
 		log.info("workingPath {}", workingPath);
 
-		final String format = parser.get("format");
-		log.info("format {}", format);
-
 		SparkConf sconf = new SparkConf();
 
+		Configuration conf = new Configuration();
+		conf.set("fs.defaultFS", hdfsNameNode);
+
+		FileSystem fileSystem = FileSystem.get(conf);
 		final String delimiter = Optional
 			.ofNullable(parser.get("delimiter"))
 			.orElse(DEFAULT_DELIMITER);
@@ -66,20 +66,21 @@ public class ReadCOCI implements Serializable {
 				doRead(
 					spark,
 					workingPath,
-					inputFile,
+					fileSystem,
 					outputPath,
-					delimiter,
+					delimiter);
-					format);
 			});
 	}
 
-	private static void doRead(SparkSession spark, String workingPath, String[] inputFiles,
+	private static void doRead(SparkSession spark, String workingPath, FileSystem fileSystem,
 		String outputPath,
-		String delimiter, String format) {
+		String delimiter) throws IOException {
-
+		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
-		for (String inputFile : inputFiles) {
+			.listFiles(
-			String pString = workingPath + "/" + inputFile + ".gz";
+				new Path(workingPath), true);
-
+		while (fileStatusListIterator.hasNext()) {
+			LocatedFileStatus fileStatus = fileStatusListIterator.next();
+			log.info("extracting file {}", fileStatus.getPath().toString());
 			Dataset<Row> cociData = spark
 				.read()
 				.format("csv")
@@ -87,26 +88,26 @@ public class ReadCOCI implements Serializable {
 				.option("inferSchema", "true")
 				.option("header", "true")
 				.option("quotes", "\"")
-				.load(pString)
+				.load(fileStatus.getPath().toString())
 				.repartition(100);
 
 			cociData.map((MapFunction<Row, COCI>) row -> {
+
 				COCI coci = new COCI();
-				if (format.equals("COCI")) {
+
 				coci.setCiting(row.getString(1));
 				coci.setCited(row.getString(2));
-				} else {
+
-					coci.setCiting(String.valueOf(row.getInt(1)));
-					coci.setCited(String.valueOf(row.getInt(2)));
-				}
 				coci.setOci(row.getString(0));
 
 				return coci;
 			}, Encoders.bean(COCI.class))
+				.filter((FilterFunction<COCI>) c -> c != null)
 				.write()
-				.mode(SaveMode.Overwrite)
+				.mode(SaveMode.Append)
 				.option("compression", "gzip")
-				.json(outputPath + inputFile);
+				.json(outputPath);
+			fileSystem.rename(fileStatus.getPath(), new Path("/tmp/miriam/OC/DONE"));
 		}
 
 	}

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

@@ -9,8 +9,10 @@ public class COCI implements Serializable {
 	private String oci;
 
 	private String citing;
+	private String citing_pid;
 
 	private String cited;
+	private String cited_pid;
 
 	public String getOci() {
 		return oci;
@@ -25,6 +27,8 @@ public class COCI implements Serializable {
 	}
 
 	public void setCiting(String citing) {
+		if (citing != null && citing.startsWith("omid:"))
+			citing = citing.substring(5);
 		this.citing = citing;
 	}
 
@@ -33,7 +37,24 @@ public class COCI implements Serializable {
 	}
 
 	public void setCited(String cited) {
+		if (cited != null && cited.startsWith("omid:"))
+			cited = cited.substring(5);
 		this.cited = cited;
 	}
 
+	public String getCiting_pid() {
+		return citing_pid;
+	}
+
+	public void setCiting_pid(String citing_pid) {
+		this.citing_pid = citing_pid;
+	}
+
+	public String getCited_pid() {
+		return cited_pid;
+	}
+
+	public void setCited_pid(String cited_pid) {
+		this.cited_pid = cited_pid;
+	}
 }

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

@@ -1,7 +1,26 @@
 
 package eu.dnetlib.dhp.actionmanager.project;
 
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.util.Arrays;
+import java.util.Objects;
+import java.util.Optional;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.api.java.function.MapGroupsFunction;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import com.fasterxml.jackson.databind.ObjectMapper;
+
 import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme;
 import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject;
 import eu.dnetlib.dhp.actionmanager.project.utils.model.JsonTopic;
@@ -15,25 +34,8 @@ import eu.dnetlib.dhp.schema.oaf.OafEntity;
 import eu.dnetlib.dhp.schema.oaf.Project;
 import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
 import eu.dnetlib.dhp.utils.DHPUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.mapred.SequenceFileOutputFormat;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.api.java.function.MapGroupsFunction;
-import org.apache.spark.sql.Dataset;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SparkSession;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import scala.Tuple2;
 
-import java.util.Arrays;
-import java.util.Objects;
-import java.util.Optional;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
 /**
  * Class that makes the ActionSet. To prepare the AS two joins are needed
  *

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

@@ -0,0 +1,195 @@
+
+package eu.dnetlib.dhp.actionmanager.transformativeagreement;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.*;
+
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.GzipCodec;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.transformativeagreement.model.TransformativeAgreementModel;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Country;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.utils.*;
+import scala.Tuple2;
+
+public class CreateActionSetSparkJob implements Serializable {
+
+	private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static final String IREL_PROJECT = "40|100018998___::1e5e62235d094afd01cd56e65112fc63";
+	private static final String TRANSFORMATIVE_AGREEMENT = "openapc::transformativeagreement";
+
+	public static void main(final String[] args) throws IOException, ParseException {
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					Objects
+						.requireNonNull(
+							CreateActionSetSparkJob.class
+								.getResourceAsStream(
+									"/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json"))));
+
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String inputPath = parser.get("inputPath");
+		log.info("inputPath {}", inputPath);
+
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}", outputPath);
+
+		SparkConf conf = new SparkConf();
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> createActionSet(spark, inputPath, outputPath));
+
+	}
+
+	private static void createActionSet(SparkSession spark, String inputPath, String outputPath) {
+		JavaRDD<AtomicAction> relations = spark
+			.read()
+			.textFile(inputPath)
+			.map(
+				(MapFunction<String, TransformativeAgreementModel>) value -> OBJECT_MAPPER
+					.readValue(value, TransformativeAgreementModel.class),
+				Encoders.bean(TransformativeAgreementModel.class))
+			.flatMap(
+				(FlatMapFunction<TransformativeAgreementModel, Relation>) value -> createRelation(
+					value)
+						.iterator(),
+				Encoders.bean(Relation.class))
+			.filter((FilterFunction<Relation>) Objects::nonNull)
+			.toJavaRDD()
+			.map(p -> new AtomicAction(p.getClass(), p));
+//TODO relations in stand-by waiting to know if we need to create them or not In case we need just make a union before saving the sequence file
+		spark
+			.read()
+			.textFile(inputPath)
+			.map(
+				(MapFunction<String, TransformativeAgreementModel>) value -> OBJECT_MAPPER
+					.readValue(value, TransformativeAgreementModel.class),
+				Encoders.bean(TransformativeAgreementModel.class))
+			.map(
+				(MapFunction<TransformativeAgreementModel, Result>) value -> createResult(
+					value),
+				Encoders.bean(Result.class))
+			.filter((FilterFunction<Result>) r -> r != null)
+			.toJavaRDD()
+			.map(p -> new AtomicAction(p.getClass(), p))
+			.mapToPair(
+				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+			.saveAsHadoopFile(
+				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+
+	}
+
+	private static Result createResult(TransformativeAgreementModel value) {
+		Result r = new Result();
+		r
+			.setId(
+				"50|doi_________::"
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi())));
+		r.setTransformativeAgreement(value.getAgreement());
+		Country country = new Country();
+		country.setClassid(value.getCountry());
+		country.setClassname(value.getCountry());
+		country
+			.setDataInfo(
+				OafMapperUtils
+					.dataInfo(
+						false, ModelConstants.SYSIMPORT_ACTIONSET, false, false,
+						OafMapperUtils
+							.qualifier(
+								"openapc::transformativeagreement",
+								"Harvested from Trnasformative Agreement file from OpenAPC",
+								ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
+						"0.9"));
+		country.setSchemeid(ModelConstants.DNET_COUNTRY_TYPE);
+		country.setSchemename(ModelConstants.DNET_COUNTRY_TYPE);
+		r.setCountry(Arrays.asList(country));
+		return r;
+	}
+
+	private static List<Relation> createRelation(TransformativeAgreementModel value) {
+
+		List<Relation> relationList = new ArrayList<>();
+
+		if (value.getAgreement().startsWith("IReL")) {
+			String paper;
+
+			paper = "50|doi_________::"
+				+ IdentifierFactory
+					.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi()));
+
+			relationList
+				.add(
+					getRelation(
+						paper,
+						IREL_PROJECT, ModelConstants.IS_PRODUCED_BY));
+
+			relationList.add(getRelation(IREL_PROJECT, paper, ModelConstants.PRODUCES));
+		}
+		return relationList;
+	}
+
+	public static Relation getRelation(
+		String source,
+		String target,
+		String relClass) {
+
+		return OafMapperUtils
+			.getRelation(
+				source,
+				target,
+				ModelConstants.RESULT_PROJECT,
+				ModelConstants.OUTCOME,
+				relClass,
+				Arrays
+					.asList(
+						OafMapperUtils.keyValue(ModelConstants.OPEN_APC_ID, ModelConstants.OPEN_APC_NAME)),
+				OafMapperUtils
+					.dataInfo(
+						false, null, false, false,
+						OafMapperUtils
+							.qualifier(
+								TRANSFORMATIVE_AGREEMENT, "Transformative Agreement",
+								ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
+						"0.9"),
+				null);
+	}
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java

