optimization of normalization stage in openorgs workflow, implementation of new comparators replacing older versions, openorgs configuration update, addition of inference flag in model definition, new test classes

Reviewed-on: D-Net/dnet-hadoop#451

.gitignore

@@ -27,3 +27,4 @@ spark-warehouse
 /**/.factorypath
 /**/.scalafmt.conf
 /.java-version
+/dhp-shade-package/dependency-reduced-pom.xml

dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java

@@ -80,7 +80,15 @@ class WritePredefinedProjectPropertiesTest {
 		mojo.outputFile = testFolder;
 
 		// execute
-		Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
+		try {
+			mojo.execute();
+			Assertions.assertTrue(false); // not reached
+		} catch (Exception e) {
+			Assertions
+				.assertTrue(
+					MojoExecutionException.class.isAssignableFrom(e.getClass()) ||
+						IllegalArgumentException.class.isAssignableFrom(e.getClass()));
+		}
 	}
 
 	@Test

dhp-common/pom.xml

@@ -70,10 +70,7 @@
 			<groupId>com.ibm.icu</groupId>
 			<artifactId>icu4j</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.hadoop</groupId>
-			<artifactId>hadoop-common</artifactId>
-		</dependency>
+
 		<dependency>
 			<groupId>com.github.sisyphsu</groupId>
 			<artifactId>dateparser</artifactId>
@@ -163,7 +160,7 @@
 
 		<dependency>
 			<groupId>eu.dnetlib.dhp</groupId>
-			<artifactId>${dhp-schemas.artifact}</artifactId>
+			<artifactId>dhp-schemas</artifactId>
 		</dependency>
 
 		<dependency>
@@ -172,4 +169,23 @@
 		</dependency>
 	</dependencies>
 
+	<!-- dependencies required on JDK9+ because J2EE has been removed -->
+	<profiles>
+		<profile>
+			<id>spark-34</id>
+			<dependencies>
+				<dependency>
+					<groupId>javax.xml.bind</groupId>
+					<artifactId>jaxb-api</artifactId>
+					<version>2.2.11</version>
+				</dependency>
+				<dependency>
+					<groupId>com.sun.xml.ws</groupId>
+					<artifactId>jaxws-ri</artifactId>
+					<version>2.3.3</version>
+					<type>pom</type>
+				</dependency>
+			</dependencies>
+		</profile>
+	</profiles>
 </project>

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

@@ -38,7 +38,7 @@ public class PacePerson {
 					PacePerson.class
 						.getResourceAsStream(
 							"/eu/dnetlib/dhp/common/name_particles.txt")));
-		} catch (IOException e) {
+		} catch (Exception e) {
 			throw new RuntimeException(e);
 		}
 	}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java

@@ -217,8 +217,6 @@ public class ZenodoAPIClient implements Serializable {
 	 *            part of the url for the DOI Zenodo suggests to use to cite all versions: DOI: 10.xxx/zenodo.656930
 	 *            concept_rec_id = 656930
 	 * @return response code
-	 * @throws IOException
-	 * @throws MissingConceptDoiException
 	 */
 	public int newVersion(String concept_rec_id) throws IOException, MissingConceptDoiException {
 		setDepositionId(concept_rec_id, 1);

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

@@ -12,9 +12,7 @@ import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.math.NumberUtils;
-import org.apache.commons.lang3.time.DateUtils;
 import org.apache.http.HttpHeaders;
-import org.joda.time.Instant;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

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

@@ -0,0 +1,106 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import java.util.*;
+
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+public class MergeEntitiesComparator implements Comparator<Oaf> {
+	static final List<String> PID_AUTHORITIES = Arrays
+		.asList(
+			ModelConstants.ARXIV_ID,
+			ModelConstants.PUBMED_CENTRAL_ID,
+			ModelConstants.EUROPE_PUBMED_CENTRAL_ID,
+			ModelConstants.DATACITE_ID,
+			ModelConstants.CROSSREF_ID);
+
+	static final List<String> RESULT_TYPES = Arrays
+		.asList(
+			ModelConstants.ORP_RESULTTYPE_CLASSID,
+			ModelConstants.SOFTWARE_RESULTTYPE_CLASSID,
+			ModelConstants.DATASET_RESULTTYPE_CLASSID,
+			ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
+
+	public static final Comparator<Oaf> INSTANCE = new MergeEntitiesComparator();
+
+	@Override
+	public int compare(Oaf left, Oaf right) {
+		if (left == null && right == null)
+			return 0;
+		if (left == null)
+			return -1;
+		if (right == null)
+			return 1;
+
+		int res = 0;
+
+		// pid authority
+		int cfp1 = Optional
+			.ofNullable(left.getCollectedfrom())
+			.map(
+				cf -> cf
+					.stream()
+					.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
+					.max(Integer::compare)
+					.orElse(-1))
+			.orElse(-1);
+		int cfp2 = Optional
+			.ofNullable(right.getCollectedfrom())
+			.map(
+				cf -> cf
+					.stream()
+					.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
+					.max(Integer::compare)
+					.orElse(-1))
+			.orElse(-1);
+
+		if (cfp1 >= 0 && cfp1 > cfp2) {
+			return 1;
+		} else if (cfp2 >= 0 && cfp2 > cfp1) {
+			return -1;
+		}
+
+		// trust
+		if (left.getDataInfo() != null && right.getDataInfo() != null) {
+			res = left.getDataInfo().getTrust().compareTo(right.getDataInfo().getTrust());
+		}
+
+		// result type
+		if (res == 0) {
+			if (left instanceof Result && right instanceof Result) {
+				Result r1 = (Result) left;
+				Result r2 = (Result) right;
+
+				if (r1.getResulttype() == null || r1.getResulttype().getClassid() == null) {
+					if (r2.getResulttype() != null && r2.getResulttype().getClassid() != null) {
+						return -1;
+					}
+				} else if (r2.getResulttype() == null || r2.getResulttype().getClassid() == null) {
+					return 1;
+				}
+
+				int rt1 = RESULT_TYPES.indexOf(r1.getResulttype().getClassid());
+				int rt2 = RESULT_TYPES.indexOf(r2.getResulttype().getClassid());
+
+				if (rt1 >= 0 && rt1 > rt2) {
+					return 1;
+				} else if (rt2 >= 0 && rt2 > rt1) {
+					return -1;
+				}
+			}
+		}
+
+		// id
+		if (res == 0) {
+			if (left instanceof OafEntity && right instanceof OafEntity) {
+				res = ((OafEntity) left).getId().compareTo(((OafEntity) right).getId());
+			}
+		}
+
+		return res;
+	}
+
+}

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

@@ -40,27 +40,12 @@ public class MergeUtils {
 
 	public static <T extends Oaf> T mergeGroup(String s, Iterator<T> oafEntityIterator,
 		boolean checkDelegateAuthority) {
-		TreeSet<T> sortedEntities = new TreeSet<>((o1, o2) -> {
-			int res = 0;
 
-			if (o1.getDataInfo() != null && o2.getDataInfo() != null) {
-				res = o1.getDataInfo().getTrust().compareTo(o2.getDataInfo().getTrust());
-			}
+		ArrayList<T> sortedEntities = new ArrayList<>();
+		oafEntityIterator.forEachRemaining(sortedEntities::add);
+		sortedEntities.sort(MergeEntitiesComparator.INSTANCE.reversed());
 
-			if (res == 0) {
-				if (o1 instanceof Result && o2 instanceof Result) {
-					return ResultTypeComparator.INSTANCE.compare((Result) o1, (Result) o2);
-				}
-			}
-
-			return res;
-		});
-
-		while (oafEntityIterator.hasNext()) {
-			sortedEntities.add(oafEntityIterator.next());
-		}
-
-		Iterator<T> it = sortedEntities.descendingIterator();
+		Iterator<T> it = sortedEntities.iterator();
 		T merged = it.next();
 
 		while (it.hasNext()) {
@@ -143,7 +128,7 @@ public class MergeUtils {
 	 * https://graph.openaire.eu/docs/data-model/pids-and-identifiers#delegated-authorities and in that case it prefers
 	 * such version.
 	 * <p>
-	 * Otherwise, it considers a resulttype priority order implemented in {@link ResultTypeComparator}
+	 * Otherwise, it considers a resulttype priority order implemented in {@link MergeEntitiesComparator}
 	 * and proceeds with the canonical property merging.
 	 *
 	 * @param left
@@ -161,8 +146,9 @@ public class MergeUtils {
 		if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
 			return right;
 		}
+
 		// TODO: raise trust to have preferred fields from one or the other??
-		if (new ResultTypeComparator().compare(left, right) < 0) {
+		if (MergeEntitiesComparator.INSTANCE.compare(left, right) > 0) {
 			return mergeResultFields(left, right);
 		} else {
 			return mergeResultFields(right, left);
@@ -225,9 +211,9 @@ public class MergeUtils {
 
 	private static <T, K> List<T> mergeLists(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) {
+		if (left == null || left.isEmpty()) {
+			return right != null ? right : new ArrayList<>();
+		} else if (right == null || right.isEmpty()) {
 			return left;
 		}
 
@@ -405,7 +391,7 @@ public class MergeUtils {
 		}
 
 		// should be an instance attribute, get the first non-null value
-		merge.setLanguage(coalesce(merge.getLanguage(), enrich.getLanguage()));
+		merge.setLanguage(coalesceQualifier(merge.getLanguage(), enrich.getLanguage()));
 
 		// distinct countries, do not manage datainfo
 		merge.setCountry(mergeQualifiers(merge.getCountry(), enrich.getCountry(), trust));
@@ -575,6 +561,13 @@ public class MergeUtils {
 		return m != null ? m : e;
 	}
 
+	private static Qualifier coalesceQualifier(Qualifier m, Qualifier e) {
+		if (m == null || m.getClassid() == null || StringUtils.isBlank(m.getClassid())) {
+			return e;
+		}
+		return m;
+	}
+
 	private static List<Author> mergeAuthors(List<Author> author, List<Author> author1, int trust) {
 		List<List<Author>> authors = new ArrayList<>();
 		if (author != null) {
@@ -587,6 +580,10 @@ public class MergeUtils {
 	}
 
 	private static String instanceKeyExtractor(Instance i) {
+		// three levels of concatenating:
+		// 1. ::
+		// 2. @@
+		// 3. ||
 		return String
 			.join(
 				"::",
@@ -594,10 +591,10 @@ public class MergeUtils {
 				kvKeyExtractor(i.getCollectedfrom()),
 				qualifierKeyExtractor(i.getAccessright()),
 				qualifierKeyExtractor(i.getInstancetype()),
-				Optional.ofNullable(i.getUrl()).map(u -> String.join("::", u)).orElse(null),
+				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("::")))
+					.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("@@")))
 					.orElse(null));
 	}
 
@@ -706,7 +703,7 @@ public class MergeUtils {
 	private static String spKeyExtractor(StructuredProperty sp) {
 		return Optional
 			.ofNullable(sp)
-			.map(s -> Joiner.on("::").join(s, qualifierKeyExtractor(s.getQualifier())))
+			.map(s -> Joiner.on("||").join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
 			.orElse(null);
 	}
 

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

@@ -1,87 +0,0 @@
-
-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> {
-
-	public static final ResultTypeComparator INSTANCE = new ResultTypeComparator();
-
-	@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;
-		}
-
-		if (left.getResulttype() == null || left.getResulttype().getClassid() == null) {
-			if (right.getResulttype() == null || right.getResulttype().getClassid() == null) {
-				return 0;
-			}
-			return 1;
-		} else if (right.getResulttype() == null || right.getResulttype().getClassid() == null) {
-			return -1;
-		}
-
-		String lClass = left.getResulttype().getClassid();
-		String rClass = right.getResulttype().getClassid();
-
-		if (!lClass.equals(rClass)) {
-			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/main/resources/eu/dnetlib/scholexplorer/relation/relations.json

@@ -154,5 +154,13 @@
   "unknown":{
     "original":"Unknown",
     "inverse":"Unknown"
+  },
+  "isamongtopnsimilardocuments": {
+    "original": "IsAmongTopNSimilarDocuments",
+    "inverse": "HasAmongTopNSimilarDocuments"
+  },
+  "hasamongtopnsimilardocuments": {
+    "original": "HasAmongTopNSimilarDocuments",
+    "inverse": "IsAmongTopNSimilarDocuments"
   }
 }

dhp-common/src/main/scala/eu/dnetlib/dhp/application/SparkScalaApplication.scala

@@ -65,12 +65,13 @@ abstract class AbstractScalaApplication(
     val conf: SparkConf = new SparkConf()
     val master = parser.get("master")
     log.info(s"Creating Spark session: Master: $master")
-    SparkSession
+    val b = SparkSession
       .builder()
       .config(conf)
       .appName(getClass.getSimpleName)
-      .master(master)
-      .getOrCreate()
+    if (master != null)
+      b.master(master)
+    b.getOrCreate()
   }
 
   def reportTotalSize(targetPath: String, outputBasePath: String): Unit = {

dhp-common/src/main/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala

@@ -65,7 +65,11 @@ object ScholixUtils extends Serializable {
   }
 
   def generateScholixResourceFromResult(r: Result): ScholixResource = {
-    generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
+    val sum = ScholixUtils.resultToSummary(r)
+    if (sum != null)
+      generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
+    else
+      null
   }
 
   val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] =
@@ -153,6 +157,14 @@ object ScholixUtils extends Serializable {
 
   }
 
+  def invRel(rel: String): String = {
+    val semanticRelation = relations.getOrElse(rel.toLowerCase, null)
+    if (semanticRelation != null)
+      semanticRelation.inverse
+    else
+      null
+  }
+
   def extractCollectedFrom(summary: ScholixResource): List[ScholixEntityId] = {
     if (summary.getCollectedFrom != null && !summary.getCollectedFrom.isEmpty) {
       val l: List[ScholixEntityId] = summary.getCollectedFrom.asScala.map { d =>
@@ -377,10 +389,7 @@ object ScholixUtils extends Serializable {
     if (persistentIdentifiers.isEmpty)
       return null
     s.setLocalIdentifier(persistentIdentifiers.asJava)
-    if (r.isInstanceOf[Publication])
-      s.setTypology(Typology.publication)
-    else
-      s.setTypology(Typology.dataset)
+//    s.setTypology(r.getResulttype.getClassid)
 
     s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)
 

dhp-pace-core/pom.xml

@@ -24,7 +24,7 @@
 				<executions>
 					<execution>
 						<id>scala-compile-first</id>
-						<phase>initialize</phase>
+						<phase>process-resources</phase>
 						<goals>
 							<goal>add-source</goal>
 							<goal>compile</goal>
@@ -59,14 +59,6 @@
 			<groupId>edu.cmu</groupId>
 			<artifactId>secondstring</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>com.google.guava</groupId>
-			<artifactId>guava</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>com.google.code.gson</groupId>
-			<artifactId>gson</artifactId>
-		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
@@ -91,10 +83,6 @@
 			<groupId>com.fasterxml.jackson.core</groupId>
 			<artifactId>jackson-databind</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>commons-math3</artifactId>
-		</dependency>
 		<dependency>
 			<groupId>com.jayway.jsonpath</groupId>
 			<artifactId>json-path</artifactId>
@@ -113,4 +101,90 @@
 		</dependency>
 	</dependencies>
 
+	<profiles>
+		<profile>
+			<id>spark-24</id>
+			<activation>
+				<activeByDefault>true</activeByDefault>
+			</activation>
+
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.codehaus.mojo</groupId>
+						<artifactId>build-helper-maven-plugin</artifactId>
+						<version>3.4.0</version>
+						<executions>
+							<execution>
+								<phase>generate-sources</phase>
+								<goals>
+									<goal>add-source</goal>
+								</goals>
+								<configuration>
+									<sources>
+										<source>src/main/spark-2</source>
+									</sources>
+								</configuration>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+
+		<profile>
+			<id>spark-34</id>
+
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.codehaus.mojo</groupId>
+						<artifactId>build-helper-maven-plugin</artifactId>
+						<version>3.4.0</version>
+						<executions>
+							<execution>
+								<phase>generate-sources</phase>
+								<goals>
+									<goal>add-source</goal>
+								</goals>
+								<configuration>
+									<sources>
+										<source>src/main/spark-2</source>
+									</sources>
+								</configuration>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+
+		<profile>
+			<id>spark-35</id>
+
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.codehaus.mojo</groupId>
+						<artifactId>build-helper-maven-plugin</artifactId>
+						<version>3.4.0</version>
+						<executions>
+							<execution>
+								<phase>generate-sources</phase>
+								<goals>
+									<goal>add-source</goal>
+								</goals>
+								<configuration>
+									<sources>
+										<source>src/main/spark-35</source>
+									</sources>
+								</configuration>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+	</profiles>
+
 </project>

dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/LegalnameClustering.java

@@ -2,31 +2,41 @@
 package eu.dnetlib.pace.clustering;
 
 import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
 
 import eu.dnetlib.pace.config.Config;
 
-@ClusteringClass("keywordsclustering")
-public class KeywordsClustering extends AbstractClusteringFunction {
+@ClusteringClass("legalnameclustering")
+public class LegalnameClustering extends AbstractClusteringFunction {
 
-	public KeywordsClustering(Map<String, Object> params) {
+	private static final Pattern CITY_CODE_PATTERN = Pattern.compile("city::\\d+");
+	private static final Pattern KEYWORD_CODE_PATTERN = Pattern.compile("key::\\d+");
+
+	public LegalnameClustering(Map<String, Object> params) {
 		super(params);
 	}
 
+	public Set<String> getRegexList(String input, Pattern codeRegex) {
+		Matcher matcher = codeRegex.matcher(input);
+		Set<String> cities = new HashSet<>();
+		while (matcher.find()) {
+			cities.add(matcher.group());
+		}
+		return cities;
+	}
+
 	@Override
 	protected Collection<String> doApply(final Config conf, String s) {
 
-		// takes city codes and keywords codes without duplicates
-		Set<String> keywords = getKeywords(s, conf.translationMap(), paramOrDefault("windowSize", 4));
-		Set<String> cities = getCities(s, paramOrDefault("windowSize", 4));
-
 		// list of combination to return as result
 		final Collection<String> combinations = new LinkedHashSet<String>();
 