@@ -0,0 +1,51 @@
+
+package eu.dnetlib.dhp.actionmanager.transformativeagreement.model;
+
+import java.io.Serializable;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+
+/**
+ * @author miriam.baglioni
+ * @Date 18/12/23
+ */
+@JsonIgnoreProperties(ignoreUnknown = true)
+
+public class TransformativeAgreementModel implements Serializable {
+	private String institution;
+	private String doi;
+	private String agreement;
+	private String country;
+
+	public String getCountry() {
+		return country;
+	}
+
+	public void setCountry(String country) {
+		this.country = country;
+	}
+
+	public String getInstitution() {
+		return institution;
+	}
+
+	public void setInstitution(String institution) {
+		this.institution = institution;
+	}
+
+	public String getDoi() {
+		return doi;
+	}
+
+	public void setDoi(String doi) {
+		this.doi = doi;
+	}
+
+	public String getAgreement() {
+		return agreement;
+	}
+
+	public void setAgreement(String agreement) {
+		this.agreement = agreement;
+	}
+}

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

@@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.actionmanager.Constants.*;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
 
 import java.io.Serializable;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
@@ -13,7 +14,9 @@ import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.api.java.function.MapGroupsFunction;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SaveMode;
@@ -68,18 +71,59 @@ public class SparkAtomicActionUsageJob implements Serializable {
 
 		final String workingPath = parser.get("workingPath");
 
+		final String datasourcePath = parser.get("datasourcePath");
+
 		runWithSparkHiveSession(
 			conf,
 			isSparkSessionManaged,
 			spark -> {
 				removeOutputDir(spark, outputPath);
-				prepareData(dbname, spark, workingPath + "/usageDb", "usage_stats", "result_id");
+				prepareResultData(
+					dbname, spark, workingPath + "/usageDb",
+					"usage_stats",
+					"result_id",
+					"repository_id",
+					datasourcePath);
 				prepareData(dbname, spark, workingPath + "/projectDb", "project_stats", "id");
 				prepareData(dbname, spark, workingPath + "/datasourceDb", "datasource_stats", "repository_id");
 				writeActionSet(spark, workingPath, outputPath);
 			});
 	}
 
+	private static void prepareResultData(String dbname, SparkSession spark, String workingPath, String tableName,
+		String resultAttributeName, String datasourceAttributeName,
+		String datasourcePath) {
+		Dataset<UsageStatsResultModel> resultModel = spark
+			.sql(
+				String
+					.format(
+						"select %s as id, %s as datasourceId, sum(downloads) as downloads, sum(views) as views " +
+							"from %s.%s group by %s, %s",
+						resultAttributeName, datasourceAttributeName, dbname, tableName, resultAttributeName,
+						datasourceAttributeName))
+			.as(Encoders.bean(UsageStatsResultModel.class));
+		Dataset<Datasource> datasource = readPath(spark, datasourcePath, Datasource.class)
+			.filter((FilterFunction<Datasource>) d -> !d.getDataInfo().getDeletedbyinference())
+			.map((MapFunction<Datasource, Datasource>) d -> {
+				d.setId(d.getId().substring(3));
+				return d;
+			}, Encoders.bean(Datasource.class));
+		resultModel
+			.joinWith(datasource, resultModel.col("datasourceId").equalTo(datasource.col("id")), "left")
+			.map((MapFunction<Tuple2<UsageStatsResultModel, Datasource>, UsageStatsResultModel>) t2 -> {
+				UsageStatsResultModel usrm = t2._1();
+				if(Optional.ofNullable(t2._2()).isPresent())
+					usrm.setDatasourceId(usrm.getDatasourceId() + "||" + t2._2().getOfficialname().getValue());
+				else
+					usrm.setDatasourceId(usrm.getDatasourceId() + "||NO_MATCH_FOUND");
+				return usrm;
+			}, Encoders.bean(UsageStatsResultModel.class))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
+			.json(workingPath);
+	}
+
 	private static void prepareData(String dbname, SparkSession spark, String workingPath, String tableName,
 		String attribute_name) {
 		spark
@@ -115,15 +159,62 @@ public class SparkAtomicActionUsageJob implements Serializable {
 
 	}
 
+	public static Measure newMeasureInstance(String id) {
+		Measure m = new Measure();
+		m.setId(id);
+		m.setUnit(new ArrayList<>());
+		return m;
+	}
+
 	private static Dataset<Result> getFinalIndicatorsResult(SparkSession spark, String inputPath) {
 
-		return readPath(spark, inputPath, UsageStatsModel.class)
+		return readPath(spark, inputPath, UsageStatsResultModel.class)
-			.map((MapFunction<UsageStatsModel, Result>) usm -> {
+			.groupByKey((MapFunction<UsageStatsResultModel, String>) usm -> usm.getId(), Encoders.STRING())
+			.mapGroups((MapGroupsFunction<String, UsageStatsResultModel, Result>) (k, it) -> {
 				Result r = new Result();
-				r.setId("50|" + usm.getId());
+				r.setId("50|" + k);
-				r.setMeasures(getMeasure(usm.getDownloads(), usm.getViews()));
+				// id = download or view and unit = list of key value pairs
+				Measure download = newMeasureInstance("downloads");
+				Measure view = newMeasureInstance("views");
+				UsageStatsResultModel first = it.next();
+				addCountForDatasource(download, first, view);
+				it.forEachRemaining(usm -> {
+					addCountForDatasource(download, usm, view);
+				});
+				r.setMeasures(Arrays.asList(download, view));
 				return r;
-			}, Encoders.bean(Result.class));
+			}, Encoders.bean(Result.class))
+//			.map((MapFunction<UsageStatsResultModel, Result>) usm -> {
+//				Result r = new Result();
+//				r.setId("50|" + usm.getId());
+//				r.setMeasures(getMeasure(usm.getDownloads(), usm.getViews()));
+//				return r;
+//			}, Encoders.bean(Result.class));
+		;
+	}
+
+	private static void addCountForDatasource(Measure download, UsageStatsResultModel usm, Measure view) {
+		DataInfo dataInfo = OafMapperUtils
+			.dataInfo(
+				false,
+				UPDATE_DATA_INFO_TYPE,
+				true,
+				false,
+				OafMapperUtils
+					.qualifier(
+						UPDATE_MEASURE_USAGE_COUNTS_CLASS_ID,
+						UPDATE_CLASS_NAME,
+						ModelConstants.DNET_PROVENANCE_ACTIONS,
+						ModelConstants.DNET_PROVENANCE_ACTIONS),
+				"");
+		download
+			.getUnit()
+			.add(
+				OafMapperUtils
+					.newKeyValueInstance(usm.getDatasourceId(), String.valueOf(usm.getDownloads()), dataInfo));
+		view
+			.getUnit()
+			.add(OafMapperUtils.newKeyValueInstance(usm.getDatasourceId(), String.valueOf(usm.getViews()), dataInfo));
 	}
 
 	private static Dataset<Project> getFinalIndicatorsProject(SparkSession spark, String inputPath) {

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

@@ -0,0 +1,18 @@
+
+package eu.dnetlib.dhp.actionmanager.usagestats;
+
+/**
+ * @author miriam.baglioni
+ * @Date 30/06/23
+ */
+public class UsageStatsResultModel extends UsageStatsModel {
+	private String datasourceId;
+
+	public String getDatasourceId() {
+		return datasourceId;
+	}
+
+	public void setDatasourceId(String datasourceId) {
+		this.datasourceId = datasourceId;
+	}
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/XSLTTransformationFunction.java

@@ -48,7 +48,7 @@ public class XSLTTransformationFunction implements MapFunction<MetadataRecord, M
 	@Override
 	public MetadataRecord call(MetadataRecord value) {
 		aggregationCounter.getTotalItems().add(1);
-		try {
+
 		Processor processor = new Processor(false);
 
 		processor.registerExtensionFunction(cleanFunction);
@@ -60,11 +60,18 @@ public class XSLTTransformationFunction implements MapFunction<MetadataRecord, M
 		comp.setParameter(datasourceIDParam, new XdmAtomicValue(value.getProvenance().getDatasourceId()));
 		QName datasourceNameParam = new QName(DATASOURCE_NAME_PARAM);
 		comp.setParameter(datasourceNameParam, new XdmAtomicValue(value.getProvenance().getDatasourceName()));
-			XsltExecutable xslt = comp
+		XsltExecutable xslt;
+		XdmNode source;
+		try {
+			xslt = comp
 				.compile(new StreamSource(IOUtils.toInputStream(transformationRule, StandardCharsets.UTF_8)));
-			XdmNode source = processor
+			source = processor
 				.newDocumentBuilder()
 				.build(new StreamSource(IOUtils.toInputStream(value.getBody(), StandardCharsets.UTF_8)));
+		} catch (Throwable e) {
+			throw new RuntimeException("Error on parsing xslt", e);
+		}
+		try {
 			XsltTransformer trans = xslt.load();
 			trans.setInitialContextNode(source);
 			final StringWriter output = new StringWriter();

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json

@@ -17,6 +17,18 @@
     "paramDescription": "the path to get the input data from Pubmed",
     "paramRequired": true
   },
+  {
+    "paramName": "oip",
+    "paramLongName": "openapcInputPath",
+    "paramDescription": "the path to get the input data from OpenAPC",
+    "paramRequired": true
+  },
+  {
+    "paramName": "dip",
+    "paramLongName": "dataciteInputPath",
+    "paramDescription": "the path to get the input data from Datacite",
+    "paramRequired": true
+  },
   {
     "paramName": "o",
     "paramLongName": "outputPath",

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties

@@ -31,6 +31,9 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
 # The following is needed as a property of a workflow
 oozie.wf.application.path=${oozieTopWfApplicationPath}
 
-crossrefInputPath=/data/bip-affiliations/data.json
+crossrefInputPath=/data/bip-affiliations/crossref-data.json
 pubmedInputPath=/data/bip-affiliations/pubmed-data.json
+openapcInputPath=/data/bip-affiliations/openapc-data.json
+dataciteInputPath=/data/bip-affiliations/datacite-data.json
+
 outputPath=/tmp/crossref-affiliations-output-v5

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

@@ -9,6 +9,14 @@
             <name>pubmedInputPath</name>
             <description>the path where to find the inferred affiliation relations from Pubmed</description>
         </property>
+        <property>
+            <name>openapcInputPath</name>
+            <description>the path where to find the inferred affiliation relations from OpenAPC</description>
+        </property>
+        <property>
+            <name>dataciteInputPath</name>
+            <description>the path where to find the inferred affiliation relations from Datacite</description>
+        </property>
         <property>
             <name>outputPath</name>
             <description>the path where to store the actionset</description>
@@ -102,6 +110,9 @@
             </spark-opts>
             <arg>--crossrefInputPath</arg><arg>${crossrefInputPath}</arg>
             <arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
+            <arg>--openapcInputPath</arg><arg>${openapcInputPath}</arg>
+            <arg>--dataciteInputPath</arg><arg>${dataciteInputPath}</arg>
+
             <arg>--outputPath</arg><arg>${outputPath}</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json

@@ -16,5 +16,10 @@
     "paramLongName": "outputPath",
     "paramDescription": "the path of the new ActionSet",
     "paramRequired": true
+  },  {
+  "paramName": "fd",
+  "paramLongName": "distributeDoi",
+  "paramDescription": "the path of the new ActionSet",
+  "paramRequired": false
 }
 ]

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

@@ -0,0 +1,20 @@
+[
+  {
+    "paramName": "sp",
+    "paramLongName": "sourcePath",
+    "paramDescription": "the zipped opencitations file",
+    "paramRequired": true
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "the working path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  }
+]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/oozie_app/config-default.xml

@@ -0,0 +1,30 @@
+<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>hiveMetastoreUris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>hiveJdbcUrl</name>
+        <value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
+    </property>
+    <property>
+        <name>hiveDbName</name>
+        <value>openaire</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+</configuration>

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

@@ -0,0 +1,153 @@
+
+<workflow-app name="FOS no doi" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>fosPath</name>
+            <description>the input path of the resources to be extended</description>
+        </property>
+        <property>
+            <name>outputPath</name>
+            <description>the path where to store the actionset</description>
+        </property>
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
+        <property>
+            <name>spark2YarnHistoryServerAddress</name>
+            <description>spark 2.* yarn history server address</description>
+        </property>
+        <property>
+            <name>spark2EventLogDir</name>
+            <description>spark 2.* event log dir location</description>
+        </property>
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+
+        </configuration>
+    </global>
+    <start to="getFOS"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+
+
+    <action name="getFOS">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Gets Data from FOS csv file</name>
+            <class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSSparkJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${fosPath}</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/input/fos</arg>
+            <arg>--delimiter</arg><arg>${delimiter}</arg>
+        </spark>
+        <ok to="prepareFos"/>
+        <error to="Kill"/>
+    </action>
+
+
+    <action name="prepareFos">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the results from FOS</name>
+            <class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareFOSSparkJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${workingDir}/input/fos</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/prepared</arg>
+            <arg>--distributeDoi</arg><arg>false</arg>
+        </spark>
+        <ok to="produceActionSet"/>
+        <error to="Kill"/>
+    </action>
+
+
+
+    <action name="produceActionSet">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Save the action set grouping results with the same id</name>
+            <class>eu.dnetlib.dhp.actionmanager.fosnodoi.CreateActionSetSparkJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${workingDir}/prepared/fos</arg>
+            <arg>--outputPath</arg><arg>${outputPath}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>

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

@@ -1,13 +1,13 @@
 [
   {
-    "paramName": "if",
+    "paramName": "ip",
-    "paramLongName": "inputFile",
+    "paramLongName": "inputPath",
     "paramDescription": "the zipped opencitations file",
     "paramRequired": true
   },
   {
-    "paramName": "wp",
+    "paramName": "op",
-    "paramLongName": "workingPath",
+    "paramLongName": "outputPath",
     "paramDescription": "the working path",
     "paramRequired": true
   },
@@ -16,11 +16,5 @@
     "paramLongName": "hdfsNameNode",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
-  },
-  {
-    "paramName": "p",
-    "paramLongName": "prefix",
-    "paramDescription": "COCI or POCI",
-    "paramRequired": true
   }
 ]

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

@@ -1,7 +1,7 @@
 [
   {
-    "paramName": "wp",
+    "paramName": "ip",
-    "paramLongName": "workingPath",
+    "paramLongName": "inputPath",
     "paramDescription": "the zipped opencitations file",
     "paramRequired": true
   },
@@ -24,15 +24,9 @@
     "paramLongName": "outputPath",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
-  },
-  {
-    "paramName": "if",
-    "paramLongName": "inputFile",
-    "paramDescription": "the hdfs name node",
-    "paramRequired": true
   },  {
-  "paramName": "f",
+  "paramName": "nn",
-  "paramLongName": "format",
+  "paramLongName": "hdfsNameNode",
   "paramDescription": "the hdfs name node",
   "paramRequired": true
 }

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

@@ -27,7 +27,9 @@
             <case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
             <case to="extract">${wf:conf('resumeFrom') eq 'ExtractContent'}</case>
             <case to="read">${wf:conf('resumeFrom') eq 'ReadContent'}</case>
-            <default to="create_actionset"/> <!-- first action to be done when downloadDump is to be performed -->
+            <case to="remap">${wf:conf('resumeFrom') eq 'MapContent'}</case>
+            <case to="create_actionset">${wf:conf('resumeFrom') eq 'CreateAS'}</case>
+            <default to="deleteoutputpath"/> <!-- first action to be done when downloadDump is to be performed -->
         </switch>
     </decision>
 
@@ -35,6 +37,15 @@
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
+    <action name="deleteoutputpath">
+        <fs>
+            <delete path='${inputPath}'/>
+            <mkdir path='${inputPath}'/>
+        </fs>
+        <ok to="download"/>
+        <error to="Kill"/>
+    </action>
+
     <action name="download">
         <shell xmlns="uri:oozie:shell-action:0.2">
             <job-tracker>${jobTracker}</job-tracker>
@@ -47,7 +58,28 @@
             </configuration>
             <exec>download.sh</exec>
             <argument>${filelist}</argument>
-            <argument>${workingPath}/${prefix}/Original</argument>
+            <argument>${inputPath}/Original</argument>
+            <env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
+            <file>download.sh</file>
+            <capture-output/>
+        </shell>
+        <ok to="download_correspondence"/>
+        <error to="Kill"/>
+    </action>
+<!--    downloads the correspondence from the omid and the pid (doi, pmid etc)-->
+    <action name="download_correspondence">
+        <shell xmlns="uri:oozie:shell-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <configuration>
+                <property>
+                    <name>mapred.job.queue.name</name>
+                    <value>${queueName}</value>
+                </property>
+            </configuration>
+            <exec>download_corr.sh</exec>
+            <argument>${filecorrespondence}</argument>
+            <argument>${inputPath}/correspondence</argument>
             <env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
             <file>download.sh</file>
             <capture-output/>
@@ -60,9 +92,19 @@
         <java>
             <main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
             <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
-            <arg>--inputFile</arg><arg>${inputFile}</arg>
+            <arg>--inputPath</arg><arg>${inputPath}/Original</arg>
-            <arg>--workingPath</arg><arg>${workingPath}/${prefix}</arg>
+            <arg>--outputPath</arg><arg>${inputPath}/Extracted</arg>
-            <arg>--prefix</arg><arg>${prefix}</arg>
+        </java>
+        <ok to="read"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="extract_correspondence">
+        <java>
+            <main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
+            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
+            <arg>--inputPath</arg><arg>${inputPath}/correspondence</arg>
+            <arg>--outputPath</arg><arg>${inputPath}/correspondence_extracted</arg>
         </java>
         <ok to="read"/>
         <error to="Kill"/>
@@ -85,11 +127,35 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
             </spark-opts>
-            <arg>--workingPath</arg><arg>${workingPath}/${prefix}/${prefix}</arg>
+            <arg>--inputPath</arg><arg>${inputPath}/Extracted</arg>
-            <arg>--outputPath</arg><arg>${workingPath}/${prefix}/${prefix}_JSON/</arg>
+            <arg>--outputPath</arg><arg>${inputPath}/JSON</arg>
             <arg>--delimiter</arg><arg>${delimiter}</arg>
-            <arg>--inputFile</arg><arg>${inputFileCoci}</arg>
+            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
-            <arg>--format</arg><arg>${prefix}</arg>
+        </spark>
+        <ok to="remap"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="remap">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the AS for OC</name>
+            <class>eu.dnetlib.dhp.actionmanager.opencitations.MapOCIdsInPids</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}</arg>
+            <arg>--outputPath</arg><arg>${outputPathExtraction}</arg>
+            <arg>--nameNode</arg><arg>${nameNode}</arg>
         </spark>
         <ok to="create_actionset"/>
         <error to="Kill"/>
@@ -112,7 +178,7 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
             </spark-opts>
-            <arg>--inputPath</arg><arg>${workingPath}</arg>
+            <arg>--inputPath</arg><arg>${outputPathExtraction}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
         </spark>
         <ok to="End"/>

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

@@ -0,0 +1,25 @@
+[
+  {
+    "paramName": "ip",
+    "paramLongName": "inputPath",
+    "paramDescription": "the zipped opencitations file",
+    "paramRequired": true
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "the working path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManged",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  },{
+  "paramName": "nn",
+  "paramLongName": "nameNode",
+  "paramDescription": "the hdfs name node",
+  "paramRequired": true
+}
+]

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

@@ -0,0 +1,20 @@
+[
+  {
+    "paramName": "ip",
+    "paramLongName": "inputPath",
+    "paramDescription": "the zipped opencitations file",
+    "paramRequired": true
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "the working path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  }
+]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/input_read_parameters.json

@@ -0,0 +1,30 @@
+[
+
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  },
+  {
+    "paramName": "d",
+    "paramLongName": "delimiter",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": true
+  },
+  {
+    "paramName": "if",
+    "paramLongName": "inputFile",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": true
+  }
+]
+
+
+

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/config-default.xml

@@ -0,0 +1,58 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+    <property>
+        <name>hive_metastore_uris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>spark2YarnHistoryServerAddress</name>
+        <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
+    </property>
+    <property>
+        <name>spark2ExtraListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+    </property>
+    <property>
+        <name>spark2SqlQueryExecutionListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>sparkExecutorNumber</name>
+        <value>4</value>
+    </property>
+    <property>
+        <name>spark2EventLogDir</name>
+        <value>/user/spark/spark2ApplicationHistory</value>
+    </property>
+    <property>
+        <name>sparkDriverMemory</name>
+        <value>15G</value>
+    </property>
+    <property>
+        <name>sparkExecutorMemory</name>
+        <value>6G</value>
+    </property>
+    <property>
+        <name>sparkExecutorCores</name>
+        <value>1</value>
+    </property>
+</configuration>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/download.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+curl -L $1  | hdfs dfs -put - $2