-		for (String keyword : keywordsToCodes(keywords, conf.translationMap())) {
-			for (String city : citiesToCodes(cities)) {
+		for (String keyword : getRegexList(s, KEYWORD_CODE_PATTERN)) {
+			for (String city : getRegexList(s, CITY_CODE_PATTERN)) {
 				combinations.add(keyword + "-" + city);
 				if (combinations.size() >= paramOrDefault("max", 2)) {
 					return combinations;
@@ -42,9 +52,6 @@ public class KeywordsClustering extends AbstractClusteringFunction {
 		return fields
 			.stream()
 			.filter(f -> !f.isEmpty())
-			.map(KeywordsClustering::cleanup)
-			.map(KeywordsClustering::normalize)
-			.map(s -> filterAllStopWords(s))
 			.map(s -> doApply(conf, s))
 			.map(c -> filterBlacklisted(c, ngramBlacklist))
 			.flatMap(c -> c.stream())

dhp-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java

@@ -1,12 +1,6 @@
 
 package eu.dnetlib.pace.common;
 
-import com.google.common.base.Joiner;
-import com.google.common.collect.Sets;
-import com.ibm.icu.text.Transliterator;
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
-
 import java.io.IOException;
 import java.io.StringWriter;
 import java.nio.charset.StandardCharsets;
@@ -15,6 +9,13 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+
+import com.google.common.base.Joiner;
+import com.google.common.collect.Sets;
+import com.ibm.icu.text.Transliterator;
+
 /**
  * Set of common functions for the framework
  *
@@ -26,6 +27,14 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 	private static Map<String, String> cityMap = AbstractPaceFunctions
 		.loadMapFromClasspath("/eu/dnetlib/pace/config/city_map.csv");
 
+	// keywords map to be used when translating the keyword names into codes
+	private static Map<String, String> keywordMap = AbstractPaceFunctions
+		.loadMapFromClasspath("/eu/dnetlib/pace/config/translation_map.csv");
+
+	// country map to be used when inferring the country from the city name
+	private static Map<String, String> countryMap = AbstractPaceFunctions
+		.loadCountryMapFromClasspath("/eu/dnetlib/pace/config/country_map.csv");
+
 	// list of stopwords in different languages
 	protected static Set<String> stopwords_gr = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_gr.txt");
 	protected static Set<String> stopwords_en = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_en.txt");
@@ -73,6 +82,64 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return s12;
 	}
 
+	public static String countryInference(final String original, String inferFrom) {
+		if (!original.equalsIgnoreCase("unknown"))
+			return original;
+
+		inferFrom = cleanup(inferFrom);
+		inferFrom = normalize(inferFrom);
+		inferFrom = filterAllStopWords(inferFrom);
+		Set<String> cities = getCities(inferFrom, 4);
+		return citiesToCountry(cities).stream().findFirst().orElse("UNKNOWN");
+	}
+
+	public static String cityInference(String original) {
+		original = cleanup(original);
+		original = normalize(original);
+		original = filterAllStopWords(original);
+
+		Set<String> cities = getCities(original, 4);
+
+		for (String city : cities) {
+			original = original.replaceAll(city, cityMap.get(city));
+		}
+
+		return original;
+	}
+
+	public static String keywordInference(String original) {
+		original = cleanup(original);
+		original = normalize(original);
+		original = filterAllStopWords(original);
+
+		Set<String> keywords = getKeywords(original, keywordMap, 4);
+
+		for (String keyword : keywords) {
+			original = original.replaceAll(keyword, keywordMap.get(keyword));
+		}
+
+		return original;
+	}
+
+	public static String cityKeywordInference(String original) {
+		original = cleanup(original);
+		original = normalize(original);
+		original = filterAllStopWords(original);
+
+		Set<String> keywords = getKeywords(original, keywordMap, 4);
+		Set<String> cities = getCities(original, 4);
+
+		for (String keyword : keywords) {
+			original = original.replaceAll(keyword, keywordMap.get(keyword));
+		}
+
+		for (String city : cities) {
+			original = original.replaceAll(city, cityMap.get(city));
+		}
+
+		return original;
+	}
+
 	protected static String fixXML(final String a) {
 
 		return a
@@ -207,6 +274,30 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return m;
 	}
 
+	public static Map<String, String> loadCountryMapFromClasspath(final String classpath) {
+
+		Transliterator transliterator = Transliterator.getInstance("Any-Eng");
+
+		final Map<String, String> m = new HashMap<>();
+		try {
+			for (final String s : IOUtils
+				.readLines(AbstractPaceFunctions.class.getResourceAsStream(classpath), StandardCharsets.UTF_8)) {
+				// string is like this: country_code;city1;city2;city3
+				String[] line = s.split(";");
+				String value = line[0];
+				for (int i = 1; i < line.length; i++) {
+					String city = fixAliases(transliterator.transliterate(line[i].toLowerCase()));
+					String code = cityMap.get(city);
+					m.put(code, value);
+				}
+			}
+		} catch (final Throwable e) {
+			return new HashMap<>();
+		}
+		return m;
+
+	}
+
 	public static String removeKeywords(String s, Set<String> keywords) {
 
 		s = " " + s + " ";
@@ -236,6 +327,10 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return toCodes(keywords, cityMap);
 	}
 
+	public static Set<String> citiesToCountry(Set<String> cities) {
+		return toCodes(toCodes(cities, cityMap), countryMap);
+	}
+
 	protected static String firstLC(final String s) {
 		return StringUtils.substring(s, 0, 1).toLowerCase();
 	}

dhp-pace-core/src/main/java/eu/dnetlib/pace/model/FieldDef.java

@@ -47,9 +47,21 @@ public class FieldDef implements Serializable {
 
 	private String clean;
 
+	private String infer;
+
+	private String inferenceFrom;
+
 	public FieldDef() {
 	}
 
+	public String getInferenceFrom() {
+		return inferenceFrom;
+	}
+
+	public void setInferenceFrom(final String inferenceFrom) {
+		this.inferenceFrom = inferenceFrom;
+	}
+
 	public String getName() {
 		return name;
 	}
@@ -126,6 +138,14 @@ public class FieldDef implements Serializable {
 		this.clean = clean;
 	}
 
+	public String getInfer() {
+		return infer;
+	}
+
+	public void setInfer(String infer) {
+		this.infer = infer;
+	}
+
 	@Override
 	public String toString() {
 		try {

dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala

@@ -3,7 +3,7 @@ package eu.dnetlib.pace.model
 import com.jayway.jsonpath.{Configuration, JsonPath}
 import eu.dnetlib.pace.common.AbstractPaceFunctions
 import eu.dnetlib.pace.config.{DedupConfig, Type}
-import eu.dnetlib.pace.util.MapDocumentUtil
+import eu.dnetlib.pace.util.{MapDocumentUtil, SparkCompatUtils}
 import org.apache.commons.lang3.StringUtils
 import org.apache.spark.sql.catalyst.encoders.RowEncoder
 import org.apache.spark.sql.catalyst.expressions.GenericRowWithSchema
@@ -52,7 +52,7 @@ case class SparkModel(conf: DedupConfig) {
   val orderingFieldPosition: Int = schema.fieldIndex(orderingFieldName)
 
   val parseJsonDataset: (Dataset[String] => Dataset[Row]) = df => {
-    df.map(r => rowFromJson(r))(RowEncoder(schema))
+    df.map(r => rowFromJson(r))(SparkCompatUtils.encoderFor(schema))
   }
 
   def rowFromJson(json: String): Row = {
@@ -123,9 +123,19 @@ case class SparkModel(conf: DedupConfig) {
               case _ => res(index)
             }
           }
+
+          if (StringUtils.isNotBlank(fdef.getInfer)) {
+            val inferFrom : String = if (StringUtils.isNotBlank(fdef.getInferenceFrom)) fdef.getInferenceFrom else fdef.getPath
+            res(index) = res(index) match {
+              case x: Seq[String] => x.map(inference(_, MapDocumentUtil.getJPathString(inferFrom, documentContext), fdef.getInfer))
+              case _ => inference(res(index).toString, MapDocumentUtil.getJPathString(inferFrom, documentContext), fdef.getInfer)
+            }
+          }
+
         }
 
         res
+
     }
 
     new GenericRowWithSchema(values, schema)
@@ -146,5 +156,17 @@ case class SparkModel(conf: DedupConfig) {
     res
   }
 
+  def inference(value: String, inferfrom: String, infertype: String) : String = {
+    val res = infertype match {
+      case "country" => AbstractPaceFunctions.countryInference(value, inferfrom)
+      case "city" => AbstractPaceFunctions.cityInference(value)
+      case "keyword" => AbstractPaceFunctions.keywordInference(value)
+      case "city_keyword" => AbstractPaceFunctions.cityKeywordInference(value)
+      case _ => value
+    }
+
+    res
+  }
+
 }
 

dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CityMatch.java

@@ -1,48 +0,0 @@
-
-package eu.dnetlib.pace.tree;
-
-import java.util.Map;
-import java.util.Set;
-
-import eu.dnetlib.pace.config.Config;
-import eu.dnetlib.pace.tree.support.AbstractStringComparator;
-import eu.dnetlib.pace.tree.support.ComparatorClass;
-
-@ComparatorClass("cityMatch")
-public class CityMatch extends AbstractStringComparator {
-
-	private Map<String, String> params;
-
-	public CityMatch(Map<String, String> params) {
-		super(params);
-		this.params = params;
-	}
-
-	@Override
-	public double distance(final String a, final String b, final Config conf) {
-
-		String ca = cleanup(a);
-		String cb = cleanup(b);
-
-		ca = normalize(ca);
-		cb = normalize(cb);
-
-		ca = filterAllStopWords(ca);
-		cb = filterAllStopWords(cb);
-
-		Set<String> cities1 = getCities(ca, Integer.parseInt(params.getOrDefault("windowSize", "4")));
-		Set<String> cities2 = getCities(cb, Integer.parseInt(params.getOrDefault("windowSize", "4")));
-
-		Set<String> codes1 = citiesToCodes(cities1);
-		Set<String> codes2 = citiesToCodes(cities2);
-
-		// if no cities are detected, the comparator gives 1.0
-		if (codes1.isEmpty() && codes2.isEmpty())
-			return 1.0;
-		else {
-			if (codes1.isEmpty() ^ codes2.isEmpty())
-				return -1; // undefined if one of the two has no cities
-			return commonElementsPercentage(codes1, codes2);
-		}
-	}
-}

dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CodeMatch.java

@@ -0,0 +1,51 @@
+
+package eu.dnetlib.pace.tree;
+
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import eu.dnetlib.pace.config.Config;
+import eu.dnetlib.pace.tree.support.AbstractStringComparator;
+import eu.dnetlib.pace.tree.support.ComparatorClass;
+
+@ComparatorClass("codeMatch")
+public class CodeMatch extends AbstractStringComparator {
+
+	private Map<String, String> params;
+
+	private Pattern CODE_REGEX;
+
+	public CodeMatch(Map<String, String> params) {
+		super(params);
+		this.params = params;
+		this.CODE_REGEX = Pattern.compile(params.getOrDefault("codeRegex", "[a-zA-Z]::\\d+"));
+	}
+
+	public Set<String> getRegexList(String input) {
+		Matcher matcher = this.CODE_REGEX.matcher(input);
+		Set<String> cities = new HashSet<>();
+		while (matcher.find()) {
+			cities.add(matcher.group());
+		}
+		return cities;
+	}
+
+	@Override
+	public double distance(final String a, final String b, final Config conf) {
+
+		Set<String> codes1 = getRegexList(a);
+		Set<String> codes2 = getRegexList(b);
+
+		// if no codes are detected, the comparator gives 1.0
+		if (codes1.isEmpty() && codes2.isEmpty())
+			return 1.0;
+		else {
+			if (codes1.isEmpty() ^ codes2.isEmpty())
+				return -1; // undefined if one of the two has no codes
+			return commonElementsPercentage(codes1, codes2);
+		}
+	}
+}

dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java

@@ -0,0 +1,54 @@
+
+package eu.dnetlib.pace.tree;
+
+import java.util.Map;
+import java.util.Set;
+
+import com.wcohen.ss.AbstractStringDistance;
+
+import eu.dnetlib.pace.config.Config;
+import eu.dnetlib.pace.tree.support.AbstractStringComparator;
+import eu.dnetlib.pace.tree.support.ComparatorClass;
+
+@ComparatorClass("countryMatch")
+public class CountryMatch extends AbstractStringComparator {
+
+	private Map<String, String> params;
+
+	public CountryMatch(Map<String, String> params) {
+		super(params, new com.wcohen.ss.JaroWinkler());
+		this.params = params;
+	}
+
+	public CountryMatch(final double weight) {
+		super(weight, new com.wcohen.ss.JaroWinkler());
+	}
+
+	protected CountryMatch(final double weight, final AbstractStringDistance ssalgo) {
+		super(weight, ssalgo);
+	}
+
+	@Override
+	public double distance(final String a, final String b, final Config conf) {
+
+		if (a.isEmpty() || b.isEmpty()) {
+			return -1.0; // return -1 if a field is missing
+		}
+		if (a.equalsIgnoreCase("unknown") || b.equalsIgnoreCase("unknown")) {
+			return -1.0; // return -1 if a country is UNKNOWN
+		}
+
+		return a.equals(b) ? 1.0 : 0;
+	}
+
+	@Override
+	public double getWeight() {
+		return super.weight;
+	}
+
+	@Override
+	protected double normalize(final double d) {
+		return d;
+	}
+
+}

dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JaroWinklerLegalname.java

@@ -0,0 +1,59 @@
+
+package eu.dnetlib.pace.tree;
+
+import java.util.Map;
+import java.util.Set;
+
+import com.wcohen.ss.AbstractStringDistance;
+
+import eu.dnetlib.pace.config.Config;
+import eu.dnetlib.pace.tree.support.AbstractStringComparator;
+import eu.dnetlib.pace.tree.support.ComparatorClass;
+
+@ComparatorClass("jaroWinklerLegalname")
+public class JaroWinklerLegalname extends AbstractStringComparator {
+
+	private Map<String, String> params;
+
+	private final String CITY_CODE_REGEX = "city::\\d+";
+	private final String KEYWORD_CODE_REGEX = "key::\\d+";
+
+	public JaroWinklerLegalname(Map<String, String> params) {
+		super(params, new com.wcohen.ss.JaroWinkler());
+		this.params = params;
+	}
+
+	public JaroWinklerLegalname(double weight) {
+		super(weight, new com.wcohen.ss.JaroWinkler());
+	}
+
+	protected JaroWinklerLegalname(double weight, AbstractStringDistance ssalgo) {
+		super(weight, ssalgo);
+	}
+
+	@Override
+	public double distance(String a, String b, final Config conf) {
+
+		String ca = a.replaceAll(CITY_CODE_REGEX, "").replaceAll(KEYWORD_CODE_REGEX, " ");
+		String cb = b.replaceAll(CITY_CODE_REGEX, "").replaceAll(KEYWORD_CODE_REGEX, " ");
+
+		ca = ca.replaceAll("[ ]{2,}", " ");
+		cb = cb.replaceAll("[ ]{2,}", " ");
+
+		if (ca.isEmpty() && cb.isEmpty())
+			return 1.0;
+		else
+			return normalize(ssalgo.score(ca, cb));
+	}
+
+	@Override
+	public double getWeight() {
+		return super.weight;
+	}
+
+	@Override
+	protected double normalize(double d) {
+		return d;
+	}
+
+}

dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JaroWinklerNormalizedName.java

@@ -1,74 +0,0 @@
-
-package eu.dnetlib.pace.tree;
-
-import java.util.Map;
-import java.util.Set;
-
-import com.wcohen.ss.AbstractStringDistance;
-
-import eu.dnetlib.pace.config.Config;
-import eu.dnetlib.pace.tree.support.AbstractStringComparator;
-import eu.dnetlib.pace.tree.support.ComparatorClass;
-
-@ComparatorClass("jaroWinklerNormalizedName")
-public class JaroWinklerNormalizedName extends AbstractStringComparator {
-
-	private Map<String, String> params;
-
-	public JaroWinklerNormalizedName(Map<String, String> params) {
-		super(params, new com.wcohen.ss.JaroWinkler());
-		this.params = params;
-	}
-
-	public JaroWinklerNormalizedName(double weight) {
-		super(weight, new com.wcohen.ss.JaroWinkler());
-	}
-
-	protected JaroWinklerNormalizedName(double weight, AbstractStringDistance ssalgo) {
-		super(weight, ssalgo);
-	}
-
-	@Override
-	public double distance(String a, String b, final Config conf) {
-		String ca = cleanup(a);
-		String cb = cleanup(b);
-
-		ca = normalize(ca);
-		cb = normalize(cb);
-
-		ca = filterAllStopWords(ca);
-		cb = filterAllStopWords(cb);
-
-		Set<String> keywords1 = getKeywords(
-			ca, conf.translationMap(), Integer.parseInt(params.getOrDefault("windowSize", "4")));
-		Set<String> keywords2 = getKeywords(
-			cb, conf.translationMap(), Integer.parseInt(params.getOrDefault("windowSize", "4")));
-
-		Set<String> cities1 = getCities(ca, Integer.parseInt(params.getOrDefault("windowSize", "4")));
-		Set<String> cities2 = getCities(cb, Integer.parseInt(params.getOrDefault("windowSize", "4")));
-
-		ca = removeKeywords(ca, keywords1);
-		ca = removeKeywords(ca, cities1);
-		cb = removeKeywords(cb, keywords2);
-		cb = removeKeywords(cb, cities2);
-
-		ca = ca.replaceAll("[ ]{2,}", " ");
-		cb = cb.replaceAll("[ ]{2,}", " ");
-
-		if (ca.isEmpty() && cb.isEmpty())
-			return 1.0;
-		else
-			return normalize(ssalgo.score(ca, cb));
-	}
-
-	@Override
-	public double getWeight() {
-		return super.weight;
-	}
-
-	@Override
-	protected double normalize(double d) {
-		return d;
-	}
-
-}

dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/KeywordMatch.java

@@ -1,50 +0,0 @@
-
-package eu.dnetlib.pace.tree;
-
-import java.util.Map;
-import java.util.Set;
-
-import eu.dnetlib.pace.config.Config;
-import eu.dnetlib.pace.tree.support.AbstractStringComparator;
-import eu.dnetlib.pace.tree.support.ComparatorClass;
-
-@ComparatorClass("keywordMatch")
-public class KeywordMatch extends AbstractStringComparator {
-
-	Map<String, String> params;
-
-	public KeywordMatch(Map<String, String> params) {
-		super(params);
-		this.params = params;
-	}
-
-	@Override
-	public double distance(final String a, final String b, final Config conf) {
-
-		String ca = cleanup(a);
-		String cb = cleanup(b);
-
-		ca = normalize(ca);
-		cb = normalize(cb);
-
-		ca = filterAllStopWords(ca);
-		cb = filterAllStopWords(cb);
-
-		Set<String> keywords1 = getKeywords(
-			ca, conf.translationMap(), Integer.parseInt(params.getOrDefault("windowSize", "4")));
-		Set<String> keywords2 = getKeywords(
-			cb, conf.translationMap(), Integer.parseInt(params.getOrDefault("windowSize", "4")));
-
-		Set<String> codes1 = toCodes(keywords1, conf.translationMap());
-		Set<String> codes2 = toCodes(keywords2, conf.translationMap());
-
-		// if no cities are detected, the comparator gives 1.0
-		if (codes1.isEmpty() && codes2.isEmpty())
-			return 1.0;
-		else {
-			if (codes1.isEmpty() ^ codes2.isEmpty())
-				return -1.0; // undefined if one of the two has no keywords
-			return commonElementsPercentage(codes1, codes2);
-		}
-	}
-}

dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeDef.java

@@ -48,7 +48,7 @@ public class TreeNodeDef implements Serializable {
 	// function for the evaluation of the node
 	public TreeNodeStats evaluate(Row doc1, Row doc2, Config conf) {
 