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

@@ -0,0 +1,82 @@
+<workflow-app name="Transfomative Agreement Integration" xmlns="uri:oozie:workflow:0.5">
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+
+        </configuration>
+    </global>
+
+    <start to="resume_from"/>
+
+    <decision name="resume_from">
+        <switch>
+            <case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
+            <default to="create_actionset"/> <!-- first action to be done when downloadDump is to be performed -->
+        </switch>
+    </decision>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="download">
+        <shell xmlns="uri:oozie:shell-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <configuration>
+                <property>
+                    <name>mapred.job.queue.name</name>
+                    <value>${queueName}</value>
+                </property>
+            </configuration>
+            <exec>download.sh</exec>
+            <argument>${inputFile}</argument>
+            <argument>${workingDir}/transformativeagreement/transformativeAgreement.json</argument>
+            <env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
+            <file>download.sh</file>
+            <capture-output/>
+        </shell>
+        <ok to="create_actionset"/>
+        <error to="Kill"/>
+    </action>
+
+
+    <action name="create_actionset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the AS for the Transformative Agreement</name>
+            <class>eu.dnetlib.dhp.actionmanager.transformativeagreement.CreateActionSetSparkJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${workingDir}/transformativeagreement/</arg>
+            <arg>--outputPath</arg><arg>${outputPath}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+    <end name="End"/>
+</workflow-app>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json

@@ -28,5 +28,11 @@
     "paramLongName": "workingPath",
     "paramDescription": "the workingPath where to save the content of the usage_stats table",
     "paramRequired": true
+  },
+  {
+    "paramName": "dp",
+    "paramLongName": "datasourcePath",
+    "paramDescription": "the workingPath where to save the content of the usage_stats table",
+    "paramRequired": true
   }
 ]

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

@@ -90,6 +90,7 @@
             <arg>--outputPath</arg><arg>${outputPath}</arg>
             <arg>--usagestatsdb</arg><arg>${usagestatsdb}</arg>
             <arg>--workingPath</arg><arg>${workingDir}</arg>
+            <arg>--datasourcePath</arg><arg>${datasourcePath}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java

@@ -78,10 +78,6 @@ public class PrepareAffiliationRelationsTest {
 			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
 			.getPath();
 
-		String pubmedAffiliationRelationsPath = getClass()
-			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
-			.getPath();
-
 		String outputPath = workingDir.toString() + "/actionSet";
 
 		PrepareAffiliationRelations
@@ -89,7 +85,9 @@ public class PrepareAffiliationRelationsTest {
 				new String[] {
 					"-isSparkSessionManaged", Boolean.FALSE.toString(),
 					"-crossrefInputPath", crossrefAffiliationRelationPath,
-					"-pubmedInputPath", pubmedAffiliationRelationsPath,
+					"-pubmedInputPath", crossrefAffiliationRelationPath,
+					"-openapcInputPath", crossrefAffiliationRelationPath,
+					"-dataciteInputPath", crossrefAffiliationRelationPath,
 					"-outputPath", outputPath
 				});
 
@@ -106,7 +104,7 @@ public class PrepareAffiliationRelationsTest {
 //            );
 //        }
 		// count the number of relations
-		assertEquals(40, tmp.count());
+		assertEquals(80, tmp.count());
 
 		Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
 		dataset.createOrReplaceTempView("result");
@@ -117,7 +115,7 @@ public class PrepareAffiliationRelationsTest {
 		// verify that we have equal number of bi-directional relations
 		Assertions
 			.assertEquals(
-				20, execVerification
+				40, execVerification
 					.filter(
 						"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
 					.collectAsList()
@@ -125,7 +123,7 @@ public class PrepareAffiliationRelationsTest {
 
 		Assertions
 			.assertEquals(
-				20, execVerification
+				40, execVerification
 					.filter(
 						"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
 					.collectAsList()

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

@@ -0,0 +1,104 @@
+
+package eu.dnetlib.dhp.actionmanager.fosnodoi;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.LocalFileSystem;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSSparkJob;
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareTest;
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.ProduceTest;
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
+
+/**
+ * @author miriam.baglioni
+ * @Date 13/02/23
+ */
+public class GetFosTest {
+
+	private static final Logger log = LoggerFactory.getLogger(ProduceTest.class);
+
+	private static Path workingDir;
+	private static SparkSession spark;
+	private static LocalFileSystem fs;
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files.createTempDirectory(PrepareTest.class.getSimpleName());
+
+		fs = FileSystem.getLocal(new Configuration());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(ProduceTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(PrepareTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	@Disabled
+	void test3() throws Exception {
+		final String sourcePath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.csv")
+			.getPath();
+
+		final String outputPath = workingDir.toString() + "/fos.json";
+		GetFOSSparkJob
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--sourcePath", sourcePath,
+
+					"-outputPath", outputPath,
+					"-delimiter", ","
+
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<FOSDataModel> tmp = sc
+			.textFile(outputPath)
+			.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
+
+		tmp.foreach(t -> Assertions.assertTrue(t.getOaid() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
+
+		tmp.foreach(t -> System.out.println(new ObjectMapper().writeValueAsString(t)));
+
+	}
+
+}

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

@@ -0,0 +1,99 @@
+
+package eu.dnetlib.dhp.actionmanager.fosnodoi;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.LocalFileSystem;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareFOSSparkJob;
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareSDGSparkJob;
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.ProduceTest;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+public class PrepareTest {
+
+	private static final Logger log = LoggerFactory.getLogger(ProduceTest.class);
+
+	private static Path workingDir;
+	private static SparkSession spark;
+	private static LocalFileSystem fs;
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files.createTempDirectory(PrepareTest.class.getSimpleName());
+
+		fs = FileSystem.getLocal(new Configuration());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(ProduceTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(PrepareTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void fosPrepareTest() throws Exception {
+		final String sourcePath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.json")
+			.getPath();
+
+		PrepareFOSSparkJob
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--sourcePath", sourcePath,
+
+					"-outputPath", workingDir.toString() + "/work",
+					"-distributeDoi", Boolean.FALSE.toString()
+
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Result> tmp = sc
+			.textFile(workingDir.toString() + "/work/fos")
+			.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
+
+		tmp.foreach(t -> System.out.println(new ObjectMapper().writeValueAsString(t)));
+
+	}
+
+}

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java

@@ -76,7 +76,7 @@ public class CreateOpenCitationsASTest {
 
 		String inputPath = getClass()
 			.getResource(
-				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/jsonforas")
 			.getPath();
 
 		CreateActionSetSparkJob
@@ -84,8 +84,6 @@ public class CreateOpenCitationsASTest {
 				new String[] {
 					"-isSparkSessionManaged",
 					Boolean.FALSE.toString(),
-					"-shouldDuplicateRels",
-					Boolean.TRUE.toString(),
 					"-inputPath",
 					inputPath,
 					"-outputPath",
@@ -99,9 +97,10 @@ public class CreateOpenCitationsASTest {
 			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
 			.map(aa -> ((Relation) aa.getPayload()));
 
-		assertEquals(31, tmp.count());
+		Assertions.assertEquals(27, tmp.count());
+		tmp.foreach(r -> Assertions.assertEquals(1, r.getCollectedfrom().size()));
 
-		// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
+		tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
 
 	}
 

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/RemapTest.java

@@ -0,0 +1,90 @@
+
+package eu.dnetlib.dhp.actionmanager.opencitations;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.LocalFileSystem;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
+
+/**
+ * @author miriam.baglioni
+ * @Date 07/03/24
+ */
+public class RemapTest {
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+	private static final Logger log = LoggerFactory
+		.getLogger(RemapTest.class);
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files
+			.createTempDirectory(RemapTest.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(RemapTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(RemapTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void testRemap() throws Exception {
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap")
+			.getPath();
+
+		MapOCIdsInPids
+			.main(
+				new String[] {
+					"-isSparkSessionManged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/out/",
+					"-nameNode", "input1;input2;input3;input4;input5"
+				});
+
+	}
+}

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java

@@ -0,0 +1,324 @@
+
+package eu.dnetlib.dhp.actionmanager.transformativeagreement;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob;
+import eu.dnetlib.dhp.actionmanager.opencitations.CreateOpenCitationsASTest;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+
+/**
+ * @author miriam.baglioni
+ * @Date 13/02/24
+ */
+public class CreateTAActionSetTest {
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+	private static final Logger log = LoggerFactory
+		.getLogger(CreateOpenCitationsASTest.class);
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files
+			.createTempDirectory(CreateTAActionSetTest.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(CreateTAActionSetTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(CreateTAActionSetTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void createActionSet() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/transformativeagreement/facts.json")
+			.getPath();
+
+		eu.dnetlib.dhp.actionmanager.transformativeagreement.CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet1"
+				});
+
+	}
+
+	@Test
+	void testNumberofRelations2() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+			.getPath();
+
+		eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet2"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet2", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		assertEquals(23, tmp.count());
+
+		// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
+
+	}
+
+	@Test
+	void testRelationsCollectedFrom() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+			.getPath();
+
+		eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet3"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet3", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		tmp.foreach(r -> {
+			assertEquals(ModelConstants.OPENOCITATIONS_NAME, r.getCollectedfrom().get(0).getValue());
+			assertEquals(ModelConstants.OPENOCITATIONS_ID, r.getCollectedfrom().get(0).getKey());
+		});
+
+	}
+
+	@Test
+	void testRelationsDataInfo() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+			.getPath();
+
+		eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet4"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet4", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		tmp.foreach(r -> {
+			assertEquals(false, r.getDataInfo().getInferred());
+			assertEquals(false, r.getDataInfo().getDeletedbyinference());
+			assertEquals("0.91", r.getDataInfo().getTrust());
+			assertEquals(
+				eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob.OPENCITATIONS_CLASSID,
+				r.getDataInfo().getProvenanceaction().getClassid());
+			assertEquals(
+				eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob.OPENCITATIONS_CLASSNAME,
+				r.getDataInfo().getProvenanceaction().getClassname());
+			assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemeid());
+			assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemename());
+		});
+
+	}
+
+	@Test
+	void testRelationsSemantics() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+			.getPath();
+
+		eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet5"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet5", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		tmp.foreach(r -> {
+			assertEquals("citation", r.getSubRelType());
+			assertEquals("resultResult", r.getRelType());
+		});
+		assertEquals(23, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
+		assertEquals(0, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
+
+	}
+
+	@Test
+	void testRelationsSourceTargetPrefix() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+			.getPath();
+
+		eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet6"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet6", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		tmp.foreach(r -> {
+			assertEquals("50|doi_________::", r.getSource().substring(0, 17));
+			assertEquals("50|doi_________::", r.getTarget().substring(0, 17));
+		});
+
+	}
+
+	@Test
+	void testRelationsSourceTargetCouple() throws Exception {
+		final String doi1 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x"));
+		final String doi2 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x"));
+		final String doi3 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9"));
+		final String doi4 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069"));
+		final String doi5 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4"));
+		final String doi6 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5"));
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+			.getPath();
+
+		CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet7"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet7", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		JavaRDD<Relation> check = tmp.filter(r -> r.getSource().equals(doi1) || r.getTarget().equals(doi1));
+
+		assertEquals(5, check.count());
+
+//		check.foreach(r -> {
+//			if (r.getSource().equals(doi2) || r.getSource().equals(doi3) || r.getSource().equals(doi4) ||
+//				r.getSource().equals(doi5) || r.getSource().equals(doi6)) {
+//				assertEquals(ModelConstants.IS_CITED_BY, r.getRelClass());
+//				assertEquals(doi1, r.getTarget());
+//			}
+//		});
+
+		assertEquals(5, check.filter(r -> r.getSource().equals(doi1)).count());
+		check.filter(r -> r.getSource().equals(doi1)).foreach(r -> assertEquals(ModelConstants.CITES, r.getRelClass()));
+
+	}
+}

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java

@@ -24,6 +24,7 @@ import org.slf4j.LoggerFactory;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.oaf.Measure;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
 import eu.dnetlib.dhp.schema.oaf.Result;
 
@@ -66,10 +67,380 @@ public class SparkAtomicActionCountJobTest {
 		spark.stop();
 	}
 
+	@Test
+	void testUsageStatsDb2() {
+		String usageScoresPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/usagestats/test2")
+			.getPath();
+
+		SparkAtomicActionUsageJob.writeActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet");
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<AtomicAction> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
+			.map(usm -> OBJECT_MAPPER.readValue(usm._2.getBytes(), AtomicAction.class));
+		// .map(aa -> (Result) aa.getPayload());
+
+		Assertions.assertEquals(7, tmp.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("50|")).count());
+		Assertions.assertEquals(9, tmp.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("10|")).count());
+		Assertions.assertEquals(9, tmp.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("40|")).count());
+
+		tmp.foreach(r -> Assertions.assertEquals(2, ((OafEntity) r.getPayload()).getMeasures().size()));
+		tmp
+			.foreach(
+				r -> ((OafEntity) r.getPayload())
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m
+							.getUnit()
+							.stream()
+							.forEach(u -> Assertions.assertFalse(u.getDataInfo().getDeletedbyinference()))));
+		tmp
+			.foreach(
+				r -> ((OafEntity) r.getPayload())
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m.getUnit().stream().forEach(u -> Assertions.assertTrue(u.getDataInfo().getInferred()))));
+		tmp
+			.foreach(
+				r -> ((OafEntity) r.getPayload())
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m
+							.getUnit()
+							.stream()
+							.forEach(u -> Assertions.assertFalse(u.getDataInfo().getInvisible()))));
+
+		tmp
+			.foreach(
+				r -> ((OafEntity) r.getPayload())
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m
+							.getUnit()
+							.stream()
+							.forEach(
+								u -> Assertions
+									.assertEquals(
+										"measure:usage_counts",
+										u.getDataInfo().getProvenanceaction().getClassid()))));
+		tmp
+			.foreach(
+				r -> ((OafEntity) r.getPayload())
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m
+							.getUnit()
+							.stream()
+							.forEach(
+								u -> Assertions
+									.assertEquals(
+										"Inferred by OpenAIRE",
+										u.getDataInfo().getProvenanceaction().getClassname()))));
+
+		tmp
+			.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("40|"))
+			.foreach(
+				r -> ((OafEntity) r.getPayload())
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m
+							.getUnit()
+							.stream()
+							.forEach(
+								u -> Assertions
+									.assertEquals(
+										"count",
+										u.getKey()))));
+
+		Assertions
+			.assertEquals(
+				1,
+				tmp
+					.filter(
+						r -> ((OafEntity) r.getPayload())
+							.getId()
+							.equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6"))
+					.count());
+
+		OafEntity entity = (OafEntity) tmp
+			.filter(
+				aa -> ((OafEntity) aa.getPayload()).getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6"))
+			.first()
+			.getPayload();
+
+		entity
+			.getMeasures()
+			.stream()
+			.forEach(
+				m -> Assertions.assertEquals(3, m.getUnit().size()));
+
+		Measure downloads = entity
+			.getMeasures()
+			.stream()
+			.filter(m -> m.getId().equals("downloads"))
+			.findFirst()
+			.get();
+
+		Assertions
+			.assertEquals(
+				String.valueOf(0),
+				downloads.getUnit().stream().filter(u -> u.getKey().equals("10|fake1")).findFirst().get().getValue());
+		Assertions
+			.assertEquals(
+				String.valueOf(0),
+				downloads.getUnit().stream().filter(u -> u.getKey().equals("10|fake2")).findFirst().get().getValue());
+		Assertions
+			.assertEquals(
+				String.valueOf(1),
+				downloads.getUnit().stream().filter(u -> u.getKey().equals("10|fake3")).findFirst().get().getValue());
+
+		Measure views = entity
+			.getMeasures()
+			.stream()
+			.filter(m -> m.getId().equals("views"))
+			.findFirst()
+			.get();
+
+		Assertions
+			.assertEquals(
+				String.valueOf(5),
+				views.getUnit().stream().filter(u -> u.getKey().equals("10|fake1")).findFirst().get().getValue());
+		Assertions
+			.assertEquals(
+				String.valueOf(1),
+				views.getUnit().stream().filter(u -> u.getKey().equals("10|fake2")).findFirst().get().getValue());
+		Assertions
+			.assertEquals(
+				String.valueOf(3),
+				views.getUnit().stream().filter(u -> u.getKey().equals("10|fake3")).findFirst().get().getValue());
+
+		tmp
+			.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("10|"))
+			.foreach(
+				r -> ((OafEntity) r.getPayload())
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m
+							.getUnit()
+							.stream()
+							.forEach(
+								u -> Assertions
+									.assertEquals(
+										"count",
+										u.getKey()))));
+
+		Assertions
+			.assertEquals(
+				"0",
+				tmp
+					.map(r -> ((OafEntity) r.getPayload()))
+					.filter(r -> r.getId().equals("40|f1__________::53575dc69e9ace947e02d47ecd54a7a6"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("downloads"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+		Assertions
+			.assertEquals(
+				"5",
+				tmp
+					.map(r -> ((OafEntity) r.getPayload()))
+					.filter(r -> r.getId().equals("40|f1__________::53575dc69e9ace947e02d47ecd54a7a6"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("views"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+
+		Assertions
+			.assertEquals(
+				"0",
+				tmp
+					.map(r -> ((OafEntity) r.getPayload()))
+					.filter(r -> r.getId().equals("40|f11_________::17eda2ff77407538fbe5d3d719b9d1c0"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("downloads"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+		Assertions
+			.assertEquals(
+				"1",
+				tmp
+					.map(r -> ((OafEntity) r.getPayload()))
+					.filter(r -> r.getId().equals("40|f11_________::17eda2ff77407538fbe5d3d719b9d1c0"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("views"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+
+		Assertions
+			.assertEquals(
+				"2",
+				tmp
+					.map(r -> ((OafEntity) r.getPayload()))
+					.filter(r -> r.getId().equals("40|f12_________::3085e4c6e051378ca6157fe7f0430c1f"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("downloads"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+		Assertions
+			.assertEquals(
+				"6",
+				tmp
+					.map(r -> ((OafEntity) r.getPayload()))
+					.filter(r -> r.getId().equals("40|f12_________::3085e4c6e051378ca6157fe7f0430c1f"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("views"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+
+		Assertions
+			.assertEquals(
+				"0",
+				tmp
+					.map(r -> ((OafEntity) r.getPayload()))
+					.filter(r -> r.getId().equals("10|d1__________::53575dc69e9ace947e02d47ecd54a7a6"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("downloads"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+		Assertions
+			.assertEquals(
+				"5",
+				tmp
+					.map(r -> ((OafEntity) r.getPayload()))
+					.filter(r -> r.getId().equals("10|d1__________::53575dc69e9ace947e02d47ecd54a7a6"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("views"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+
+		Assertions
+			.assertEquals(
+				"0",
+				tmp
+					.map(r -> ((OafEntity) r.getPayload()))
+					.filter(r -> r.getId().equals("10|d11_________::17eda2ff77407538fbe5d3d719b9d1c0"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("downloads"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+		Assertions
+			.assertEquals(
+				"1",
+				tmp
+					.map(r -> ((OafEntity) r.getPayload()))
+					.filter(r -> r.getId().equals("10|d11_________::17eda2ff77407538fbe5d3d719b9d1c0"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("views"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+
+		Assertions
+			.assertEquals(
+				"2",
+				tmp
+					.map(r -> ((OafEntity) r.getPayload()))
+					.filter(r -> r.getId().equals("10|d12_________::3085e4c6e051378ca6157fe7f0430c1f"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("downloads"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+		Assertions
+			.assertEquals(
+				"6",
+				tmp
+					.map(r -> ((OafEntity) r.getPayload()))
+					.filter(r -> r.getId().equals("10|d12_________::3085e4c6e051378ca6157fe7f0430c1f"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("views"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+	}
+
 	@Test
 	void testMatch() {
 		String usageScoresPath = getClass()
-			.getResource("/eu/dnetlib/dhp/actionmanager/usagestats")
+			.getResource("/eu/dnetlib/dhp/actionmanager/usagestats/test1")
 			.getPath();
 