-		TreeNodeStats stats = new TreeNodeStats();
+		TreeNodeStats stats = new TreeNodeStats(ignoreUndefined);
 
 		// for each field in the node, it computes the
 		for (FieldConf fieldConf : fields) {

dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java

@@ -9,8 +9,11 @@ public class TreeNodeStats implements Serializable {
 
 	private Map<String, FieldStats> results; // this is an accumulator for the results of the node
 
-	public TreeNodeStats() {
+	private final boolean ignoreUndefined;
+
+	public TreeNodeStats(boolean ignoreUndefined) {
 		this.results = new HashMap<>();
+		this.ignoreUndefined = ignoreUndefined;
 	}
 
 	public Map<String, FieldStats> getResults() {
@@ -22,7 +25,10 @@ public class TreeNodeStats implements Serializable {
 	}
 
 	public int fieldsCount() {
-		return this.results.size();
+		if(ignoreUndefined)
+			return this.results.size();
+		else
+			return this.results.size() - undefinedCount();	//do not count undefined
 	}
 
 	public int undefinedCount() {
@@ -78,11 +84,25 @@ public class TreeNodeStats implements Serializable {
 		double min = 100.0; // random high value
 		for (FieldStats fs : this.results.values()) {
 			if (fs.getResult() < min) {
-				if (fs.getResult() >= 0.0 || (fs.getResult() == -1 && fs.isCountIfUndefined()))
+				if (fs.getResult() == -1) {
+					if (fs.isCountIfUndefined()) {
+						min = 0.0;
+					}
+					else {
+						min = -1;
+					}
+				}
+				else {
 					min = fs.getResult();
+				}
 			}
 		}
-		return min;
+		if (ignoreUndefined) {
+			return min==-1.0? 0.0 : min;
+		}
+		else {
+			return min;
+		}
 	}
 
 	// if at least one is true, return 1.0
@@ -91,7 +111,11 @@ public class TreeNodeStats implements Serializable {
 			if (fieldStats.getResult() >= fieldStats.getThreshold())
 				return 1.0;
 		}
-		return 0.0;
+		if (!ignoreUndefined && undefinedCount()>0){
+			return -1.0;
+		} else {
+			return 0.0;
+		}
 	}
 
 	// if at least one is false, return 0.0
@@ -100,7 +124,7 @@ public class TreeNodeStats implements Serializable {
 
 			if (fieldStats.getResult() == -1) {
 				if (fieldStats.isCountIfUndefined())
-					return 0.0;
+					return ignoreUndefined? 0.0 : -1.0;
 			} else {
 				if (fieldStats.getResult() < fieldStats.getThreshold())
 					return 0.0;

dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java

@@ -43,18 +43,17 @@ public class TreeProcessor {
 
 			TreeNodeStats stats = currentNode.evaluate(doc1, doc2, config);
 			treeStats.addNodeStats(nextNodeName, stats);
-
-			// if ignoreUndefined=false the miss is considered as undefined
-			if (!currentNode.isIgnoreUndefined() && stats.undefinedCount() > 0) {
+			
+			double finalScore = stats.getFinalScore(currentNode.getAggregation());
+			if(finalScore == -1.0)
 				nextNodeName = currentNode.getUndefined();
-			}
-			// if ignoreUndefined=true the miss is ignored and the score computed anyway
-			else if (stats.getFinalScore(currentNode.getAggregation()) >= currentNode.getThreshold()) {
+			else if (finalScore >= currentNode.getThreshold()) {
 				nextNodeName = currentNode.getPositive();
 			} else {
 				nextNodeName = currentNode.getNegative();
 			}
 
+
 		} while (MatchType.parse(nextNodeName) == MatchType.UNDEFINED);
 
 		treeStats.setResult(MatchType.parse(nextNodeName));

dhp-pace-core/src/main/spark-2/eu/dnetlib/pace/util/SparkCompatUtils.scala

@@ -0,0 +1,12 @@
+package eu.dnetlib.pace.util
+
+import org.apache.spark.sql.Row
+import org.apache.spark.sql.catalyst.encoders.{ExpressionEncoder, RowEncoder}
+import org.apache.spark.sql.types.StructType
+
+object SparkCompatUtils {
+
+  def encoderFor(schema: StructType): ExpressionEncoder[Row] = {
+    RowEncoder(schema)
+  }
+}

dhp-pace-core/src/main/spark-35/eu/dnetlib/pace/util/SparkCompatUtils.scala

@@ -0,0 +1,12 @@
+package eu.dnetlib.pace.util
+
+import org.apache.spark.sql.Row
+import org.apache.spark.sql.catalyst.encoders.ExpressionEncoder
+import org.apache.spark.sql.types.StructType
+
+object SparkCompatUtils {
+
+  def encoderFor(schema: StructType): ExpressionEncoder[Row] = {
+    ExpressionEncoder(schema)
+  }
+}

dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java

@@ -3,6 +3,7 @@ package eu.dnetlib.pace.clustering;
 
 import java.util.Map;
 
+import com.mongodb.connection.Cluster;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
 
@@ -177,41 +178,16 @@ public class ClusteringFunctionTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void testKeywordsClustering() {
+	public void legalnameClustering() {
 
-		final ClusteringFunction cf = new KeywordsClustering(params);
-		final String s = "Polytechnic University of Turin";
+		final ClusteringFunction cf = new LegalnameClustering(params);
+		String s = "key::1 key::2 city::1";
 		System.out.println(s);
 		System.out.println(cf.apply(conf, Lists.newArrayList(s)));
 
-		final String s1 = "POLITECNICO DI TORINO";
-		System.out.println(s1);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s1)));
-
-		final String s2 = "Universita farmaceutica culturale di milano bergamo";
-		System.out.println("s2 = " + s2);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s2)));
-
-		final String s3 = "universita universita milano milano";
-		System.out.println("s3 = " + s3);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s3)));
-
-		final String s4 = "Politechniki Warszawskiej (Warsaw University of Technology)";
-		System.out.println("s4 = " + s4);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s4)));
-
-		final String s5 = "İstanbul Ticarət Universiteti";
-		System.out.println("s5 = " + s5);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s5)));
-
-		final String s6 = "National and Kapodistrian University of Athens";
-		System.out.println("s6 = " + s6);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s6)));
-
-		final String s7 = "Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών";
-		System.out.println("s7 = " + s7);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s7)));
-
+		s = "key::1 key::2 city::1 city::2";
+		System.out.println(s);
+		System.out.println(cf.apply(conf, Lists.newArrayList(s)));
 	}
 
 	@Test

dhp-pace-core/src/test/java/eu/dnetlib/pace/common/PaceFunctionTest.java

@@ -54,4 +54,47 @@ public class PaceFunctionTest extends AbstractPaceFunctions {
 		System.out.println("Fixed aliases  : " + fixAliases(TEST_STRING));
 	}
 
+	@Test
+	public void countryInferenceTest() {
+		assertEquals("IT", countryInference("UNKNOWN", "Università di Bologna"));
+		assertEquals("UK", countryInference("UK", "Università di Bologna"));
+		assertEquals("IT", countryInference("UNKNOWN", "Universiteé de Naples"));
+		assertEquals("UNKNOWN", countryInference("UNKNOWN", "Università del Lavoro"));
+	}
+
+	@Test
+	public void cityInferenceTest() {
+		assertEquals("universita city::3181928", cityInference("Università di Bologna"));
+		assertEquals("university city::3170647", cityInference("University of Pisa"));
+		assertEquals("universita", cityInference("Università del lavoro"));
+		assertEquals("universita city::3173331 city::3169522", cityInference("Università di Modena e Reggio Emilia"));
+	}
+
+	@Test
+	public void keywordInferenceTest() {
+		assertEquals("key::41 turin", keywordInference("Polytechnic University of Turin"));
+		assertEquals("key::41 torino", keywordInference("POLITECNICO DI TORINO"));
+		assertEquals(
+			"key::1 key::60 key::81 milano bergamo",
+			keywordInference("Universita farmaceutica culturale di milano bergamo"));
+		assertEquals("key::1 key::1 milano milano", keywordInference("universita universita milano milano"));
+		assertEquals(
+			"key::10 kapodistriako panepistemio athenon",
+			keywordInference("Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών"));
+	}
+
+	@Test
+	public void cityKeywordInferenceTest() {
+		assertEquals("key::41 city::3165524", cityKeywordInference("Polytechnic University of Turin"));
+		assertEquals("key::41 city::3165524", cityKeywordInference("POLITECNICO DI TORINO"));
+		assertEquals(
+			"key::1 key::60 key::81 city::3173435 city::3182164",
+			cityKeywordInference("Universita farmaceutica culturale di milano bergamo"));
+		assertEquals(
+			"key::1 key::1 city::3173435 city::3173435", cityKeywordInference("universita universita milano milano"));
+		assertEquals(
+			"key::10 kapodistriako panepistemio city::264371",
+			cityKeywordInference("Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών"));
+	}
+
 }

dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java

@@ -35,6 +35,7 @@ public class ComparatorTest extends AbstractPaceTest {
 		params.put("name_th", "0.95");
 		params.put("jpath_value", "$.value");
 		params.put("jpath_classid", "$.qualifier.classid");
+		params.put("codeRegex", "key::\\d+");
 	}
 
 	@Test
@@ -44,52 +45,23 @@ public class ComparatorTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void cityMatchTest() {
-		final CityMatch cityMatch = new CityMatch(params);
+	public void codeMatchTest() {
+		CodeMatch codeMatch = new CodeMatch(params);
 
-		// both names with no cities
-		assertEquals(1.0, cityMatch.distance("Università", "Centro di ricerca", conf));
+		// both names with no codes
+		assertEquals(1.0, codeMatch.distance("testing1", "testing2", conf));
 
-		// one of the two names with no cities
-		assertEquals(-1.0, cityMatch.distance("Università di Bologna", "Centro di ricerca", conf));
+		// one of the two names with no codes
+		assertEquals(-1.0, codeMatch.distance("testing1 key::1", "testing", conf));
 
-		// both names with cities (same)
-		assertEquals(1.0, cityMatch.distance("Universita di Bologna", "Biblioteca di Bologna", conf));
+		// both names with codes (same)
+		assertEquals(1.0, codeMatch.distance("testing1 key::1", "testing2 key::1", conf));
 
-		// both names with cities (different)
-		assertEquals(0.0, cityMatch.distance("Universita di Bologna", "Universita di Torino", conf));
-		assertEquals(0.0, cityMatch.distance("Franklin College", "Concordia College", conf));
+		// both names with codes (different)
+		assertEquals(0.0, codeMatch.distance("testing1 key::1", "testing2 key::2", conf));
 
-		// particular cases
-		assertEquals(1.0, cityMatch.distance("Free University of Bozen-Bolzano", "Università di Bolzano", conf));
-		assertEquals(
-			1.0,
-			cityMatch
-				.distance(
-					"Politechniki Warszawskiej (Warsaw University of Technology)", "Warsaw University of Technology",
-					conf));
-
-		// failing becasuse 'Allen' is a transliterrated greek stopword
-		// assertEquals(-1.0, cityMatch.distance("Allen (United States)", "United States Military Academy", conf));
-		assertEquals(-1.0, cityMatch.distance("Washington (United States)", "United States Military Academy", conf));
-	}
-
-	@Test
-	public void keywordMatchTest() {
-		params.put("threshold", "0.5");
-
-		final KeywordMatch keywordMatch = new KeywordMatch(params);
-
-		assertEquals(
-			0.5, keywordMatch.distance("Biblioteca dell'Universita di Bologna", "Università di Bologna", conf));
-		assertEquals(1.0, keywordMatch.distance("Universita degli studi di Pisa", "Universita di Pisa", conf));
-		assertEquals(1.0, keywordMatch.distance("Polytechnic University of Turin", "POLITECNICO DI TORINO", conf));
-		assertEquals(1.0, keywordMatch.distance("Istanbul Commerce University", "İstanbul Ticarət Universiteti", conf));
-		assertEquals(1.0, keywordMatch.distance("Franklin College", "Concordia College", conf));
-		assertEquals(2.0 / 3.0, keywordMatch.distance("University of Georgia", "Georgia State University", conf));
-		assertEquals(0.5, keywordMatch.distance("University College London", "University of London", conf));
-		assertEquals(0.5, keywordMatch.distance("Washington State University", "University of Washington", conf));
-		assertEquals(-1.0, keywordMatch.distance("Allen (United States)", "United States Military Academy", conf));
+		// both names with codes (1 same, 1 different)
+		assertEquals(0.5,codeMatch.distance("key::1 key::2 testing1", "key::1 testing", conf));
 
 	}
 
@@ -155,15 +127,15 @@ public class ComparatorTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void jaroWinklerNormalizedNameTest() {
+	public void jaroWinklerLegalnameTest() {
 
-		final JaroWinklerNormalizedName jaroWinklerNormalizedName = new JaroWinklerNormalizedName(params);
+		final JaroWinklerLegalname jaroWinklerLegalname = new JaroWinklerLegalname(params);
 
-		double result = jaroWinklerNormalizedName
-			.distance("AT&T (United States)", "United States Military Academy", conf);
+		double result = jaroWinklerLegalname
+			.distance("AT&T (United States)", "United States key::2 key::1", conf);
 		System.out.println("result = " + result);
 
-		result = jaroWinklerNormalizedName.distance("NOAA - Servicio Meteorol\\u00f3gico Nacional", "NOAA - NWS", conf);
+		result = jaroWinklerLegalname.distance("NOAA - Servicio Meteorol\\u00f3gico Nacional", "NOAA - NWS", conf);
 		System.out.println("result = " + result);
 
 	}
@@ -336,4 +308,23 @@ public class ComparatorTest extends AbstractPaceTest {
 		System.out.println("compare = " + compare);
 	}
 