 		SparkAtomicActionUsageJob.writeActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet");
@@ -144,6 +515,39 @@ public class SparkAtomicActionCountJobTest {
 										u.getDataInfo().getProvenanceaction().getClassname()))));
 
 		tmp
+			.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("40|"))
+			.foreach(
+				r -> ((OafEntity) r.getPayload())
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m
+							.getUnit()
+							.stream()
+							.forEach(
+								u -> Assertions
+									.assertEquals(
+										"count",
+										u.getKey()))));
+
+		tmp
+			.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("50|"))
+			.foreach(
+				r -> ((OafEntity) r.getPayload())
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m
+							.getUnit()
+							.stream()
+							.forEach(
+								u -> Assertions
+									.assertEquals(
+										"10|fake1",
+										u.getKey()))));
+
+		tmp
+			.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("10|"))
 			.foreach(
 				r -> ((OafEntity) r.getPayload())
 					.getMeasures()
@@ -465,5 +869,4 @@ public class SparkAtomicActionCountJobTest {
 					.get(0)
 					.getValue());
 	}
-
 }

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java

@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.transformation;
 
 import static eu.dnetlib.dhp.common.Constants.MDSTORE_DATA_PATH;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertThrows;
 
 import java.io.IOException;
 import java.nio.file.Path;
@@ -279,6 +280,19 @@ class TransformationJobTest extends AbstractVocabularyTest {
 		// TODO Create significant Assert
 	}
 
+	@Test
+	public void testInvalidXSLT() throws Exception {
+		final MetadataRecord mr = new MetadataRecord();
+
+		mr.setProvenance(new Provenance("openaire____::cnr_explora", "CNR ExploRA", "cnr_________"));
+		mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_cnr_explora.xml")));
+		// We Load the XSLT transformation Rule from the classpath
+		final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/invalid.xslt");
+
+		assertThrows(RuntimeException.class, () -> tr.call(mr));
+
+	}
+
 	private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception {
 		final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path));
 		final LongAccumulator la = new LongAccumulator();

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.csv

@@ -0,0 +1,19 @@
+DOI,OAID,level1,level2,level3,level4,score_for_L3,score_for_L4
+N/A,78975075580c::e680668c98366c9cd6349afc62486a7f,03 medical and health sciences,0301 basic medicine,030104 developmental biology,N/A,0.5,0.0
+N/A,78975075580c::e680668c98366c9cd6349afc62486a7f,03 medical and health sciences,0303 health sciences,030304 developmental biology,N/A,0.5,0.0
+N/A,od______2806::a1da9d2678b12969a9ab5f50b5e71d0a,05 social sciences,0501 psychology and cognitive sciences,050109 social psychology,05010904 Group processes/Collective identity,0.5589094161987305,0.5166763067245483
+N/A,od______2806::a1da9d2678b12969a9ab5f50b5e71d0a,05 social sciences,0501 psychology and cognitive sciences,050105 experimental psychology,05010501 Emotion/Affective science,0.44109055399894714,0.4833236634731293
+N/A,doajarticles::76535d77fd2a5fe9810aefafffb8ef6c,05 social sciences,0502 economics and business,050203 business & management,05020302 Supply chain management/Business terms,0.5459638833999634,0.5460261106491089
+N/A,doajarticles::76535d77fd2a5fe9810aefafffb8ef6c,05 social sciences,0502 economics and business,050211 marketing,05021102 Services marketing/Retailing,0.4540362060070038,0.4539738595485687
+N/A,od_______156::a3a0119c6d9d3a66943f8da042e97a5e,01 natural sciences,0105 earth and related environmental sciences,010504 meteorology & atmospheric sciences,01050407 Geomagnetism/Ionosphere,0.5131047964096069,0.4990350902080536
+N/A,od_______156::a3a0119c6d9d3a66943f8da042e97a5e,01 natural sciences,0105 earth and related environmental sciences,010502 geochemistry & geophysics,01050203 Seismology/Seismology measurement,0.4868951737880707,0.500964879989624
+N/A,od______2806::4b9a664dd6b8b04204cb613e7bc9c873,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,03022002 Medical imaging/Medical physics,0.5068133473396301,0.10231181626910052
+N/A,od______2806::4b9a664dd6b8b04204cb613e7bc9c873,03 medical and health sciences,0302 clinical medicine,030204 cardiovascular system & hematology,N/A,0.49318668246269226,0.0
+N/A,od______3341::ef754de29464abf9bc9b99664630ce74,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,03022012 Oncology/Infectious causes of cancer,0.5,0.5
+N/A,od______3341::ef754de29464abf9bc9b99664630ce74,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,03022012 Oncology/Infectious causes of cancer,0.5,0.5
+N/A,od______3978::6704dcced0fe3dd6fbf985dc2507f61c,03 medical and health sciences,0302 clinical medicine,030217 neurology & neurosurgery,03021702 Aging-associated diseases/Cognitive disorders,0.5134317874908447,0.09614889098529535
+N/A,od______3978::6704dcced0fe3dd6fbf985dc2507f61c,03 medical and health sciences,0301 basic medicine,030104 developmental biology,N/A,0.48656824231147766,0.0
+N/A,dedup_wf_001::b77264819800b90c0328c4d17eea5c1a,02 engineering and technology,0209 industrial biotechnology,020901 industrial engineering & automation,02090105 Control theory/Advanced driver assistance systems,0.5178514122962952,0.5198937654495239
+N/A,dedup_wf_001::b77264819800b90c0328c4d17eea5c1a,02 engineering and technology,"0202 electrical engineering, electronic engineering, information engineering",020201 artificial intelligence & image processing,02020108 Fuzzy logic/Artificial neural networks/Computational neuroscience,0.48214852809906006,0.4801062345504761
+N/A,od______2806::a938609e9f36ada6629a1bcc50c88230,03 medical and health sciences,0302 clinical medicine,030217 neurology & neurosurgery,03021708 Neurotrauma/Stroke,0.5014800429344177,0.5109656453132629
+N/A,od______2806::a938609e9f36ada6629a1bcc50c88230,02 engineering and technology,0206 medical engineering,020601 biomedical engineering,02060102 Medical terminology/Patient,0.4985199570655823,0.4890343248844147

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.json

@@ -0,0 +1,18 @@
+{"doi":"n/a","oaid":"od______3341::ef754de29464abf9bc9b99664630ce74","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030220 oncology & carcinogenesis","level4":"03022012 Oncology/Infectious causes of cancer","scoreL3":"0.5","scoreL4":"0.5"}
+{"doi":"n/a","oaid":"78975075580c::e680668c98366c9cd6349afc62486a7f","level1":"03 medical and health sciences","level2":"0301 basic medicine","level3":"030104 developmental biology","level4":"N/A","scoreL3":"0.5","scoreL4":"0.0"}
+{"doi":"n/a","oaid":"od______3341::ef754de29464abf9bc9b99664630ce74","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030220 oncology & carcinogenesis","level4":"03022012 Oncology/Infectious causes of cancer","scoreL3":"0.5","scoreL4":"0.5"}
+{"doi":"n/a","oaid":"78975075580c::e680668c98366c9cd6349afc62486a7f","level1":"03 medical and health sciences","level2":"0303 health sciences","level3":"030304 developmental biology","level4":"N/A","scoreL3":"0.5","scoreL4":"0.0"}
+{"doi":"n/a","oaid":"od______3978::6704dcced0fe3dd6fbf985dc2507f61c","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030217 neurology & neurosurgery","level4":"03021702 Aging-associated diseases/Cognitive disorders","scoreL3":"0.5134317874908447","scoreL4":"0.09614889098529535"}
+{"doi":"n/a","oaid":"od______2806::a1da9d2678b12969a9ab5f50b5e71d0a","level1":"05 social sciences","level2":"0501 psychology and cognitive sciences","level3":"050109 social psychology","level4":"05010904 Group processes/Collective identity","scoreL3":"0.5589094161987305","scoreL4":"0.5166763067245483"}
+{"doi":"n/a","oaid":"od______3978::6704dcced0fe3dd6fbf985dc2507f61c","level1":"03 medical and health sciences","level2":"0301 basic medicine","level3":"030104 developmental biology","level4":"N/A","scoreL3":"0.48656824231147766","scoreL4":"0.0"}
+{"doi":"n/a","oaid":"od______2806::a1da9d2678b12969a9ab5f50b5e71d0a","level1":"05 social sciences","level2":"0501 psychology and cognitive sciences","level3":"050105 experimental psychology","level4":"05010501 Emotion/Affective science","scoreL3":"0.44109055399894714","scoreL4":"0.4833236634731293"}
+{"doi":"n/a","oaid":"dedup_wf_001::b77264819800b90c0328c4d17eea5c1a","level1":"02 engineering and technology","level2":"0209 industrial biotechnology","level3":"020901 industrial engineering & automation","level4":"02090105 Control theory/Advanced driver assistance systems","scoreL3":"0.5178514122962952","scoreL4":"0.5198937654495239"}
+{"doi":"n/a","oaid":"doajarticles::76535d77fd2a5fe9810aefafffb8ef6c","level1":"05 social sciences","level2":"0502 economics and business","level3":"050203 business & management","level4":"05020302 Supply chain management/Business terms","scoreL3":"0.5459638833999634","scoreL4":"0.5460261106491089"}
+{"doi":"n/a","oaid":"doajarticles::76535d77fd2a5fe9810aefafffb8ef6c","level1":"05 social sciences","level2":"0502 economics and business","level3":"050211 marketing","level4":"05021102 Services marketing/Retailing","scoreL3":"0.4540362060070038","scoreL4":"0.4539738595485687"}
+{"doi":"n/a","oaid":"dedup_wf_001::b77264819800b90c0328c4d17eea5c1a","level1":"02 engineering and technology","level2":"0202 electrical engineering, electronic engineering, information engineering","level3":"020201 artificial intelligence & image processing","level4":"02020108 Fuzzy logic/Artificial neural networks/Computational neuroscience","scoreL3":"0.48214852809906006","scoreL4":"0.4801062345504761"}
+{"doi":"n/a","oaid":"od_______156::a3a0119c6d9d3a66943f8da042e97a5e","level1":"01 natural sciences","level2":"0105 earth and related environmental sciences","level3":"010504 meteorology & atmospheric sciences","level4":"01050407 Geomagnetism/Ionosphere","scoreL3":"0.5131047964096069","scoreL4":"0.4990350902080536"}
+{"doi":"n/a","oaid":"od______2806::a938609e9f36ada6629a1bcc50c88230","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030217 neurology & neurosurgery","level4":"03021708 Neurotrauma/Stroke","scoreL3":"0.5014800429344177","scoreL4":"0.5109656453132629"}
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+{"doi":"n/a","oaid":"od______2806::a938609e9f36ada6629a1bcc50c88230","level1":"02 engineering and technology","level2":"0206 medical engineering","level3":"020601 biomedical engineering","level4":"02060102 Medical terminology/Patient","scoreL3":"0.4985199570655823","scoreL4":"0.4890343248844147"}
+{"doi":"n/a","oaid":"od______2806::4b9a664dd6b8b04204cb613e7bc9c873","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030220 oncology & carcinogenesis","level4":"03022002 Medical imaging/Medical physics","scoreL3":"0.5068133473396301","scoreL4":"0.10231181626910052"}
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dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/JSON/part-00000

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dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/correspondence/omid.csv

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+{"oci":"oci:06420189328-061202007182","citing":"10.1098/rspa.2006.1747","citing_pid":"doi","cited":"10.1007/978-3-642-38844-6_25","cited_pid":"doi"}
+{"oci":"oci:062603906965-061701362658","citing":"16104945","citing_pid":"pmid","cited":"2682767","cited_pid":"pmid"}
+{"oci":"oci:062603906965-061701362658","citing":"10.1111/j.1523-5378.2005.00327.x","citing_pid":"doi","cited":"2682767","cited_pid":"pmid"}
+{"oci":"oci:0670294309-06104327031","citing":"10.3390/nano10040644","citing_pid":"doi","cited":"2682767","cited_pid":"pmid"}
+{"oci":"oci:0670294309-06104327031","citing":"32235596","citing_pid":"pmid","cited":"2682767","cited_pid":"pmid"}
+{"oci":"oci:061702060228-061301712529","citing":"10.1098/rspa.2006.1747","citing_pid":"doi","cited":"2682767","cited_pid":"pmid"}
+{"oci":"oci:06901104174-06503692526","citing":"10.1016/j.foodpol.2021.102189","citing_pid":"doi","cited":"10.1016/j.ymeth.2014.07.008","cited_pid":"doi"}
+{"oci":"oci:06901104174-06503692526","citing":"10.1016/j.foodpol.2021.102189","citing_pid":"doi","cited":"25088780","cited_pid":"pmid"}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/test1/usageDb

@@ -0,0 +1,9 @@
+{"id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","datasourceId":"10|fake1","downloads":0,"views":5}
+{"id":"doi_________::17eda2ff77407538fbe5d3d719b9d1c0","datasourceId":"10|fake1","downloads":0,"views":1}
+{"id":"doi_________::1d4dc08605fd0a2be1105d30c63bfea1","datasourceId":"10|fake1","downloads":1,"views":3}
+{"id":"doi_________::2e3527822854ca9816f6dfea5bff61a8","datasourceId":"10|fake1","downloads":1,"views":1}
+{"id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","datasourceId":"10|fake1","downloads":2,"views":6}
+{"id":"doi_________::33f710e6dd30cc5e67e35b371ddc33cf","datasourceId":"10|fake1","downloads":0,"views":1}
+{"id":"doi_________::39738ebf10654732dd3a7af9f24655f8","datasourceId":"10|fake1","downloads":1,"views":3}
+{"id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","datasourceId":"10|fake1","downloads":1,"views":10}
+{"id":"doi_________::4938a71a884dd481d329657aa543b850","datasourceId":"10|fake1","downloads":0,"views":3}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/test2/datasourceDb

@@ -0,0 +1,9 @@
+{"id":"d1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":5}
+{"id":"d11_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1}
+{"id":"d11_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3}
+{"id":"d11_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1}
+{"id":"d12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":6}
+{"id":"d12_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1}
+{"id":"d12_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3}
+{"id":"d13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":10}
+{"id":"d13_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/test2/projectDb

@@ -0,0 +1,9 @@
+{"id":"f1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":5}
+{"id":"f11_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1}
+{"id":"f11_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3}
+{"id":"f11_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1}
+{"id":"f12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":6}
+{"id":"f12_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1}
+{"id":"f12_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3}
+{"id":"f13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":10}
+{"id":"f13_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/test2/usageDb

@@ -0,0 +1,9 @@
+{"id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","datasourceId":"10|fake1","downloads":0,"views":5}
+{"id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","datasourceId":"10|fake2","downloads":0,"views":1}
+{"id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","datasourceId":"10|fake3","downloads":1,"views":3}
+{"id":"doi_________::2e3527822854ca9816f6dfea5bff61a8","datasourceId":"10|fake1","downloads":1,"views":1}
+{"id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","datasourceId":"10|fake1","downloads":2,"views":6}
+{"id":"doi_________::33f710e6dd30cc5e67e35b371ddc33cf","datasourceId":"10|fake1","downloads":0,"views":1}
+{"id":"doi_________::39738ebf10654732dd3a7af9f24655f8","datasourceId":"10|fake1","downloads":1,"views":3}
+{"id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","datasourceId":"10|fake1","downloads":1,"views":10}
+{"id":"doi_________::4938a71a884dd481d329657aa543b850","datasourceId":"10|fake1","downloads":0,"views":3}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usageDb

@@ -1,9 +0,0 @@
-{"id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":5}
-{"id":"doi_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1}
-{"id":"doi_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3}
-{"id":"doi_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1}
-{"id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":6}
-{"id":"doi_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1}
-{"id":"doi_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3}
-{"id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":10}
-{"id":"doi_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/invalid.xslt