+	@Test
+	public void countryMatch() {
+
+		CountryMatch countryMatch = new CountryMatch(params);
+
+		double result = countryMatch.distance("UNKNOWN", "UNKNOWN", conf);
+		assertEquals(-1.0, result);
+
+		result = countryMatch.distance("CL", "UNKNOWN", conf);
+		assertEquals(-1.0, result);
+
+		result = countryMatch.distance("CL", "IT", conf);
+		assertEquals(0.0, result);
+
+		result = countryMatch.distance("CL", "CL", conf);
+		assertEquals(1.0, result);
+
+	}
+
 }

dhp-pace-core/src/test/java/eu/dnetlib/pace/util/UtilTest.java

@@ -11,6 +11,7 @@ import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
 import eu.dnetlib.pace.model.Person;
+import jdk.nashorn.internal.ir.annotations.Ignore;
 
 public class UtilTest {
 

dhp-shade-package/dependency-reduced-pom.xml

@@ -0,0 +1,113 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <parent>
+    <artifactId>dhp</artifactId>
+    <groupId>eu.dnetlib.dhp</groupId>
+    <version>1.2.5-SNAPSHOT</version>
+  </parent>
+  <modelVersion>4.0.0</modelVersion>
+  <artifactId>dhp-shade-package</artifactId>
+  <description>This module create a jar of all module dependencies</description>
+  <build>
+    <plugins>
+      <plugin>
+        <artifactId>maven-shade-plugin</artifactId>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>shade</goal>
+            </goals>
+            <configuration>
+              <transformers>
+                <transformer>
+                  <mainClass>eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels</mainClass>
+                </transformer>
+                <transformer />
+                <transformer>
+                  <resource>META-INF/cxf/bus-extensions.txt</resource>
+                </transformer>
+              </transformers>
+              <filters>
+                <filter>
+                  <artifact>*:*</artifact>
+                  <excludes>
+                    <exclude>META-INF/maven/**</exclude>
+                    <exclude>META-INF/*.SF</exclude>
+                    <exclude>META-INF/*.DSA</exclude>
+                    <exclude>META-INF/*.RSA</exclude>
+                  </excludes>
+                </filter>
+              </filters>
+              <relocations>
+                <relocation>
+                  <pattern>com</pattern>
+                  <shadedPattern>repackaged.com.google.common</shadedPattern>
+                  <includes>
+                    <include>com.google.common.**</include>
+                  </includes>
+                </relocation>
+              </relocations>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+  <dependencies>
+    <dependency>
+      <groupId>org.projectlombok</groupId>
+      <artifactId>lombok</artifactId>
+      <version>1.18.28</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter</artifactId>
+      <version>5.6.1</version>
+      <scope>test</scope>
+      <exclusions>
+        <exclusion>
+          <artifactId>junit-jupiter-api</artifactId>
+          <groupId>org.junit.jupiter</groupId>
+        </exclusion>
+        <exclusion>
+          <artifactId>junit-jupiter-params</artifactId>
+          <groupId>org.junit.jupiter</groupId>
+        </exclusion>
+        <exclusion>
+          <artifactId>junit-jupiter-engine</artifactId>
+          <groupId>org.junit.jupiter</groupId>
+        </exclusion>
+      </exclusions>
+    </dependency>
+    <dependency>
+      <groupId>org.mockito</groupId>
+      <artifactId>mockito-core</artifactId>
+      <version>3.3.3</version>
+      <scope>test</scope>
+      <exclusions>
+        <exclusion>
+          <artifactId>byte-buddy</artifactId>
+          <groupId>net.bytebuddy</groupId>
+        </exclusion>
+        <exclusion>
+          <artifactId>byte-buddy-agent</artifactId>
+          <groupId>net.bytebuddy</groupId>
+        </exclusion>
+      </exclusions>
+    </dependency>
+    <dependency>
+      <groupId>org.mockito</groupId>
+      <artifactId>mockito-junit-jupiter</artifactId>
+      <version>3.3.3</version>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
+  <distributionManagement>
+    <site>
+      <id>DHPSite</id>
+      <url>${dhp.site.stage.path}/dhp-common</url>
+    </site>
+  </distributionManagement>
+</project>

dhp-shade-package/pom.xml

@@ -0,0 +1,169 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>eu.dnetlib.dhp</groupId>
+        <artifactId>dhp</artifactId>
+        <version>1.2.5-SNAPSHOT</version>
+        <relativePath>../pom.xml</relativePath>
+
+    </parent>
+
+    <artifactId>dhp-shade-package</artifactId>
+    <packaging>jar</packaging>
+
+    <distributionManagement>
+        <site>
+            <id>DHPSite</id>
+            <url>${dhp.site.stage.path}/dhp-common</url>
+        </site>
+    </distributionManagement>
+
+    <description>This module create a jar of all module dependencies</description>
+
+
+    <dependencies>
+
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-actionmanager</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-aggregation</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-blacklist</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-broker-events</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-dedup-openaire</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-enrichment</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-graph-mapper</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-graph-provision</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-impact-indicators</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-stats-actionsets</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-stats-hist-snaps</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-stats-monitor-irish</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-stats-promote</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-stats-update</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-swh</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-usage-raw-data-update</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-usage-stats-build</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+    </dependencies>
+
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>shade</goal>
+                        </goals>
+                        <configuration>
+                            <transformers>
+                                <transformer
+                                        implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                    <mainClass>eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels</mainClass>
+                                </transformer>
+                                <!-- This is needed if you have dependencies that use Service Loader. Most Google Cloud client libraries do. -->
+                                <transformer
+                                        implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
+                                <transformer
+                                        implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
+                                    <resource>META-INF/cxf/bus-extensions.txt</resource>
+                                </transformer>
+                            </transformers>
+                            <filters>
+                                <filter>
+                                    <artifact>*:*</artifact>
+                                    <excludes>
+                                        <exclude>META-INF/maven/**</exclude>
+                                        <exclude>META-INF/*.SF</exclude>
+                                        <exclude>META-INF/*.DSA</exclude>
+                                        <exclude>META-INF/*.RSA</exclude>
+                                    </excludes>
+                                </filter>
+                            </filters>
+                            <relocations>
+                                <relocation>
+                                    <pattern>com</pattern>
+                                    <shadedPattern>repackaged.com.google.common</shadedPattern>
+                                    <includes>
+                                        <include>com.google.common.**</include>
+                                    </includes>
+                                </relocation>
+                            </relocations>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+</project>

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml

@@ -103,6 +103,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -156,6 +157,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml

@@ -95,6 +95,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

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

@@ -125,6 +125,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml

@@ -95,6 +95,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml

@@ -103,6 +103,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -155,11 +156,12 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=2560
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${workingDir}/otherresearchproduct</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml

@@ -95,6 +95,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml

@@ -103,11 +103,12 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7000
+                --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/publication</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
@@ -156,11 +157,12 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7000
+                --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${workingDir}/publication</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml

@@ -95,11 +95,12 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=10000
+                --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/relation</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml

@@ -103,6 +103,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -155,11 +156,12 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=2560
+                --conf spark.sql.shuffle.partitions=4000
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${workingDir}/software</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>

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

@@ -9,6 +9,7 @@ import java.util.List;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.BZip2Codec;
 import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
@@ -106,7 +107,7 @@ public class PrepareAffiliationRelations implements Serializable {
 					.union(openAPCRelations)
 					.union(dataciteRelations)
 					.saveAsHadoopFile(
-						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
 
 			});
 	}

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

@@ -10,6 +10,7 @@ import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.BZip2Codec;
 import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
@@ -83,7 +84,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
 				resultsRDD
 					.union(projectsRDD)
 					.saveAsHadoopFile(
-						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
 			});
 	}
 

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

@@ -115,19 +115,7 @@ public class PrepareFOSSparkJob implements Serializable {
 			.forEach(
 				l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true)));
 		r.setSubject(sbjs);
-		r
-			.setDataInfo(
-				OafMapperUtils
-					.dataInfo(
-						false, null, true,
-						false,
-						OafMapperUtils
-							.qualifier(
-								ModelConstants.PROVENANCE_ENRICH,
-								null,
-								ModelConstants.DNET_PROVENANCE_ACTIONS,
-								ModelConstants.DNET_PROVENANCE_ACTIONS),
-						null));
+
 		return r;
 	}
 

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

@@ -81,19 +81,7 @@ public class PrepareSDGSparkJob implements Serializable {
 						s -> sbjs
 							.add(getSubject(s.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
 				r.setSubject(sbjs);
-				r
-					.setDataInfo(
-						OafMapperUtils
-							.dataInfo(
-								false, null, true,
-								false,
-								OafMapperUtils
-									.qualifier(
-										ModelConstants.PROVENANCE_ENRICH,
-										null,
-										ModelConstants.DNET_PROVENANCE_ACTIONS,
-										ModelConstants.DNET_PROVENANCE_ACTIONS),
-								null));
+
 				return r;
 			}, Encoders.bean(Result.class))
 			.write()

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

@@ -12,6 +12,7 @@ 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.function.FilterFunction;
 import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.sql.*;
 import org.apache.spark.sql.types.StructType;
@@ -70,6 +71,9 @@ public class CreateActionSetFromWebEntries implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
+		final String blackListInputPath = parser.get("blackListPath");
+		log.info("blackListInputPath: {}", blackListInputPath);
+
 		SparkConf conf = new SparkConf();
 
 		runWithSparkSession(
@@ -77,29 +81,35 @@ public class CreateActionSetFromWebEntries implements Serializable {
 			isSparkSessionManaged,
 			spark -> {
 
-				createActionSet(spark, inputPath, outputPath);
+				createActionSet(spark, inputPath, outputPath, blackListInputPath);
 
 			});
 	}
 
 	public static void createActionSet(SparkSession spark, String inputPath,
-		String outputPath) {
+		String outputPath, String blackListInputPath) {
 
 		final Dataset<Row> dataset = readWebCrawl(spark, inputPath)
-			.filter("publication_year <= 2020 or country_code=='IE'")
+			.filter("country_code=='IE'")
 			.drop("publication_year");
 
-		dataset.flatMap((FlatMapFunction<Row, Relation>) row -> {
-			List<Relation> ret = new ArrayList<>();
-			final String ror = ROR_PREFIX
-				+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
-			ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
-			ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
-			ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
+		final Dataset<Row> blackList = readBlackList(spark, blackListInputPath);
 
-			return ret
-				.iterator();
-		}, Encoders.bean(Relation.class))
+		dataset
+			.join(blackList, dataset.col("id").equalTo(blackList.col("OpenAlexId")), "left")
+			.filter((FilterFunction<Row>) r -> r.getAs("OpenAlexId") == null)
+			.drop("OpenAlexId")
+			.flatMap((FlatMapFunction<Row, Relation>) row -> {
+				List<Relation> ret = new ArrayList<>();
+				final String ror = ROR_PREFIX
+					+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
+				ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
+				ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
+				ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
+
+				return ret
+					.iterator();
+			}, Encoders.bean(Relation.class))
 			.toJavaRDD()
 			.map(p -> new AtomicAction(p.getClass(), p))
 			.mapToPair(
@@ -136,6 +146,15 @@ public class CreateActionSetFromWebEntries implements Serializable {
 
 	}
 
+	private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {
+
+		return spark
+			.read()
+			.option("header", true)
+			.csv(inputPath)
+			.select("OpenAlexId");
+	}
+
 	private static List<Relation> createAffiliationRelationPairPMCID(String pmcid, String ror) {
 		if (pmcid == null)
 			return new ArrayList<>();

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestCollectorPlugin.java

@@ -1,6 +1,7 @@
 
 package eu.dnetlib.dhp.collection.plugin.rest;
 
+import java.util.Map;
 import java.util.Optional;
 import java.util.Spliterator;
 import java.util.Spliterators;
@@ -9,6 +10,8 @@ import java.util.stream.StreamSupport;
 
 import org.apache.commons.lang3.StringUtils;
 
+import com.google.gson.Gson;
+
 import eu.dnetlib.dhp.collection.ApiDescriptor;
 import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
 import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
@@ -47,6 +50,9 @@ public class RestCollectorPlugin implements CollectorPlugin {
 		final String entityXpath = api.getParams().get("entityXpath");
 		final String authMethod = api.getParams().get("authMethod");
 		final String authToken = api.getParams().get("authToken");
+		final String requestHeaderMap = api.getParams().get("requestHeaderMap");
+		Gson gson = new Gson();
+		Map requestHeaders = gson.fromJson(requestHeaderMap, Map.class);
 		final String resultSizeValue = Optional
 			.ofNullable(api.getParams().get("resultSizeValue"))
 			.filter(StringUtils::isNotBlank)
@@ -64,9 +70,6 @@ public class RestCollectorPlugin implements CollectorPlugin {
 		if (StringUtils.isBlank(resultFormatValue)) {
 			throw new CollectorException("Param 'resultFormatValue' is null or empty");
 		}
-		if (StringUtils.isBlank(queryParams)) {
-			throw new CollectorException("Param 'queryParams' is null or empty");
-		}
 		if (StringUtils.isBlank(entityXpath)) {
 			throw new CollectorException("Param 'entityXpath' is null or empty");
 		}
@@ -92,7 +95,8 @@ public class RestCollectorPlugin implements CollectorPlugin {
 			entityXpath,
 			authMethod,
 			authToken,
-			resultOutputFormat);
+			resultOutputFormat,
+			requestHeaders);
 
 		return StreamSupport
 			.stream(

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java

@@ -9,8 +9,11 @@ import java.net.URL;
 import java.net.URLEncoder;
 import java.nio.charset.StandardCharsets;
 import java.util.Iterator;
+import java.util.Map;
 import java.util.Queue;
 import java.util.concurrent.PriorityBlockingQueue;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import javax.xml.transform.OutputKeys;
 import javax.xml.transform.Transformer;
@@ -22,20 +25,20 @@ import javax.xml.xpath.*;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.http.HttpHeaders;
-import org.apache.http.entity.ContentType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 import org.xml.sax.InputSource;
 
+import com.google.common.collect.Maps;
+
 import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils;
 import eu.dnetlib.dhp.common.collection.CollectorException;
 import eu.dnetlib.dhp.common.collection.HttpClientParams;
 
 /**
- * log.info(...) equal to  log.trace(...) in the application-logs
+ * log.info(...) equal to log.trace(...) in the application-logs
  * <p>
  * known bug: at resumptionType 'discover' if the (resultTotal % resultSizeValue) == 0 the collecting fails -> change the resultSizeValue
  *
@@ -44,24 +47,29 @@ import eu.dnetlib.dhp.common.collection.HttpClientParams;
  *
  */
 public class RestIterator implements Iterator<String> {
-
 	private static final Logger log = LoggerFactory.getLogger(RestIterator.class);
 	public static final String UTF_8 = "UTF-8";
+	private static final int MAX_ATTEMPTS = 5;
 
 	private final HttpClientParams clientParams;
 
-	private final String BASIC = "basic";
+	private final String AUTHBASIC = "basic";
+
+	private static final String XML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
+	private static final String EMPTY_XML = XML_HEADER + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG
+		+ ">";
 
 	private final String baseUrl;
 	private final String resumptionType;
 	private final String resumptionParam;
 	private final String resultFormatValue;
-	private String queryParams;
+	private String queryParams = "";
 	private final int resultSizeValue;
 	private int resumptionInt = 0; // integer resumption token (first record to harvest)
 	private int resultTotal = -1;
-	private String resumptionStr = Integer.toString(resumptionInt); // string resumption token (first record to harvest
-																	// or token scanned from results)
+	private String resumptionStr = Integer.toString(this.resumptionInt); // string resumption token (first record to
+																			// harvest
+	// or token scanned from results)
 	private InputStream resultStream;
 	private Transformer transformer;
 	private XPath xpath;
@@ -73,7 +81,7 @@ public class RestIterator implements Iterator<String> {
 	private final String querySize;
 	private final String authMethod;
 	private final String authToken;
-	private final Queue<String> recordQueue = new PriorityBlockingQueue<String>();
+	private final Queue<String> recordQueue = new PriorityBlockingQueue<>();
 	private int discoverResultSize = 0;
 	private int pagination = 1;
 	/*
@@ -83,8 +91,13 @@ public class RestIterator implements Iterator<String> {
 	 */
 	private final String resultOutputFormat;
 
-	/** RestIterator class
-	 *  compatible to version 1.3.33
+	/*
+	 * Can be used to set additional request headers, like for content negotiation
+	 */
+	private Map<String, String> requestHeaders;
+
+	/**
+	 * RestIterator class compatible to version 1.3.33
 	 */
 	public RestIterator(
 		final HttpClientParams clientParams,
@@ -101,47 +114,56 @@ public class RestIterator implements Iterator<String> {
 		final String entityXpath,
 		final String authMethod,
 		final String authToken,
-		final String resultOutputFormat) {
+		final String resultOutputFormat,
+		final Map<String, String> requestHeaders) {
 
 		this.clientParams = clientParams;
 		this.baseUrl = baseUrl;
 		this.resumptionType = resumptionType;
 		this.resumptionParam = resumptionParam;
 		this.resultFormatValue = resultFormatValue;
-		this.resultSizeValue = Integer.valueOf(resultSizeValueStr);
+		this.resultSizeValue = Integer.parseInt(resultSizeValueStr);
 		this.queryParams = queryParams;
 		this.authMethod = authMethod;
 		this.authToken = authToken;
 		this.resultOutputFormat = resultOutputFormat;
+		this.requestHeaders = requestHeaders != null ? requestHeaders : Maps.newHashMap();
 
-		queryFormat = StringUtils.isNotBlank(resultFormatParam) ? "&" + resultFormatParam + "=" + resultFormatValue
+		this.queryFormat = StringUtils.isNotBlank(resultFormatParam) ? "&" + resultFormatParam + "=" + resultFormatValue
+			: "";
+		this.querySize = StringUtils.isNotBlank(resultSizeParam) ? "&" + resultSizeParam + "=" + resultSizeValueStr
 			: "";
-		querySize = StringUtils.isNotBlank(resultSizeParam) ? "&" + resultSizeParam + "=" + resultSizeValueStr : "";
 
 		try {
 			initXmlTransformation(resultTotalXpath, resumptionXpath, entityXpath);
-		} catch (Exception e) {
+		} catch (final Exception e) {
 			throw new IllegalStateException("xml transformation init failed: " + e.getMessage());
 		}
 
 		initQueue();
 	}
 
-	private void initXmlTransformation(String resultTotalXpath, String resumptionXpath, String entityXpath)
+	private void initXmlTransformation(final String resultTotalXpath, final String resumptionXpath,
+		final String entityXpath)
 		throws TransformerConfigurationException, XPathExpressionException {
 		final TransformerFactory factory = TransformerFactory.newInstance();
-		transformer = factory.newTransformer();
-		transformer.setOutputProperty(OutputKeys.INDENT, "yes");
-		transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
-		xpath = XPathFactory.newInstance().newXPath();
-		xprResultTotalPath = xpath.compile(resultTotalXpath);
-		xprResumptionPath = xpath.compile(StringUtils.isBlank(resumptionXpath) ? "/" : resumptionXpath);
-		xprEntity = xpath.compile(entityXpath);
+		this.transformer = factory.newTransformer();
+		this.transformer.setOutputProperty(OutputKeys.INDENT, "yes");
+		this.transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
+		this.xpath = XPathFactory.newInstance().newXPath();
+		this.xprResultTotalPath = this.xpath.compile(resultTotalXpath);
+		this.xprResumptionPath = this.xpath.compile(StringUtils.isBlank(resumptionXpath) ? "/" : resumptionXpath);
+		this.xprEntity = this.xpath.compile(entityXpath);
 	}
 
 	private void initQueue() {
-		query = baseUrl + "?" + queryParams + querySize + queryFormat;
-		log.info("REST calls starting with {}", query);
+		if (queryParams.equals("") && querySize.equals("") && queryFormat.equals("")) {
+			query = baseUrl;
+		} else {
+			query = baseUrl + "?" + queryParams + querySize + queryFormat;
+		}
+
+		log.info("REST calls starting with {}", this.query);
 	}
 
 	private void disconnect() {
@@ -154,11 +176,22 @@ public class RestIterator implements Iterator<String> {
 	 */
 	@Override
 	public boolean hasNext() {
-		if (recordQueue.isEmpty() && query.isEmpty()) {
+		synchronized (this.recordQueue) {
+			while (this.recordQueue.isEmpty() && !this.query.isEmpty()) {
+				try {
+					this.query = downloadPage(this.query, 0);
+				} catch (final CollectorException e) {
+					log.debug("CollectorPlugin.next()-Exception: {}", e);
+					throw new RuntimeException(e);
+				}
+			}
+
+			if (!this.recordQueue.isEmpty()) {
+				return true;
+			}
+
 			disconnect();
 			return false;
-		} else {
-			return true;
 		}
 	}
 
@@ -168,214 +201,248 @@ public class RestIterator implements Iterator<String> {
 	 */
 	@Override
 	public String next() {
-		synchronized (recordQueue) {
-			while (recordQueue.isEmpty() && !query.isEmpty()) {
-				try {
-					query = downloadPage(query);
-				} catch (CollectorException e) {
-					log.debug("CollectorPlugin.next()-Exception: {}", e);
-					throw new RuntimeException(e);
-				}
-			}
-			return recordQueue.poll();
+		synchronized (this.recordQueue) {
+			return this.recordQueue.poll();
 		}
 	}
 
 	/*
-	 * download page and return nextQuery
+	 * download page and return nextQuery (with number of attempt)
 	 */
-	private String downloadPage(String query) throws CollectorException {
-		String resultJson;
-		String resultXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
-		String nextQuery = "";
-		String emptyXml = resultXml + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG + ">";
-		Node resultNode = null;
-		NodeList nodeList = null;
-		String qUrlArgument = "";
-		int urlOldResumptionSize = 0;
-		InputStream theHttpInputStream;
+	private String downloadPage(String query, final int attempt) throws CollectorException {
 
-		// check if cursor=* is initial set otherwise add it to the queryParam URL
-		if (resumptionType.equalsIgnoreCase("deep-cursor")) {
-			log.debug("check resumptionType deep-cursor and check cursor=*?{}", query);
-			if (!query.contains("&cursor=")) {
-				query += "&cursor=*";
+		if (attempt > MAX_ATTEMPTS) {
+			throw new CollectorException("Max Number of attempts reached, query:" + query);
+		}
+
+		if (attempt > 0) {
+			final int delay = (attempt * 5000);
+			log.debug("Attempt {} with delay {}", attempt, delay);
+			try {
+				Thread.sleep(delay);
+			} catch (final InterruptedException e) {
+				new CollectorException(e);
 			}
 		}
 
 		try {
-			log.info("requestig URL [{}]", query);
+			String resultJson;
+			String resultXml = XML_HEADER;
+			String nextQuery = "";
+			Node resultNode = null;
+			NodeList nodeList = null;
+			String qUrlArgument = "";
+			int urlOldResumptionSize = 0;
+			InputStream theHttpInputStream;
 
-			URL qUrl = new URL(query);
-			log.debug("authMethod: {}", authMethod);
-			if ("bearer".equalsIgnoreCase(this.authMethod)) {
-				log.trace("authMethod before inputStream: {}", resultXml);
-				HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
-				conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + authToken);
-				conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.getMimeType());
-				conn.setRequestMethod("GET");
-				theHttpInputStream = conn.getInputStream();
-			} else if (BASIC.equalsIgnoreCase(this.authMethod)) {
-				log.trace("authMethod before inputStream: {}", resultXml);
-				HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
-				conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Basic " + authToken);
-				conn.setRequestProperty(HttpHeaders.ACCEPT, ContentType.APPLICATION_XML.getMimeType());
-				conn.setRequestMethod("GET");
-				theHttpInputStream = conn.getInputStream();
-			} else {
-				theHttpInputStream = qUrl.openStream();
-			}
-
-			resultStream = theHttpInputStream;
-			if ("json".equals(resultOutputFormat)) {
-				resultJson = IOUtils.toString(resultStream, StandardCharsets.UTF_8);
-				resultXml = JsonUtils.convertToXML(resultJson);
-				resultStream = IOUtils.toInputStream(resultXml, UTF_8);
-			}
-
-			if (!(emptyXml).equalsIgnoreCase(resultXml)) {
-				resultNode = (Node) xpath.evaluate("/", new InputSource(resultStream), XPathConstants.NODE);
-				nodeList = (NodeList) xprEntity.evaluate(resultNode, XPathConstants.NODESET);
-				log.debug("nodeList.length: {}", nodeList.getLength());
-				for (int i = 0; i < nodeList.getLength(); i++) {
-					StringWriter sw = new StringWriter();
-					transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
-					String toEnqueue = sw.toString();
-					if (toEnqueue == null || StringUtils.isBlank(toEnqueue) || emptyXml.equalsIgnoreCase(toEnqueue)) {
-						log.warn("The following record resulted in empty item for the feeding queue: {}", resultXml);
-					} else {
-						recordQueue.add(sw.toString());
-					}
+			// check if cursor=* is initial set otherwise add it to the queryParam URL
+			if ("deep-cursor".equalsIgnoreCase(this.resumptionType)) {
+				log.debug("check resumptionType deep-cursor and check cursor=*?{}", query);
+				if (!query.contains("&cursor=")) {
+					query += "&cursor=*";
 				}
-			} else {
-				log.warn("resultXml is equal with emptyXml");
 			}
 
-			resumptionInt += resultSizeValue;
+			// find pagination page start number in queryParam and remove before start the first query
+			if ((resumptionType.toLowerCase().equals("pagination") || resumptionType.toLowerCase().equals("page"))
+				&& (query.contains("paginationStart="))) {
 
-			switch (resumptionType.toLowerCase()) {
-				case "scan": // read of resumptionToken , evaluate next results, e.g. OAI, iterate over items
-					resumptionStr = xprResumptionPath.evaluate(resultNode);
-					break;
+				final Matcher m = Pattern.compile("paginationStart=([0-9]+)").matcher(query);
+				m.find(); // guaranteed to be true for this regex
 
-				case "count": // begin at one step for all records, iterate over items
-					resumptionStr = Integer.toString(resumptionInt);
-					break;
+				String[] pageVal = m.group(0).split("=");
+				pagination = Integer.parseInt(pageVal[1]);
 
-				case "discover": // size of result items unknown, iterate over items (for openDOAR - 201808)
-					if (resultSizeValue < 2) {
-						throw new CollectorException("Mode: discover, Param 'resultSizeValue' is less than 2");
+				// remove page start number from query and queryParams
+				queryParams = queryParams.replaceFirst("&?paginationStart=[0-9]+", "");
+				query = query.replaceFirst("&?paginationStart=[0-9]+", "");
+
+			}
+
+			try {
+				log.info("requesting URL [{}]", query);
+
+				final URL qUrl = new URL(query);
+				log.debug("authMethod: {}", this.authMethod);
+				if (this.authMethod == "bearer") {
+					log.trace("RestIterator.downloadPage():: authMethod before inputStream: " + resultXml);
+					requestHeaders.put("Authorization", "Bearer " + authToken);
+					// requestHeaders.put("Content-Type", "application/json");
+				} else if (AUTHBASIC.equalsIgnoreCase(this.authMethod)) {
+					log.trace("RestIterator.downloadPage():: authMethod before inputStream: " + resultXml);
+					requestHeaders.put("Authorization", "Basic " + authToken);
+					// requestHeaders.put("accept", "application/xml");
+				}
+				HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
+				conn.setRequestMethod("GET");
+				this.setRequestHeader(conn);
+				resultStream = conn.getInputStream();
+
+				if ("json".equals(this.resultOutputFormat)) {
+					resultJson = IOUtils.toString(this.resultStream, StandardCharsets.UTF_8);
+					resultXml = JsonUtils.convertToXML(resultJson);
+					this.resultStream = IOUtils.toInputStream(resultXml, UTF_8);
+				}
+
+				if (!isEmptyXml(resultXml)) {
+					resultNode = (Node) this.xpath
+						.evaluate("/", new InputSource(this.resultStream), XPathConstants.NODE);
+					nodeList = (NodeList) this.xprEntity.evaluate(resultNode, XPathConstants.NODESET);
+					log.debug("nodeList.length: {}", nodeList.getLength());
+					for (int i = 0; i < nodeList.getLength(); i++) {
+						final StringWriter sw = new StringWriter();
+						this.transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
+						final String toEnqueue = sw.toString();
+						if ((toEnqueue == null) || StringUtils.isBlank(toEnqueue) || isEmptyXml(toEnqueue)) {
+							log
+								.warn(
+									"The following record resulted in empty item for the feeding queue: {}", resultXml);
+						} else {
+							this.recordQueue.add(sw.toString());
+						}
 					}
-					qUrlArgument = qUrl.getQuery();
-					String[] arrayQUrlArgument = qUrlArgument.split("&");
-					for (String arrayUrlArgStr : arrayQUrlArgument) {
-						if (arrayUrlArgStr.startsWith(resumptionParam)) {
-							String[] resumptionKeyValue = arrayUrlArgStr.split("=");
-							if (isInteger(resumptionKeyValue[1])) {
-								urlOldResumptionSize = Integer.parseInt(resumptionKeyValue[1]);
-								log.debug("discover OldResumptionSize from Url (int): {}", urlOldResumptionSize);
-							} else {
-								log.debug("discover OldResumptionSize from Url (str): {}", resumptionKeyValue[1]);
+				} else {
+					log.warn("resultXml is equal with emptyXml");
+				}
+
+				this.resumptionInt += this.resultSizeValue;
+
+				switch (this.resumptionType.toLowerCase()) {
+					case "scan": // read of resumptionToken , evaluate next results, e.g. OAI, iterate over items
+						this.resumptionStr = this.xprResumptionPath.evaluate(resultNode);
+						break;
+
+					case "count": // begin at one step for all records, iterate over items
+						this.resumptionStr = Integer.toString(this.resumptionInt);
+						break;
+
+					case "discover": // size of result items unknown, iterate over items (for openDOAR - 201808)
+						if (this.resultSizeValue < 2) {
+							throw new CollectorException("Mode: discover, Param 'resultSizeValue' is less than 2");
+						}
+						qUrlArgument = qUrl.getQuery();
+
+						final String[] arrayQUrlArgument = qUrlArgument.split("&");
+						for (final String arrayUrlArgStr : arrayQUrlArgument) {
+							if (arrayUrlArgStr.startsWith(this.resumptionParam)) {
+								final String[] resumptionKeyValue = arrayUrlArgStr.split("=");
+								if (isInteger(resumptionKeyValue[1])) {
+									urlOldResumptionSize = Integer.parseInt(resumptionKeyValue[1]);
+									log.debug("discover OldResumptionSize from Url (int): {}", urlOldResumptionSize);
+								} else {
+									log.debug("discover OldResumptionSize from Url (str): {}", resumptionKeyValue[1]);
+								}
 							}
 						}
-					}
 
-					if (((emptyXml).equalsIgnoreCase(resultXml))
-						|| ((nodeList != null) && (nodeList.getLength() < resultSizeValue))) {
-						// resumptionStr = "";
-						if (nodeList != null) {
-							discoverResultSize += nodeList.getLength();
+						if (isEmptyXml(resultXml)
+							|| ((nodeList != null) && (nodeList.getLength() < this.resultSizeValue))) {
+							// resumptionStr = "";
+							if (nodeList != null) {
+								this.discoverResultSize += nodeList.getLength();
+							}
+							this.resultTotal = this.discoverResultSize;
+						} else {
+							this.resumptionStr = Integer.toString(this.resumptionInt);
+							this.resultTotal = this.resumptionInt + 1;
+							if (nodeList != null) {
+								this.discoverResultSize += nodeList.getLength();
+							}
 						}
-						resultTotal = discoverResultSize;
-					} else {
-						resumptionStr = Integer.toString(resumptionInt);
-						resultTotal = resumptionInt + 1;
-						if (nodeList != null) {
-							discoverResultSize += nodeList.getLength();
+						log.info("discoverResultSize: {}", this.discoverResultSize);
+						break;
+
+					case "pagination":
+					case "page": // pagination, iterate over page numbers
+						if (nodeList != null && nodeList.getLength() > 0) {
+							this.discoverResultSize += nodeList.getLength();
+						} else {
+							this.resultTotal = this.discoverResultSize;
+							this.pagination = this.discoverResultSize;
 						}
-					}
-					log.info("discoverResultSize: {}", discoverResultSize);
-					break;
+						this.pagination += 1;
+						this.resumptionInt = this.pagination;
+						this.resumptionStr = Integer.toString(this.resumptionInt);
+						break;
 
-				case "pagination":
-				case "page": // pagination, iterate over page numbers
-					pagination += 1;
-					if (nodeList != null) {
-						discoverResultSize += nodeList.getLength();
-					} else {
-						resultTotal = discoverResultSize;
-						pagination = discoverResultSize;
-					}
-					resumptionInt = pagination;
-					resumptionStr = Integer.toString(resumptionInt);
-					break;
+					case "deep-cursor": // size of result items unknown, iterate over items (for supporting deep cursor
+										// in
+										// solr)
+						// isn't relevant -- if (resultSizeValue < 2) {throw new CollectorServiceException("Mode:
+						// deep-cursor, Param 'resultSizeValue' is less than 2");}
 
-				case "deep-cursor": // size of result items unknown, iterate over items (for supporting deep cursor in
-									// solr)
-					// isn't relevant -- if (resultSizeValue < 2) {throw new CollectorServiceException("Mode:
-					// deep-cursor, Param 'resultSizeValue' is less than 2");}
+						this.resumptionStr = encodeValue(this.xprResumptionPath.evaluate(resultNode));
+						this.queryParams = this.queryParams.replace("&cursor=*", "");
 
-					resumptionStr = encodeValue(xprResumptionPath.evaluate(resultNode));
-					queryParams = queryParams.replace("&cursor=*", "");
+						// terminating if length of nodeList is 0
+						if ((nodeList != null) && (nodeList.getLength() < this.discoverResultSize)) {
+							this.resumptionInt += ((nodeList.getLength() + 1) - this.resultSizeValue);
+						} else {
+							this.resumptionInt += (nodeList.getLength() - this.resultSizeValue); // subtract the
+																									// resultSizeValue
+							// because the iteration is over
+							// real length and the
+							// resultSizeValue is added before
+							// the switch()
+						}
 
-					// terminating if length of nodeList is 0
-					if ((nodeList != null) && (nodeList.getLength() < discoverResultSize)) {
-						resumptionInt += (nodeList.getLength() + 1 - resultSizeValue);
-					} else {
-						resumptionInt += (nodeList.getLength() - resultSizeValue); // subtract the resultSizeValue
-																					// because the iteration is over
-																					// real length and the
-																					// resultSizeValue is added before
-																					// the switch()
-					}
+						this.discoverResultSize = nodeList.getLength();
 
-					discoverResultSize = nodeList.getLength();
+						log
+							.debug(
+								"downloadPage().deep-cursor: resumptionStr=" + this.resumptionStr + " ; queryParams="
+									+ this.queryParams + " resumptionLengthIncreased: " + this.resumptionInt);
 
-					log
-						.debug(
-							"downloadPage().deep-cursor: resumptionStr=" + resumptionStr + " ; queryParams="
-								+ queryParams + " resumptionLengthIncreased: " + resumptionInt);
+						break;
 
-					break;
+					default: // otherwise: abort
+						// resultTotal = resumptionInt;
+						break;
+				}
 
-				default: // otherwise: abort
-					// resultTotal = resumptionInt;
-					break;
+			} catch (final Exception e) {
+				log.error(e.getMessage(), e);
+				throw new IllegalStateException("collection failed: " + e.getMessage());
 			}
 
-		} catch (Exception e) {
-			log.error(e.getMessage(), e);
-			throw new IllegalStateException("collection failed: " + e.getMessage());
-		}
-
-		try {
-			if (resultTotal == -1) {
-				resultTotal = Integer.parseInt(xprResultTotalPath.evaluate(resultNode));
-				if (resumptionType.equalsIgnoreCase("page") && !BASIC.equalsIgnoreCase(authMethod)) {
-					resultTotal += 1;
-				} // to correct the upper bound
-				log.info("resultTotal was -1 is now: " + resultTotal);
+			try {
+				if (this.resultTotal == -1) {
+					this.resultTotal = Integer.parseInt(this.xprResultTotalPath.evaluate(resultNode));
+					if ("page".equalsIgnoreCase(this.resumptionType)
+						&& !this.AUTHBASIC.equalsIgnoreCase(this.authMethod)) {
+						this.resultTotal += 1;
+					} // to correct the upper bound
+					log.info("resultTotal was -1 is now: " + this.resultTotal);
+				}
+			} catch (final Exception e) {
+				log.error(e.getMessage(), e);
+				throw new IllegalStateException("downloadPage resultTotal couldn't parse: " + e.getMessage());
 			}
-		} catch (Exception e) {
-			log.error(e.getMessage(), e);
-			throw new IllegalStateException("downloadPage resultTotal couldn't parse: " + e.getMessage());
+			log.debug("resultTotal: " + this.resultTotal);
+			log.debug("resInt: " + this.resumptionInt);
+			if (this.resumptionInt <= this.resultTotal) {
+				nextQuery = this.baseUrl + "?" + this.queryParams + this.querySize + "&" + this.resumptionParam + "="
+					+ this.resumptionStr
+					+ this.queryFormat;
+			} else {
+				nextQuery = "";
+				// if (resumptionType.toLowerCase().equals("deep-cursor")) { resumptionInt -= 1; } // correct the
+				// resumptionInt and prevent a NullPointer Exception at mdStore
+			}
+			log.debug("nextQueryUrl: " + nextQuery);
+			return nextQuery;
+		} catch (final Throwable e) {
+			log.warn(e.getMessage(), e);
+			return downloadPage(query, attempt + 1);
 		}
-		log.debug("resultTotal: " + resultTotal);
-		log.debug("resInt: " + resumptionInt);
-		if (resumptionInt <= resultTotal) {
-			nextQuery = baseUrl + "?" + queryParams + querySize + "&" + resumptionParam + "=" + resumptionStr
-				+ queryFormat;
-		} else {
-			nextQuery = "";
-			// if (resumptionType.toLowerCase().equals("deep-cursor")) { resumptionInt -= 1; } // correct the
-			// resumptionInt and prevent a NullPointer Exception at mdStore
-		}
-		log.debug("nextQueryUrl: " + nextQuery);
-		return nextQuery;
 
 	}
 
-	private boolean isInteger(String s) {
+	private boolean isEmptyXml(String s) {
+		return EMPTY_XML.equalsIgnoreCase(s);
+	}
+
+	private boolean isInteger(final String s) {
 		boolean isValidInteger = false;
 		try {
 			Integer.parseInt(s);
@@ -383,7 +450,7 @@ public class RestIterator implements Iterator<String> {
 			// s is a valid integer
 
 			isValidInteger = true;
-		} catch (NumberFormatException ex) {
+		} catch (final NumberFormatException ex) {
 			// s is not an integer
 		}
 