@@ -0,0 +1,185 @@
+<xsl:stylesheet
+	xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+	xmlns:oaire="http://namespace.openaire.eu/schema/oaire/"
+	xmlns:vocabulary="http://eu/dnetlib/transform/clean"
+	xmlns:dateCleaner="http://eu/dnetlib/transform/dateISO"
+	xmlns:oaf="http://namespace.openaire.eu/oaf"
+	xmlns:oai="http://www.openarchives.org/OAI/2.0/"
+	xmlns:datacite="http://datacite.org/schema/kernel-4"
+	xmlns:dri="http://www.driver-repository.eu/namespace/dri"
+	xmlns:xs="http://www.w3.org/2001/XMLSchema"
+	xmlns:dr="http://www.driver-repository.eu/namespace/dr"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xmlns:dc="http://purl.org/dc/elements/1.1/"
+	exclude-result-prefixes="xsl vocabulary dateCleaner" version="2.0">
+	<xsl:param name="varOfficialName" />
+	<xsl:param name="varDataSourceId" />
+	<xsl:param name="varFP7" select="'corda_______::'" />
+	<xsl:param name="varH2020" select="'corda__h2020::'" />
+	<xsl:param name="repoCode"
+		select="substring-before(//*[local-name() = 'header']/*[local-name()='recordIdentifier'], ':')" />
+	<xsl:param name="index" select="0" />
+	<xsl:param name="transDate" select="current-dateTime()" />
+asdf;klamsdof'sdn &
+	<xsl:template match="/asdfasdf asdf&">
+		c:format'" />
+				</xsl:call-template>
+				<xsl:call-template name="allElements">
+					<xsl:with-param name="sourceElement" select="//dc:type" />
+					<xsl:with-param name="targetElement" select="'dc:type'" />
+				</xsl:call-template>
+				<xsl:call-template name="allElements">
+					<xsl:with-param name="sourceElement" select="//dc:source" />
+					<xsl:with-param name="targetElement" select="'dc:source'" />
+				</xsl:call-template>
+				<dc:language>
+					<xsl:value-of select="vocabulary:clean( //dc:language, 'dnet:languages')" />
+				</dc:language>
+				<xsl:call-template name="allElements">
+					<xsl:with-param name="sourceElement" select="//dc:rights" />
+					<xsl:with-param name="targetElement" select="'dc:rights'" />
+				</xsl:call-template>
+				<xsl:call-template name="allElements">
+					<xsl:with-param name="sourceElement" select="//dc:relation[not(starts-with(.,'info:cnr-pdr'))]" />
+					<xsl:with-param name="targetElement" select="'dc:relation'" />
+				</xsl:call-template>
+				
+				<xsl:call-template name="allElements">
+					<xsl:with-param name="sourceElement" select="//dc:identifier[starts-with(., 'http')]" />
+					<xsl:with-param name="targetElement" select="'dc:identifier'" />
+				</xsl:call-template>
+				<xsl:for-each select="//dc:relation">
+					<xsl:if	test="matches(normalize-space(.), '(info:eu-repo/grantagreement/ec/fp7/)(\d\d\d\d\d\d)(.*)', 'i')">
+						<oaf:projectid>
+							<xsl:value-of select="concat($varFP7, replace(normalize-space(.), '(info:eu-repo/grantagreement/ec/fp7/)(\d\d\d\d\d\d)(.*)', '$2', 'i'))" />
+						</oaf:projectid>
+					</xsl:if>
+					<xsl:if test="matches(normalize-space(.), '(info:eu-repo/grantagreement/ec/h2020/)(\d\d\d\d\d\d)(.*)', 'i')">
+						<oaf:projectid>
+							<xsl:value-of select="concat($varH2020, replace(normalize-space(.), '(info:eu-repo/grantagreement/ec/h2020/)(\d\d\d\d\d\d)(.*)', '$2', 'i'))" />
+						</oaf:projectid>
+					</xsl:if>
+				</xsl:for-each>
+				
+				<oaf:accessrights>
+					<xsl:value-of select="vocabulary:clean( //dc:rights, 'dnet:access_modes')" />
+				</oaf:accessrights>
+				
+				<xsl:variable name="varCobjCategory" select="vocabulary:clean( //dc:type, 'dnet:publication_resource')" />
+				<xsl:variable name="varSuperType" select="vocabulary:clean( $varCobjCategory, 'dnet:result_typologies')" />				
+				<dr:CobjCategory type="{$varSuperType}"><xsl:value-of select="$varCobjCategory" /></dr:CobjCategory>
+				
+				
+				<xsl:variable name="varRefereedConvt" select="for $i in (//dc:type, //dc:description, //oai:setSpec) return vocabulary:clean( normalize-space($i), 'dnet:review_levels')" />
+				<xsl:variable name="varRefereedIdntf" select="(//*[string(node-name(.)) = 'dc:identifier' and matches(lower-case(.), '(^|.*[\.\-_/\s\(\)%\d#])pre[\.\-_/\s\(\)%\d#]?prints?([\.\-_/\s\(\)%\d#].*)?$')][count(//dc:identifier) = 1]/'0002', //*[string(node-name(.)) = 'dc:identifier' and matches(lower-case(.), '(^|.*[\.\-_/\s\(\)%\d#])refereed([\.\-_/\s\(\)\d%\d#].*)?$')]/'0001', //*[string(node-name(.)) = 'dc:identifier' and matches(lower-case(.), '.*-peer-reviewed-(fulltext-)?article-.*')]/'0001')" />
+				<xsl:variable name="varRefereedSourc" select="//*[string(node-name(.)) = ('dc:source', 'dc:publisher') and matches(lower-case(.), '^(.*\s)?pre[\s\-_]*prints?([\s\.,].*)?$')]/'0002'" />
+				<xsl:variable name="varRefereedDescr" select="(//dc:description[matches(lower-case(.), '.*(this\s*book|this\s*volume|it)\s*constitutes\s*the\s*(thoroughly\s*)?refereed') or matches(lower-case(.), '.*peer[\.\-_/\s\(\)]?review\s*under\s*responsibility\s*of.*') or matches(lower-case(.), '(this|a)\s*(article|preprint)\s*(has\s*been\s*)?(peer[\-\s]*)?reviewed\s*and\s*recommended\s*by\s*peer[\-\s]*community')]/'0001', //dc:description[matches(., '^version\s*(préliminaire.*|preliminary.*|0$)')]/'0002')" />
+				<xsl:variable name="varRefereedTitle" select="(//dc:title[matches(lower-case(.), '.*\[.*peer[\s\-\._]*review\s*:.*\]\s*$')]/'0001', //dc:title[matches(lower-case(.), '.*\(\s*pre[\s\-\._]*prints?\s*\)\s*$')]/'0002')" />
+				<xsl:variable name="varRefereedSubjt" select="(//dc:subject[matches(lower-case(.), '^\s*refereed\s*$')][//oaf:datasourceprefix = 'narcis______']/'0001', //dc:subject[matches(lower-case(.), '^\s*no[nt].{0,3}refereed\s*$')][//oaf:datasourceprefix = 'narcis______']/'0002')" />
+				<xsl:variable name="varRefereed" select="($varRefereedConvt, $varRefereedIdntf, $varRefereedSourc, $varRefereedDescr, $varRefereedTitle, $varRefereedSubjt)" />
+				<xsl:choose>
+					<xsl:when test="count($varRefereed[. = '0001']) &gt; 0">
+						<oaf:refereed>
+							<xsl:value-of select="'0001'" />
+						</oaf:refereed>
+					</xsl:when>
+					<xsl:when test="count($varRefereed[. = '0002']) &gt; 0">
+						<oaf:refereed>
+							<xsl:value-of select="'0002'" />
+						</oaf:refereed>
+					</xsl:when>
+				</xsl:choose>
+				
+				<oaf:dateAccepted>
+					<xsl:value-of select="dateCleaner:dateISO( //dc:date[1] )" />
+				</oaf:dateAccepted>
+				
+				<xsl:if test="//dc:relation[starts-with(., 'http')] and //dc:rights[.='info:eu-repo/semantics/openAccess']">
+					<oaf:fulltext>
+						<xsl:value-of select="//dc:relation[starts-with(., 'http')]" />
+					</oaf:fulltext>
+				</xsl:if>
+				
+				<oaf:hostedBy name="{$varOfficialName}" id="{$varDataSourceId}" />
+				<oaf:collectedFrom name="{$varOfficialName}" id="{$varDataSourceId}" />
+
+				<xsl:variable name="varKnownFileEndings" select="('.bmp', '.doc', '.docx', '.epub', '.flv', '.jpeg', '.jpg', '.m4v', '.mp4', '.mpg', '.odp', '.pdf', '.png', '.ppt', '.tiv', '.txt', '.xls', '.xlsx', '.zip')" />
+				<xsl:variable name="varIdDoi" select="distinct-values((//dc:identifier[starts-with(., '10.')][matches(., '(10[.][0-9]{4,}[^\s/&gt;]*/[^\s&gt;]+)')], //dc:identifier[starts-with(., 'http') and (contains(., '://dx.doi.org/10.') or contains(., '://doi.org/10.'))]/substring-after(., 'doi.org/'), //dc:identifier[starts-with(lower-case(.), 'doi:10.')]/substring-after(lower-case(.), 'doi:')))" />
+				<xsl:for-each select="$varIdDoi">
+					<oaf:identifier identifierType="doi">
+						<xsl:value-of select="." />
+					</oaf:identifier>
+				</xsl:for-each>
+				
+				<xsl:variable name="varIdHdl" select="distinct-values(//dc:identifier[starts-with(., 'http') and contains(., '://hdl.handle.net/')]/substring-after(., 'hdl.handle.net/'))" />
+				<xsl:for-each select="$varIdHdl" >
+					<oaf:identifier identifierType="handle">
+						<xsl:value-of select="." />
+					</oaf:identifier>
+				</xsl:for-each>
+				
+				<xsl:variable name="varIdUrn" select="distinct-values(//dc:identifier[starts-with(., 'urn:nbn:nl:') or starts-with(., 'URN:NBN:NL:')])" />
+				<xsl:for-each select="$varIdUrn">
+					<oaf:identifier identifierType="urn">
+						<xsl:value-of select="." />
+					</oaf:identifier>
+				</xsl:for-each>
+				
+				<xsl:variable name="varOrigBaseUrl" select="//*[local-name() = 'about']/*[local-name() = 'provenance']//*[local-name() = 'originDescription' and not(./*[local-name() = 'originDescription'])]/*[local-name() = 'baseURL']" />
+				<xsl:variable name="varIdLdpg" select="distinct-values(//dc:identifier[(contains(substring-after(., '://'), '/') and contains($varOrigBaseUrl, substring-before(substring-after(., '://'), '/'))) or (contains(substring-after(., '://'), ':') and contains($varOrigBaseUrl, substring-before(substring-after(., '://'), ':')))][not(replace(lower-case(.), '.*(\.[a-z]*)$', '$1') = $varKnownFileEndings)])" />
+				<xsl:for-each select="$varIdLdpg">
+					<oaf:identifier identifierType="landingPage">
+						<xsl:value-of select="." />
+					</oaf:identifier>
+				</xsl:for-each>
+				
+				<xsl:variable name="varIdUrl" select="distinct-values(//dc:identifier[starts-with(., 'http')][not(contains(., '://dx.doi.org/') or contains(., '://doi.org/') or contains(., '://hdl.handle.net/'))][count(index-of($varIdLdpg, .)) = 0])" />
+				<xsl:for-each select="$varIdUrl">
+					<oaf:identifier identifierType="url">
+						<xsl:value-of select="." />
+					</oaf:identifier>
+				</xsl:for-each>
+				
+				<xsl:for-each select="//oai:setSpec">
+					<xsl:variable name="rorDsId" select="vocabulary:clean(., 'cnr:institutes')" />
+					<xsl:if test="contains($rorDsId, '/ror.org/')">
+						<oaf:relation relType="resultOrganization" subRelType="affiliation" relClass="hasAuthorInstitution">
+							<xsl:value-of select="concat('ror_________::', $rorDsId)" />
+						</oaf:relation>
+					</xsl:if>
+				</xsl:for-each>
+				
+			</metadata>
+			
+			<xsl:copy-of select="//*[local-name() = 'about']" />
+		</record>
+	</xsl:template>
+	
+	
+	<xsl:template name="allElements">
+		<xsl:param name="sourceElement" />
+		<xsl:param name="targetElement" />
+	
+		<xsl:for-each select="$sourceElement">
+			<xsl:element name="{$targetElement}">
+				<xsl:value-of select="normalize-space(.)" />
+			</xsl:element>
+		</xsl:for-each>
+	</xsl:template>
+	
+	<xsl:template match="//*[local-name() = 'header']">
+		<xsl:copy>
+			<xsl:apply-templates select="node()|@*" />
+			<xsl:element name="dr:dateOfTransformation">
+				<xsl:value-of select="$transDate" />
+			</xsl:element>
+		</xsl:copy>
+	</xsl:template>
+	
+	<xsl:template match="node()|@*">
+		<xsl:copy>
+			<xsl:apply-templates select="node()|@*" />
+		</xsl:copy>
+	</xsl:template>
+	
+</xsl:stylesheet>

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

@@ -4,7 +4,6 @@ package eu.dnetlib.dhp.oa.dedup;
 import java.util.*;
 import java.util.stream.Stream;
 
-import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
 import org.apache.commons.beanutils.BeanUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.spark.api.java.function.FlatMapFunction;
@@ -15,11 +14,11 @@ import org.apache.spark.sql.*;
 import eu.dnetlib.dhp.oa.dedup.model.Identifier;
 import eu.dnetlib.dhp.oa.merge.AuthorMerger;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
 import eu.dnetlib.dhp.schema.oaf.Author;
 import eu.dnetlib.dhp.schema.oaf.DataInfo;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
 import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
 import scala.Tuple2;
 import scala.Tuple3;
 import scala.collection.JavaConversions;