@@ -391,20 +458,36 @@ public class RestIterator implements Iterator<String> {
 	}
 
 	// Method to encode a string value using `UTF-8` encoding scheme
-	private String encodeValue(String value) {
+	private String encodeValue(final String value) {
 		try {
 			return URLEncoder.encode(value, StandardCharsets.UTF_8.toString());
-		} catch (UnsupportedEncodingException ex) {
+		} catch (final UnsupportedEncodingException ex) {
 			throw new RuntimeException(ex.getCause());
 		}
 	}
 
+	/**
+	 * setRequestHeader
+	 *
+	 * setRequestProperty: Sets the general request property. If a property with the key already exists, overwrite its value with the new value.
+	 * @param conn
+	 */
+	private void setRequestHeader(HttpURLConnection conn) {
+		if (requestHeaders != null) {
+			for (String key : requestHeaders.keySet()) {
+				conn.setRequestProperty(key, requestHeaders.get(key));
+			}
+			log.debug("Set Request Header with: " + requestHeaders);
+		}
+
+	}
+
 	public String getResultFormatValue() {
-		return resultFormatValue;
+		return this.resultFormatValue;
 	}
 
 	public String getResultOutputFormat() {
-		return resultOutputFormat;
+		return this.resultOutputFormat;
 	}
 
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XMLIterator.java

@@ -8,7 +8,10 @@ import java.io.StringWriter;
 import java.nio.charset.Charset;
 import java.nio.charset.CharsetDecoder;
 import java.nio.charset.CodingErrorAction;
+import java.util.Arrays;
 import java.util.Iterator;
+import java.util.List;
+import java.util.stream.Collectors;
 
 import javax.xml.stream.XMLEventFactory;
 import javax.xml.stream.XMLEventReader;
@@ -19,6 +22,7 @@ import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.events.StartElement;
 import javax.xml.stream.events.XMLEvent;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -58,13 +62,23 @@ public class XMLIterator implements Iterator<String> {
 
 	private String element;
 
+	private List<String> elements;
+
 	private InputStream inputStream;
 
 	public XMLIterator(final String element, final InputStream inputStream) {
 		super();
 		this.element = element;
+		if (element.contains(",")) {
+			elements = Arrays
+				.stream(element.split(","))
+				.filter(StringUtils::isNoneBlank)
+				.map(String::toLowerCase)
+				.collect(Collectors.toList());
+		}
 		this.inputStream = inputStream;
 		this.parser = getParser();
+
 		try {
 			this.current = findElement(parser);
 		} catch (XMLStreamException e) {
@@ -113,7 +127,7 @@ public class XMLIterator implements Iterator<String> {
 				final XMLEvent event = parser.nextEvent();
 
 				// TODO: replace with depth tracking instead of close tag tracking.
-				if (event.isEndElement() && event.asEndElement().getName().getLocalPart().equals(element)) {
+				if (event.isEndElement() && isCheckTag(event.asEndElement().getName().getLocalPart())) {
 					writer.add(event);
 					break;
 				}
@@ -142,18 +156,16 @@ public class XMLIterator implements Iterator<String> {
 		XMLEvent peek = parser.peek();
 		if (peek != null && peek.isStartElement()) {
 			String name = peek.asStartElement().getName().getLocalPart();
-			if (element.equals(name)) {
+			if (isCheckTag(name))
 				return peek;
-			}
 		}
 
 		while (parser.hasNext()) {
-			final XMLEvent event = parser.nextEvent();
+			XMLEvent event = parser.nextEvent();
 			if (event != null && event.isStartElement()) {
 				String name = event.asStartElement().getName().getLocalPart();
-				if (element.equals(name)) {
+				if (isCheckTag(name))
 					return event;
-				}
 			}
 		}
 		return null;
@@ -161,12 +173,31 @@ public class XMLIterator implements Iterator<String> {
 
 	private XMLEventReader getParser() {
 		try {
-			return inputFactory.get().createXMLEventReader(sanitize(inputStream));
+			XMLInputFactory xif = inputFactory.get();
+			xif.setProperty(XMLInputFactory.SUPPORT_DTD, false);
+			return xif.createXMLEventReader(sanitize(inputStream));
 		} catch (XMLStreamException e) {
 			throw new RuntimeException(e);
 		}
 	}
 
+	private boolean isCheckTag(final String tagName) {
+		if (elements != null) {
+			final String found = elements
+				.stream()
+				.filter(e -> e.equalsIgnoreCase(tagName))
+				.findFirst()
+				.orElse(null);
+			if (found != null)
+				return true;
+		} else {
+			if (element.equalsIgnoreCase(tagName)) {
+				return true;
+			}
+		}
+		return false;
+	}
+
 	private Reader sanitize(final InputStream in) {
 		final CharsetDecoder charsetDecoder = Charset.forName(UTF_8).newDecoder();
 		charsetDecoder.onMalformedInput(CodingErrorAction.REPLACE);

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

@@ -16,5 +16,10 @@
     "paramLongName": "isSparkSessionManaged",
     "paramDescription": "the hdfs name node",
     "paramRequired": false
-  }
+  },{
+  "paramName": "bl",
+  "paramLongName": "blackListPath",
+  "paramDescription": "the working path",
+  "paramRequired": true
+}
 ]

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

@@ -1,2 +1,3 @@
 sourcePath=/user/miriam.baglioni/openalex-snapshot/data/works/
 outputPath=/tmp/miriam/webcrawlComplete/
+blackListPath=/user/miriam.baglioni/openalex-blackList

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

@@ -45,6 +45,7 @@
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
+            <arg>--blackListPath</arg><arg>${blackListPath}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json

@@ -58,7 +58,7 @@
     "uri": "http://dx.doi.org/10.13039/100010414",
     "name": "Health Research Board",
     "synonym": [
-      "501100001590"
+      "501100001590", "501100023273"
     ]
   },
   {
@@ -85,24 +85,6 @@
     "name": "Irish College of General Practitioners",
     "synonym": []
   },
-  {
-    "id": "100012734",
-    "uri": "http://dx.doi.org/10.13039/100012734",
-    "name": "Department for Culture, Heritage and the Gaeltacht, Ireland",
-    "synonym": []
-  },
-  {
-    "id": "100012754",
-    "uri": "http://dx.doi.org/10.13039/100012754",
-    "name": "Horizon Pharma",
-    "synonym": []
-  },
-  {
-    "id": "100012891",
-    "uri": "http://dx.doi.org/10.13039/100012891",
-    "name": "Medical Research Charities Group",
-    "synonym": []
-  },
   {
     "id": "100012919",
     "uri": "http://dx.doi.org/10.13039/100012919",
@@ -233,7 +215,7 @@
     "id": "100018064",
     "uri": "http://dx.doi.org/10.13039/100018064",
     "name": "Department of Tourism, Culture, Arts, Gaeltacht, Sport and Media",
-    "synonym": []
+    "synonym": ["100012734"]
   },
   {
     "id": "100018172",
@@ -281,13 +263,13 @@
     "id": "100019637",
     "uri": "http://dx.doi.org/10.13039/100019637",
     "name": "Horizon Therapeutics",
-    "synonym": []
+    "synonym": ["100012754"]
   },
   {
     "id": "100020174",
     "uri": "http://dx.doi.org/10.13039/100020174",
     "name": "Health Research Charities Ireland",
-    "synonym": []
+    "synonym": ["100012891"]
   },
   {
     "id": "100020202",
@@ -319,12 +301,7 @@
     "name": "Centre for Ageing Research and Development in Ireland",
     "synonym": []
   },
-  {
-    "id": "501100001583",
-    "uri": "http://dx.doi.org/10.13039/501100001583",
-    "name": "Cystinosis Foundation Ireland",
-    "synonym": []
-  },
+
   {
     "id": "501100001584",
     "uri": "http://dx.doi.org/10.13039/501100001584",
@@ -521,7 +498,7 @@
     "id": "501100003037",
     "uri": "http://dx.doi.org/10.13039/501100003037",
     "name": "Elan",
-    "synonym": []
+    "synonym": ["501100021694"]
   },
   {
     "id": "501100003496",
@@ -595,17 +572,11 @@
     "name": "Technological University Dublin",
     "synonym": []
   },
-  {
-    "id": "501100009269",
-    "uri": "http://dx.doi.org/10.13039/501100009269",
-    "name": "Programme of Competitive Forestry Research for Development",
-    "synonym": []
-  },
   {
     "id": "501100009315",
     "uri": "http://dx.doi.org/10.13039/501100009315",
     "name": "Cystinosis Ireland",
-    "synonym": []
+    "synonym": ["501100001583"]
   },
   {
     "id": "501100010808",
@@ -625,12 +596,6 @@
     "name": "Alimentary Health",
     "synonym": []
   },
-  {
-    "id": "501100011103",
-    "uri": "http://dx.doi.org/10.13039/501100011103",
-    "name": "Rann\u00eds",
-    "synonym": []
-  },
   {
     "id": "501100012354",
     "uri": "http://dx.doi.org/10.13039/501100012354",
@@ -733,12 +698,6 @@
     "name": "Insight SFI Research Centre for Data Analytics",
     "synonym": []
   },
-  {
-    "id": "501100021694",
-    "uri": "http://dx.doi.org/10.13039/501100021694",
-    "name": "Elan Pharma International",
-    "synonym": []
-  },
   {
     "id": "501100021838",
     "uri": "http://dx.doi.org/10.13039/501100021838",
@@ -769,12 +728,6 @@
     "name": "Institute of Technology, Tralee",
     "synonym": []
   },
-  {
-    "id": "501100023273",
-    "uri": "http://dx.doi.org/10.13039/501100023273",
-    "name": "HRB Clinical Research Facility Galway",
-    "synonym": []
-  },
   {
     "id": "501100023378",
     "uri": "http://dx.doi.org/10.13039/501100023378",

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

@@ -1025,6 +1025,7 @@ case object Crossref2Oaf {
             tp._1 match {
               case "electronic" => journal.setIssnOnline(tp._2)
               case "print"      => journal.setIssnPrinted(tp._2)
+              case _            =>
             }
           })
         }

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/mag/MagUtility.scala

@@ -79,23 +79,6 @@ object MagUtility extends Serializable {
   private val MAGCollectedFrom = keyValue(ModelConstants.MAG_ID, ModelConstants.MAG_NAME)
 
   private val MAGDataInfo: DataInfo = {
-    val di = new DataInfo
-    di.setDeletedbyinference(false)
-    di.setInferred(false)
-    di.setInvisible(false)
-    di.setTrust("0.9")
-    di.setProvenanceaction(
-      OafMapperUtils.qualifier(
-        ModelConstants.SYSIMPORT_ACTIONSET,
-        ModelConstants.SYSIMPORT_ACTIONSET,
-        ModelConstants.DNET_PROVENANCE_ACTIONS,
-        ModelConstants.DNET_PROVENANCE_ACTIONS
-      )
-    )
-    di
-  }
-
-  private val MAGDataInfoInvisible: DataInfo = {
     val di = new DataInfo
     di.setDeletedbyinference(false)
     di.setInferred(false)
@@ -453,7 +436,6 @@ object MagUtility extends Serializable {
 
       case "repository" =>
         result = new Publication()
-        result.setDataInfo(MAGDataInfoInvisible)
         qualifier(
           "0038",
           "Other literature type",
@@ -488,8 +470,7 @@ object MagUtility extends Serializable {
     }
 
     if (result != null) {
-      if (result.getDataInfo == null)
-        result.setDataInfo(MAGDataInfo)
+      result.setDataInfo(MAGDataInfo)
       val i = new Instance
       i.setInstancetype(tp)
       i.setInstanceTypeMapping(
@@ -512,7 +493,7 @@ object MagUtility extends Serializable {
       return null
 
     result.setCollectedfrom(List(MAGCollectedFrom).asJava)
-    val pidList = List(
+    var pidList = List(
       structuredProperty(
         paper.paperId.get.toString,
         qualifier(
@@ -525,8 +506,6 @@ object MagUtility extends Serializable {
       )
     )
 
-    result.setPid(pidList.asJava)
-
     result.setOriginalId(pidList.map(s => s.getValue).asJava)
 
     result.setId(s"50|mag_________::${DHPUtils.md5(paper.paperId.get.toString)}")
@@ -618,22 +597,23 @@ object MagUtility extends Serializable {
     }
 
     val instance = result.getInstance().get(0)
-    instance.setPid(pidList.asJava)
-    if (paper.doi.orNull != null)
-      instance.setAlternateIdentifier(
-        List(
-          structuredProperty(
-            paper.doi.get,
-            qualifier(
-              PidType.doi.toString,
-              PidType.doi.toString,
-              ModelConstants.DNET_PID_TYPES,
-              ModelConstants.DNET_PID_TYPES
-            ),
-            null
-          )
-        ).asJava
+
+    if (paper.doi.orNull != null) {
+      pidList = pidList ::: List(
+        structuredProperty(
+          paper.doi.get,
+          qualifier(
+            PidType.doi.toString,
+            PidType.doi.toString,
+            ModelConstants.DNET_PID_TYPES,
+            ModelConstants.DNET_PID_TYPES
+          ),
+          null
+        )
       )
+    }
+    instance.setPid(pidList.asJava)
+    result.setPid(pidList.asJava)
     instance.setUrl(paper.urls.get.asJava)
     instance.setHostedby(ModelConstants.UNKNOWN_REPOSITORY)
     instance.setCollectedfrom(MAGCollectedFrom)

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/mag/SparkMAGtoOAF.scala

@@ -38,6 +38,7 @@ class SparkMAGtoOAF(propertyPath: String, args: Array[String], log: Logger)
     spark.read
       .load(s"$magBasePath/mag_denormalized")
       .as[MAGPaper]
+      .filter(col("doi").isNotNull)
       .map(s => MagUtility.convertMAGtoOAF(s))
       .filter(s => s != null)
       .write

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala

@@ -2,12 +2,9 @@ package eu.dnetlib.dhp.sx.bio.ebi
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.collection.CollectionUtils
-import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
-import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion
-import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
+import eu.dnetlib.dhp.schema.oaf.Oaf
 import eu.dnetlib.dhp.sx.bio.pubmed._
-import eu.dnetlib.dhp.utils.DHPUtils.{MAPPER, writeHdfsFile}
 import eu.dnetlib.dhp.utils.ISLookupClientFactory
 import org.apache.commons.io.IOUtils
 import org.apache.hadoop.conf.Configuration
@@ -17,13 +14,13 @@ import org.apache.http.client.methods.HttpGet
 import org.apache.http.impl.client.HttpClientBuilder
 import org.apache.spark.SparkConf
 import org.apache.spark.rdd.RDD
-import org.apache.spark.sql.expressions.Aggregator
 import org.apache.spark.sql._
+import org.apache.spark.sql.expressions.Aggregator
 import org.slf4j.{Logger, LoggerFactory}
 
-import java.io.InputStream
-import scala.io.Source
-import scala.xml.pull.XMLEventReader
+import java.io.{ByteArrayInputStream, InputStream}
+import java.nio.charset.Charset
+import javax.xml.stream.XMLInputFactory
 
 object SparkCreateBaselineDataFrame {
 
@@ -86,7 +83,7 @@ object SparkCreateBaselineDataFrame {
           if (response.getStatusLine.getStatusCode > 400) {
             tries -= 1
           } else
-            return IOUtils.toString(response.getEntity.getContent)
+            return IOUtils.toString(response.getEntity.getContent, Charset.defaultCharset())
         } catch {
           case e: Throwable =>
             println(s"Error on requesting ${r.getURI}")
@@ -158,7 +155,8 @@ object SparkCreateBaselineDataFrame {
       IOUtils.toString(
         SparkEBILinksToOaf.getClass.getResourceAsStream(
           "/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json"
-        )
+        ),
+        Charset.defaultCharset()
       )
     )
     parser.parseArgument(args)
@@ -167,15 +165,11 @@ object SparkCreateBaselineDataFrame {
     val workingPath = parser.get("workingPath")
     log.info("workingPath: {}", workingPath)
 
-    val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
-    log.info("mdstoreOutputVersion: {}", mdstoreOutputVersion)
-
-    val cleanedMdStoreVersion = MAPPER.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
-    val outputBasePath = cleanedMdStoreVersion.getHdfsPath
-    log.info("outputBasePath: {}", outputBasePath)
+    val targetPath = parser.get("targetPath")
+    log.info("targetPath: {}", targetPath)
 
     val hdfsServerUri = parser.get("hdfsServerUri")
-    log.info("hdfsServerUri: {}", hdfsServerUri)
+    log.info("hdfsServerUri: {}", targetPath)
 
     val skipUpdate = parser.get("skipUpdate")
     log.info("skipUpdate: {}", skipUpdate)
@@ -201,10 +195,11 @@ object SparkCreateBaselineDataFrame {
     if (!"true".equalsIgnoreCase(skipUpdate)) {
       downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri)
       val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline", 2000)
+      val inputFactory = XMLInputFactory.newInstance
       val ds: Dataset[PMArticle] = spark.createDataset(
         k.filter(i => i._1.endsWith(".gz"))
           .flatMap(i => {
-            val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
+            val xml = inputFactory.createXMLEventReader(new ByteArrayInputStream(i._2.getBytes()))
             new PMParser(xml)
           })
       )
@@ -223,11 +218,8 @@ object SparkCreateBaselineDataFrame {
         .map(a => PubMedToOaf.convert(a, vocabularies))
         .as[Oaf]
         .filter(p => p != null),
-      s"$outputBasePath/$MDSTORE_DATA_PATH"
+      targetPath
     )
 
-    val df = spark.read.text(s"$outputBasePath/$MDSTORE_DATA_PATH")
-    val mdStoreSize = df.count
-    writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$mdStoreSize", s"$outputBasePath/$MDSTORE_SIZE_PATH")
   }
 }

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala

@@ -1,7 +1,8 @@
 package eu.dnetlib.dhp.sx.bio.pubmed
 
 import scala.xml.MetaData
-import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
+import javax.xml.stream.XMLEventReader
+import scala.xml.pull.{EvElemEnd, EvElemStart, EvText}
 
 /** @param xml
   */

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

@@ -15,10 +15,7 @@ import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.sql.SparkSession;
-import org.junit.jupiter.api.AfterAll;
-import org.junit.jupiter.api.Assertions;
-import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

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

@@ -119,7 +119,9 @@ public class ReadCOCITest {
 					workingDir.toString() + "/COCI",
 					"-outputPath",
 					workingDir.toString() + "/COCI_json/",
-					"-inputFile", "input1;input2;input3;input4;input5"
+					"-inputFile", "input1;input2;input3;input4;input5",
+					"-format",
+					"COCI"
 				});
 
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java

@@ -75,7 +75,11 @@ public class CreateASTest {
 
 		String inputPath = getClass()
 			.getResource(
-				"/eu/dnetlib/dhp/actionmanager/webcrawl/")
+				"/eu/dnetlib/dhp/actionmanager/webcrawl/input/")
+			.getPath();
+		String blackListPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/webcrawl/blackList/")
 			.getPath();
 
 		CreateActionSetFromWebEntries
@@ -86,7 +90,8 @@ public class CreateASTest {
 					"-sourcePath",
 					inputPath,
 					"-outputPath",
-					workingDir.toString() + "/actionSet1"
+					workingDir.toString() + "/actionSet1",
+					"-blackListPath", blackListPath
 				});
 
 		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
@@ -96,7 +101,7 @@ public class CreateASTest {
 			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
 			.map(aa -> ((Relation) aa.getPayload()));
 
-		Assertions.assertEquals(64, tmp.count());
+		Assertions.assertEquals(58, tmp.count());
 
 	}
 
@@ -109,6 +114,10 @@ public class CreateASTest {
 			.getResource(
 				"/eu/dnetlib/dhp/actionmanager/webcrawl/")
 			.getPath();
+		String blackListPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/webcrawl/blackList/")
+			.getPath();
 
 		CreateActionSetFromWebEntries
 			.main(
@@ -118,7 +127,8 @@ public class CreateASTest {
 					"-sourcePath",
 					inputPath,
 					"-outputPath",
-					workingDir.toString() + "/actionSet1"
+					workingDir.toString() + "/actionSet1",
+					"-blackListPath", blackListPath
 				});
 
 		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
@@ -184,7 +194,7 @@ public class CreateASTest {
 
 		Assertions
 			.assertEquals(
-				5, tmp
+				2, tmp
 					.filter(
 						r -> r
 							.getSource()
@@ -197,7 +207,7 @@ public class CreateASTest {
 
 		Assertions
 			.assertEquals(
-				5, tmp
+				2, tmp
 					.filter(
 						r -> r
 							.getTarget()
@@ -210,7 +220,7 @@ public class CreateASTest {
 
 		Assertions
 			.assertEquals(
-				2, tmp
+				1, tmp
 					.filter(
 						r -> r
 							.getTarget()
@@ -224,7 +234,7 @@ public class CreateASTest {
 
 		Assertions
 			.assertEquals(
-				2, tmp
+				1, tmp
 					.filter(
 						r -> r
 							.getTarget()
@@ -238,7 +248,7 @@ public class CreateASTest {
 
 		Assertions
 			.assertEquals(
-				1, tmp
+				0, tmp
 					.filter(
 						r -> r
 							.getTarget()

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipMultipleNodeTest.java

@@ -0,0 +1,64 @@
+
+package eu.dnetlib.dhp.collection.plugin.file;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Objects;
+import java.util.stream.Stream;
+
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.junit.jupiter.api.*;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.junit.jupiter.MockitoExtension;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.collection.ApiDescriptor;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+
+@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
+@ExtendWith(MockitoExtension.class)
+public class FileGZipMultipleNodeTest {
+
+	private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class);
+
+	private final ApiDescriptor api = new ApiDescriptor();
+
+	private FileGZipCollectorPlugin plugin;
+
+	private static final String SPLIT_ON_ELEMENT = "incollection,article";
+
+	@BeforeEach
+	public void setUp() throws IOException {
+
+		final String gzipFile = Objects
+			.requireNonNull(
+				this
+					.getClass()
+					.getResource("/eu/dnetlib/dhp/collection/plugin/file/dblp.gz"))
+			.getFile();
+
+		api.setBaseUrl(gzipFile);
+
+		HashMap<String, String> params = new HashMap<>();
+		params.put("splitOnElement", SPLIT_ON_ELEMENT);
+
+		api.setParams(params);
+
+		FileSystem fs = FileSystem.get(new Configuration());
+		plugin = new FileGZipCollectorPlugin(fs);
+	}
+
+	@Test
+	void test() throws CollectorException {
+
+		final Stream<String> stream = plugin.collect(api, new AggregatorReport());
+
+		stream.limit(10).forEach(s -> {
+			Assertions.assertTrue(s.length() > 0);
+			log.info(s);
+		});
+	}
+}

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/OsfPreprintCollectorTest.java

@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.collection.plugin.rest;
 
 import java.util.HashMap;
 import java.util.concurrent.atomic.AtomicInteger;
+import java.util.concurrent.atomic.AtomicLong;
 import java.util.stream.Stream;
 
 import org.junit.jupiter.api.Assertions;
@@ -35,11 +36,11 @@ public class OsfPreprintCollectorTest {
 	private final String resultTotalXpath = "/*/*[local-name()='links']/*[local-name()='meta']/*[local-name()='total']";
 
 	private final String resumptionParam = "page";
-	private final String resumptionType = "page";
-	private final String resumptionXpath = "/*/*[local-name()='links']/*[local-name()='next']";
+	private final String resumptionType = "scan";
+	private final String resumptionXpath = "substring-before(substring-after(/*/*[local-name()='links']/*[local-name()='next'], 'page='), '&')";
 
-	private final String resultSizeParam = "";
-	private final String resultSizeValue = "";
+	private final String resultSizeParam = "page[size]";
+	private final String resultSizeValue = "100";
 
 	private final String resultFormatParam = "format";
 	private final String resultFormatValue = "json";
@@ -69,11 +70,11 @@ public class OsfPreprintCollectorTest {
 
 	@Test
 	@Disabled
-	void test() throws CollectorException {
+	void test_limited() throws CollectorException {
 		final AtomicInteger i = new AtomicInteger(0);
 		final Stream<String> stream = this.rcp.collect(this.api, new AggregatorReport());
 
-		stream.limit(200).forEach(s -> {
+		stream.limit(2000).forEach(s -> {
 			Assertions.assertTrue(s.length() > 0);
 			i.incrementAndGet();
 			log.info(s);
@@ -82,4 +83,23 @@ public class OsfPreprintCollectorTest {
 		log.info("{}", i.intValue());
 		Assertions.assertTrue(i.intValue() > 0);
 	}
+
+	@Test
+	@Disabled
+	void test_all() throws CollectorException {
+		final AtomicLong i = new AtomicLong(0);
+		final Stream<String> stream = this.rcp.collect(this.api, new AggregatorReport());
+
+		stream.forEach(s -> {
+			Assertions.assertTrue(s.length() > 0);
+			if ((i.incrementAndGet() % 1000) == 0) {
+				log.info("COLLECTED: {}", i.get());
+			}
+
+		});
+
+		log.info("TOTAL: {}", i.get());
+		Assertions.assertTrue(i.get() > 0);
+	}
+
 }

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/RestCollectorPluginTest.java

@@ -4,6 +4,11 @@
 
 package eu.dnetlib.dhp.collection.plugin.rest;
 
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.HashMap;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Stream;
@@ -12,6 +17,8 @@ import org.junit.jupiter.api.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import com.google.gson.Gson;
+
 import eu.dnetlib.dhp.collection.ApiDescriptor;
 import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
 import eu.dnetlib.dhp.common.collection.CollectorException;
@@ -25,18 +32,18 @@ class RestCollectorPluginTest {
 
 	private static final Logger log = LoggerFactory.getLogger(RestCollectorPluginTest.class);
 
-	private final String baseUrl = "https://share.osf.io/api/v2/search/creativeworks/_search";
-	private final String resumptionType = "count";
-	private final String resumptionParam = "from";
-	private final String entityXpath = "//hits/hits";
-	private final String resumptionXpath = "//hits";
-	private final String resultTotalXpath = "//hits/total";
-	private final String resultFormatParam = "format";
+	private final String baseUrl = "https://ddh-openapi.worldbank.org/search";
+	private final String resumptionType = "discover";
+	private final String resumptionParam = "skip";
+	private final String entityXpath = "//*[local-name()='data']";
+	private final String resumptionXpath = "";
+	private final String resultTotalXpath = "//*[local-name()='count']";
+	private final String resultFormatParam = "";
 	private final String resultFormatValue = "json";
-	private final String resultSizeParam = "size";
+	private final String resultSizeParam = "top";
 	private final String resultSizeValue = "10";
 	// private String query = "q=%28sources%3ASocArXiv+AND+type%3Apreprint%29";
-	private final String query = "q=%28sources%3AengrXiv+AND+type%3Apreprint%29";
+	private final String query = "";
 	// private String query = "=(sources:engrXiv AND type:preprint)";
 
 	private final String protocolDescriptor = "rest_json2xml";
@@ -56,6 +63,7 @@ class RestCollectorPluginTest {
 		params.put("resultSizeValue", resultSizeValue);
 		params.put("queryParams", query);
 		params.put("entityXpath", entityXpath);
+		params.put("requestHeaderMap", "{\"User-Agent\": \"OpenAIRE DEV\"}");
 
 		api.setBaseUrl(baseUrl);
 		api.setParams(params);
@@ -78,4 +86,19 @@ class RestCollectorPluginTest {
 		log.info("{}", i.intValue());
 		Assertions.assertTrue(i.intValue() > 0);
 	}
+
+	@Disabled
+	@Test
+	void testUrl() throws IOException {
+		String url_s = "https://ddh-openapi.worldbank.org/search?&top=10";
+		URL url = new URL(url_s);
+		final HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+		conn.setRequestMethod("GET");
+		conn.setRequestProperty("User-Agent", "OpenAIRE");
+		Gson gson = new Gson();
+		System.out.println("Request header");
+		System.out.println(gson.toJson(conn.getHeaderFields()));
+		InputStream inputStream = conn.getInputStream();
+
+	}
 }

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/RestIteratorTest.java

@@ -44,7 +44,7 @@ public class RestIteratorTest {
 
 		final RestIterator iterator = new RestIterator(clientParams, baseUrl, resumptionType, resumptionParam,
 			resumptionXpath, resultTotalXpath, resultFormatParam, resultFormatValue, resultSizeParam, resultSizeValue,
-			query, entityXpath, authMethod, authToken, resultOffsetParam);
+			query, entityXpath, authMethod, authToken, resultOffsetParam, null);
 		int i = 20;
 		while (iterator.hasNext() && i > 0) {
 			String result = iterator.next();

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/issn_pub.json

@@ -789,10 +789,6 @@
       "value": "2227-9717",
       "type": "electronic"
     },
-    {
-      "value": "VALUE",
-      "type": "PIPPO"
-    },
     {
       "value": "1063-4584",
       "type": "pu"

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala

@@ -2,7 +2,9 @@ package eu.dnetlib.dhp.collection.crossref
 
 import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
-import org.junit.jupiter.api.BeforeEach
+import eu.dnetlib.dhp.collection.crossref.Crossref2Oaf.TransformationType
+import org.apache.commons.io.IOUtils
+import org.junit.jupiter.api.{BeforeEach, Test}
 import org.junit.jupiter.api.extension.ExtendWith
 import org.mockito.junit.jupiter.MockitoExtension
 import org.slf4j.{Logger, LoggerFactory}
@@ -18,4 +20,13 @@ class CrossrefMappingTest extends AbstractVocabularyTest {
     super.setUpVocabulary()
   }
 
+  @Test
+  def mappingRecord(): Unit = {
+    val input =
+      IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/issn_pub.json"), "utf-8")
+
+    println(Crossref2Oaf.convert(input, vocabularies, TransformationType.All))
+
+  }
+
 }

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/mag/MAGMappingTest.scala

@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.collection.mag
 import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.schema.oaf.{Dataset, Publication, Result}
 import org.apache.spark.sql.SparkSession
+import org.apache.spark.sql.functions.col
 import org.junit.jupiter.api.Assertions._
 import org.junit.jupiter.api.Test
 
@@ -18,10 +19,8 @@ class MAGMappingTest {
       .master("local[*]")
       .getOrCreate()
 
-    val s = new SparkMagOrganizationAS(null, null, null)
-
-    s.generateAS(spark, "/home/sandro/Downloads/mag_test", "/home/sandro/Downloads/mag_AS")
-
+    val s = new SparkMAGtoOAF(null, null, null)
+    s.convertMAG(spark, "/Users/sandro/Downloads/", "/Users/sandro/Downloads/mag_OAF")
   }
 
   @Test

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala

@@ -16,6 +16,7 @@ import org.mockito.junit.jupiter.MockitoExtension
 
 import java.io.{BufferedReader, InputStream, InputStreamReader}
 import java.util.zip.GZIPInputStream
+import javax.xml.stream.XMLInputFactory
 import scala.collection.JavaConverters._
 import scala.collection.mutable.ListBuffer
 import scala.io.Source
@@ -49,10 +50,8 @@ class BioScholixTest extends AbstractVocabularyTest {
 
   @Test
   def testEBIData() = {
-    val inputXML = Source
-      .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
-      .mkString
-    val xml = new XMLEventReader(Source.fromBytes(inputXML.getBytes()))
+    val inputFactory = XMLInputFactory.newInstance
+    val xml = inputFactory.createXMLEventReader(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
     new PMParser(xml).foreach(s => println(mapper.writeValueAsString(s)))
   }
 
@@ -91,9 +90,10 @@ class BioScholixTest extends AbstractVocabularyTest {
 
   @Test
   def testParsingPubmedXML(): Unit = {
-    val xml = new XMLEventReader(
-      Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
-    )
+    val inputFactory = XMLInputFactory.newInstance
+
+    val xml = inputFactory.createXMLEventReader(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
+
     val parser = new PMParser(xml)
     parser.foreach(checkPMArticle)
   }
@@ -156,9 +156,9 @@ class BioScholixTest extends AbstractVocabularyTest {
   @Test
   def testPubmedMapping(): Unit = {
 
-    val xml = new XMLEventReader(
-      Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
-    )
+    val inputFactory = XMLInputFactory.newInstance
+    val xml = inputFactory.createXMLEventReader(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
+
     val parser = new PMParser(xml)
     val results = ListBuffer[Oaf]()
     parser.foreach(x => results += PubMedToOaf.convert(x, vocabularies))

dhp-workflows/dhp-dedup-openaire/pom.xml

@@ -53,24 +53,10 @@
             <artifactId>dhp-pace-core</artifactId>
             <version>${project.version}</version>
         </dependency>
-
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
         </dependency>
-
-        <dependency>
-            <groupId>org.scala-lang.modules</groupId>
-            <artifactId>scala-java8-compat_${scala.binary.version}</artifactId>
-            <version>1.0.2</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.scala-lang.modules</groupId>
-            <artifactId>scala-collection-compat_${scala.binary.version}</artifactId>
-            <version>2.11.0</version>
-        </dependency>
-
         <dependency>
             <groupId>org.apache.spark</groupId>
             <artifactId>spark-core_${scala.binary.version}</artifactId>
@@ -79,16 +65,10 @@
             <groupId>org.apache.spark</groupId>
             <artifactId>spark-sql_${scala.binary.version}</artifactId>
         </dependency>
-
         <dependency>
             <groupId>org.apache.spark</groupId>
             <artifactId>spark-graphx_${scala.binary.version}</artifactId>
         </dependency>
-
-        <dependency>
-            <groupId>com.arakelian</groupId>
-            <artifactId>java-jq</artifactId>
-        </dependency>
         <dependency>
             <groupId>dom4j</groupId>
             <artifactId>dom4j</artifactId>
@@ -101,10 +81,6 @@
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
         </dependency>
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-core</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>

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

@@ -42,6 +42,7 @@ import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import eu.dnetlib.pace.config.DedupConfig;
+import eu.dnetlib.pace.util.SparkCompatUtils;
 import scala.Tuple3;
 import scala.collection.JavaConversions;
 
@@ -148,8 +149,7 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
 			Dataset<Row> pivotHistory = spark
 				.createDataset(
 					Collections.emptyList(),
-					RowEncoder
-						.apply(StructType.fromDDL("id STRING, lastUsage STRING")));
+					SparkCompatUtils.encoderFor(StructType.fromDDL("id STRING, lastUsage STRING")));
 
 			if (StringUtils.isNotBlank(pivotHistoryDatabase)) {
 				pivotHistory = spark
@@ -203,8 +203,8 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
 			WindowSpec w = Window
 				.partitionBy("groupId")
 				.orderBy(
-					col("lastUsage").desc_nulls_last(),
 					col("pidType").asc_nulls_last(),
+					col("lastUsage").desc_nulls_last(),
 					col("collectedfrom").desc_nulls_last(),
 					col("date").asc_nulls_last(),
 					col("id").asc_nulls_last());

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

@@ -22,7 +22,9 @@ import eu.dnetlib.dhp.oa.dedup.model.OrgSimRel;
 import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.Field;
 import eu.dnetlib.dhp.schema.oaf.Organization;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@@ -164,12 +166,12 @@ public class SparkPrepareNewOrgs extends AbstractSparkAction {
 			.map(
 				(MapFunction<Tuple2<Tuple2<String, Organization>, Tuple2<String, String>>, OrgSimRel>) r -> new OrgSimRel(
 					"",
-					r._1()._2().getOriginalId().get(0),
-					r._1()._2().getLegalname() != null ? r._1()._2().getLegalname().getValue() : "",
-					r._1()._2().getLegalshortname() != null ? r._1()._2().getLegalshortname().getValue() : "",
-					r._1()._2().getCountry() != null ? r._1()._2().getCountry().getClassid() : "",
-					r._1()._2().getWebsiteurl() != null ? r._1()._2().getWebsiteurl().getValue() : "",
-					r._1()._2().getCollectedfrom().get(0).getValue(),
+					Optional.ofNullable(r._1()._2().getOriginalId()).map(oid -> oid.get(0)).orElse(null),
+					Optional.ofNullable(r._1()._2().getLegalname()).map(Field::getValue).orElse(""),
+					Optional.ofNullable(r._1()._2().getLegalshortname()).map(Field::getValue).orElse(""),
+					Optional.ofNullable(r._1()._2().getCountry()).map(Qualifier::getClassid).orElse(""),
+					Optional.ofNullable(r._1()._2().getWebsiteurl()).map(Field::getValue).orElse(""),
+					Optional.ofNullable(r._1()._2().getCollectedfrom()).map(cf -> cf.get(0).getValue()).orElse(null),
 					"",
 					structuredPropertyListToString(r._1()._2().getPid()),
 					parseECField(r._1()._2().getEclegalbody()),

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

@@ -217,7 +217,7 @@ public class SparkPrepareOrgRels extends AbstractSparkAction {
 					final Organization o = r._2()._2();
 					return new OrgSimRel(
 						r._1()._1(),
-						o.getOriginalId().get(0),
+						Optional.ofNullable(o.getOriginalId()).map(oid -> oid.get(0)).orElse(null),
 						Optional.ofNullable(o.getLegalname()).map(Field::getValue).orElse(""),
 						Optional.ofNullable(o.getLegalshortname()).map(Field::getValue).orElse(""),
 						Optional.ofNullable(o.getCountry()).map(Qualifier::getClassid).orElse(""),
@@ -249,7 +249,9 @@ public class SparkPrepareOrgRels extends AbstractSparkAction {
 			.map(
 				(MapFunction<Tuple2<Tuple2<String, OrgSimRel>, Tuple2<String, Organization>>, OrgSimRel>) r -> {
 					OrgSimRel orgSimRel = r._1()._2();
-					orgSimRel.setLocal_id(r._2()._2().getOriginalId().get(0));
+					orgSimRel
+						.setLocal_id(
+							Optional.ofNullable(r._2()._2().getOriginalId()).map(oid -> oid.get(0)).orElse(null));
 					return orgSimRel;
 				},
 				Encoders.bean(OrgSimRel.class));

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

@@ -8,7 +8,6 @@ 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.apache.spark.sql.catalyst.encoders.RowEncoder;
 import org.apache.spark.sql.types.StructType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -23,6 +22,7 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import eu.dnetlib.pace.util.SparkCompatUtils;
 import scala.Tuple2;
 import scala.Tuple3;
 
@@ -145,7 +145,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 		StructType idsSchema = StructType
 			.fromDDL("`id` STRING, `dataInfo` STRUCT<`deletedbyinference`:BOOLEAN,`invisible`:BOOLEAN>");
 
-		Dataset<Row> allIds = spark.emptyDataset(RowEncoder.apply(idsSchema));
+		Dataset<Row> allIds = spark.emptyDataset(SparkCompatUtils.encoderFor(idsSchema));
 
 		for (EntityType entityType : ModelSupport.entityTypes.keySet()) {
 			String entityPath = graphBasePath + '/' + entityType.name();

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/config-default.xml

@@ -15,4 +15,12 @@
         <name>oozie.action.sharelib.for.spark</name>
         <value>spark2</value>
     </property>
+    <property>
+        <name>hiveMetastoreUris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>pivotHistoryDatabase</name>
+        <value>&#x200B;</value>
+    </property>
 </configuration>

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/workflow.xml

@@ -198,6 +198,8 @@
             <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
             <arg>--actionSetId</arg><arg>${actionSetId}</arg>
             <arg>--cutConnectedComponent</arg><arg>${cutConnectedComponent}</arg>
+            <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
+            <arg>--pivotHistoryDatabase</arg><arg>${pivotHistoryDatabase}</arg>
         </spark>
         <ok to="PrepareOrgRels"/>
         <error to="Kill"/>

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java

@@ -0,0 +1,103 @@
+
+package eu.dnetlib.dhp.oa.dedup;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.Serializable;
+import java.lang.reflect.InvocationTargetException;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.codehaus.jackson.map.ObjectMapper;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
+import eu.dnetlib.dhp.schema.oaf.Dataset;
+import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
+import eu.dnetlib.pace.util.MapDocumentUtil;
+import scala.Tuple2;
+
+class DatasetMergerTest implements Serializable {
+
+	private List<Tuple2<String, Dataset>> datasets;
+
+	private String testEntityBasePath;
+	private DataInfo dataInfo;
+	private final String dedupId = "50|doi_________::3d18564ef27ebe9ef3bd8b4dec67e148";
+	private Dataset dataset_top;
+
+	@BeforeEach
+	public void setUp() throws Exception {
+		testEntityBasePath = Paths
+			.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/json").toURI())
+			.toFile()
+			.getAbsolutePath();
+
+		datasets = readSample(testEntityBasePath + "/dataset_merge.json", Dataset.class);
+
+		dataset_top = getTopPub(datasets);
+
+		dataInfo = setDI();
+	}
+
+	@Test
+	void datasetMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException {
+		Dataset pub_merged = MergeUtils.mergeGroup(dedupId, datasets.stream().map(Tuple2::_2).iterator());
+
+		// verify id
+		assertEquals(dedupId, pub_merged.getId());
+		assertEquals(2, pub_merged.getInstance().size());
+	}
+
+	public DataInfo setDI() {
+		DataInfo dataInfo = new DataInfo();
+		dataInfo.setTrust("0.9");
+		dataInfo.setDeletedbyinference(false);
+		dataInfo.setInferenceprovenance("testing");
+		dataInfo.setInferred(true);
+		return dataInfo;
+	}
+
+	public Dataset getTopPub(List<Tuple2<String, Dataset>> publications) {
+
+		Double maxTrust = 0.0;
+		Dataset maxPub = new Dataset();
+		for (Tuple2<String, Dataset> publication : publications) {
+			Double pubTrust = Double.parseDouble(publication._2().getDataInfo().getTrust());
+			if (pubTrust > maxTrust) {
+				maxTrust = pubTrust;
+				maxPub = publication._2();
+			}
+		}
+		return maxPub;
+	}
+
+	public <T> List<Tuple2<String, T>> readSample(String path, Class<T> clazz) {
+		List<Tuple2<String, T>> res = new ArrayList<>();
+		BufferedReader reader;
+		try {
+			reader = new BufferedReader(new FileReader(path));
+			String line = reader.readLine();
+			while (line != null) {
+				res
+					.add(
+						new Tuple2<>(
+							MapDocumentUtil.getJPathString("$.id", line),
+							new ObjectMapper().readValue(line, clazz)));
+				// read next line
+				line = reader.readLine();
+			}
+			reader.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+
+		return res;
+	}
+
+}

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java

@@ -93,14 +93,14 @@ class EntityMergerTest implements Serializable {
 		assertEquals(pub_top.getJournal().getConferencedate(), pub_merged.getJournal().getConferencedate());
 		assertEquals(pub_top.getJournal().getConferenceplace(), pub_merged.getJournal().getConferenceplace());
 		assertEquals("OPEN", pub_merged.getBestaccessright().getClassid());
-		assertEquals(pub_top.getResulttype(), pub_merged.getResulttype());
-		assertEquals(pub_top.getLanguage(), pub_merged.getLanguage());
-		assertEquals(pub_top.getPublisher(), pub_merged.getPublisher());
-		assertEquals(pub_top.getEmbargoenddate(), pub_merged.getEmbargoenddate());
+		assertEquals(pub_top.getResulttype().getClassid(), pub_merged.getResulttype().getClassid());
+		assertEquals(pub_top.getLanguage().getClassid(), pub_merged.getLanguage().getClassid());
+		assertEquals("Elsevier BV", pub_merged.getPublisher().getValue());
+		assertEquals(pub_top.getEmbargoenddate().getValue(), pub_merged.getEmbargoenddate().getValue());
 		assertEquals(pub_top.getResourcetype().getClassid(), "");
 		assertEquals(pub_top.getDateoftransformation(), pub_merged.getDateoftransformation());
 		assertEquals(pub_top.getOaiprovenance(), pub_merged.getOaiprovenance());
-		assertEquals(pub_top.getDateofcollection(), pub_merged.getDateofcollection());
+		// assertEquals(pub_top.getDateofcollection(), pub_merged.getDateofcollection());
 		assertEquals(3, pub_merged.getInstance().size());
 		assertEquals(2, pub_merged.getCountry().size());
 		assertEquals(0, pub_merged.getSubject().size());

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java

@@ -190,7 +190,7 @@ public class SparkDedupTest implements Serializable {
 		System.out.println("orp_simrel = " + orp_simrel);
 
 		if (CHECK_CARDINALITIES) {
-			assertEquals(751, orgs_simrel);
+			assertEquals(742, orgs_simrel);
 			assertEquals(566, pubs_simrel);
 			assertEquals(113, sw_simrel);
 			assertEquals(148, ds_simrel);
@@ -251,7 +251,7 @@ public class SparkDedupTest implements Serializable {
 
 		// entities simrels supposed to be equal to the number of previous step (no rels in whitelist)
 		if (CHECK_CARDINALITIES) {
-			assertEquals(751, orgs_simrel);
+			assertEquals(742, orgs_simrel);
 			assertEquals(566, pubs_simrel);
 			assertEquals(148, ds_simrel);
 			assertEquals(280, orp_simrel);
@@ -442,7 +442,7 @@ public class SparkDedupTest implements Serializable {
 		final List<Relation> merges = pubs
 			.filter("source == '50|arXiv_dedup_::c93aeb433eb90ed7a86e29be00791b7c'")
 			.collectAsList();
-		assertEquals(3, merges.size());
+		assertEquals(1, merges.size());
 		Set<String> dups = Sets
 			.newHashSet(
 				"50|doi_________::3b1d0d8e8f930826665df9d6b82fbb73",
@@ -451,7 +451,7 @@ public class SparkDedupTest implements Serializable {
 		merges.forEach(r -> {
 			assertEquals(ModelConstants.RESULT_RESULT, r.getRelType());
 			assertEquals(ModelConstants.DEDUP, r.getSubRelType());
-			assertEquals(ModelConstants.MERGES, r.getRelClass());
+			assertEquals(ModelConstants.IS_MERGED_IN, r.getRelClass());
 			assertTrue(dups.contains(r.getTarget()));
 		});
 
@@ -561,7 +561,7 @@ public class SparkDedupTest implements Serializable {
 		System.out.println("orp_mergerel = " + orp_mergerel);
 
 		if (CHECK_CARDINALITIES) {
-			assertEquals(1268, orgs_mergerel);
+			assertEquals(1278, orgs_mergerel);
 			assertEquals(1156, pubs.count());
 			assertEquals(292, sw_mergerel);
 			assertEquals(476, ds_mergerel);
@@ -618,7 +618,7 @@ public class SparkDedupTest implements Serializable {
 		System.out.println("orp_deduprecord = " + orp_deduprecord);
 
 		if (CHECK_CARDINALITIES) {
-			assertEquals(86, orgs_deduprecord);
+			assertEquals(78, orgs_deduprecord);
 			assertEquals(96, pubs.count());
 			assertEquals(47, sw_deduprecord);
 			assertEquals(97, ds_deduprecord);
@@ -761,7 +761,7 @@ public class SparkDedupTest implements Serializable {
 
 		if (CHECK_CARDINALITIES) {
 			assertEquals(930, publications);
-			assertEquals(839, organizations);
+			assertEquals(831, organizations);
 			assertEquals(100, projects);
 			assertEquals(100, datasource);
 			assertEquals(196, softwares);

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java

@@ -22,8 +22,11 @@ import java.util.Properties;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.Row;
 import org.apache.spark.sql.SparkSession;
 import org.junit.jupiter.api.*;
 import org.junit.jupiter.api.extension.ExtendWith;
@@ -143,7 +146,7 @@ public class SparkOpenorgsDedupTest implements Serializable {
 			.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
 			.count();
 
-		assertEquals(86, orgs_simrel);
+		assertEquals(92, orgs_simrel);
 	}
 
 	@Test
@@ -172,7 +175,7 @@ public class SparkOpenorgsDedupTest implements Serializable {
 			.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
 			.count();
 
-		assertEquals(122, orgs_simrel);
+		assertEquals(128, orgs_simrel);
 	}
 
 	@Test
@@ -207,7 +210,7 @@ public class SparkOpenorgsDedupTest implements Serializable {
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
 			.count();
-		assertEquals(132, orgs_mergerel);
+		assertEquals(128, orgs_mergerel);
 
 		// verify that a DiffRel is in the mergerels (to be sure that the job supposed to remove them has something to
 		// do)

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java

@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.dedup.jpath;
 
 import java.io.IOException;
 
+import eu.dnetlib.dhp.oa.dedup.SparkOpenorgsDedupTest;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.sql.Row;
 import org.junit.jupiter.api.Assertions;
@@ -24,6 +25,30 @@ class JsonPathTest {
 
 		Row row = SparkModel.apply(conf).rowFromJson(org);
 
+		System.out.println("row = " + row);
+		Assertions.assertNotNull(row);
+		Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier")));
+
+		System.out.println("row = " + row.getAs("countrytitle"));
+	}
+
+	@Test
+	void jsonToModelTest() throws IOException{
+		DedupConfig conf = DedupConfig
+				.load(IOUtils
+						.toString(
+								SparkOpenorgsDedupTest.class
+										.getResourceAsStream(
+												"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
+
+		final String org = IOUtils.toString(getClass().getResourceAsStream("organization_example1.json"));
+
+		Row row = SparkModel.apply(conf).rowFromJson(org);
+		// to check that the same parsing returns the same row
+		Row row1 = SparkModel.apply(conf).rowFromJson(org);
+
+		Assertions.assertEquals(row, row1);
+		System.out.println("row = " + row);
 		Assertions.assertNotNull(row);
 		Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier")));
 	}

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json

@@ -4,8 +4,8 @@
     "dedupRun" : "001",
     "entityType" : "organization",
     "subEntityValue": "organization",
-    "orderField" : "legalname",
-    "queueMaxSize" : "2000",
+    "orderField" : "original_legalname",
+    "queueMaxSize" : "100000",
     "groupMaxSize" : "50",
     "slidingWindowSize" : "200",
     "idPath":"$.id",
@@ -15,10 +15,10 @@
   },
   "pace" : {
     "clustering" : [
-      { "name" : "sortedngrampairs", "fields" : [ "legalname" ], "params" : { "max" : 2, "ngramLen" : "3"} },
-      { "name" : "suffixprefix", "fields" : [ "legalname" ], "params" : { "max" : 1, "len" : "3" } },
+      { "name" : "sortedngrampairs", "fields" : [ "original_legalname" ], "params" : { "max" : 2, "ngramLen" : "3"} },
+      { "name" : "suffixprefix", "fields" : [ "original_legalname" ], "params" : { "max" : 1, "len" : "3" } },
       { "name" : "urlclustering", "fields" : [ "websiteurl" ], "params" : { } },
-      { "name" : "keywordsclustering", "fields" : [ "legalname" ], "params" : { "max": 2, "windowSize": 4} }
+      { "name" : "legalnameclustering", "fields" : [ "legalname" ], "params" : { "max": 2} }
     ],
     "decisionTree" : {
       "start": {
@@ -29,16 +29,23 @@
             "weight": 1,
             "countIfUndefined": "false",
             "params": {}
+          },
+          {
+            "field": "rorid",
+            "comparator": "exactMatch",
+            "weight": 1,
+            "countIfUndefined": "false",
+            "params": {}
           }
         ],
         "threshold": 1,
-        "aggregation": "AVG",
+        "aggregation": "OR",
         "positive": "MATCH",
         "negative": "NO_MATCH",
-        "undefined": "layer2",
+        "undefined": "necessaryConditions",
         "ignoreUndefined": "false"
       },
-      "layer2": {
+      "necessaryConditions": {
         "fields": [
           {
             "field": "websiteurl",
@@ -49,20 +56,20 @@
           },
           {
             "field": "country",
-            "comparator": "exactMatch",
+            "comparator": "countryMatch",
             "weight": 1,
             "countIfUndefined": "true",
             "params": {}
           },
           {
-            "field": "legalname",
+            "field": "original_legalname",
             "comparator": "numbersMatch",
             "weight": 1,
             "countIfUndefined": "true",
             "params": {}
           },
           {
-            "field": "legalname",
+            "field": "original_legalname",
             "comparator": "romansMatch",
             "weight": 1,
             "countIfUndefined": "true",
@@ -71,68 +78,64 @@
         ],
         "threshold": 1,
         "aggregation": "AND",
-        "positive": "layer3",
+        "positive": "cityCheck",
         "negative": "NO_MATCH",
-        "undefined": "layer3",
+        "undefined": "cityCheck",
         "ignoreUndefined": "true"
       },
-      "layer3": {
+      "cityCheck": {
         "fields": [
           {
             "field": "legalname",
-            "comparator": "cityMatch",
+            "comparator": "codeMatch",
             "weight": 1.0,
             "countIfUndefined": "true",
             "params": {
-              "windowSize": "4"
+              "codeRegex": "city::\\d+"
             }
           }
         ],
         "threshold": 0.1,
         "aggregation": "AVG",
-        "positive": "layer4",
+        "positive": "keywordCheck",
         "negative": "NO_MATCH",
         "undefined": "NO_MATCH",
         "ignoreUndefined": "true"
       },
-      "layer4": {
+      "keywordCheck": {
         "fields": [
           {
             "field": "legalname",
-            "comparator": "keywordMatch",
+            "comparator": "codeMatch",
             "weight": 1.0,
             "countIfUndefined": "true",
             "params": {
-              "windowSize": "4"
+              "codeRegex": "key::\\d+"
             }
           }
         ],
         "threshold": 0.7,
         "aggregation": "AVG",
-        "positive": "layer5",
+        "positive": "nameCheck",
         "negative": "NO_MATCH",
-        "undefined": "layer5",
+        "undefined": "nameCheck",
         "ignoreUndefined": "true"
       },
-      "layer5": {
+      "nameCheck": {
         "fields": [
           {
             "field": "legalname",
-            "comparator": "jaroWinklerNormalizedName",
+            "comparator": "jaroWinklerLegalname",
             "weight": 0.9,
             "countIfUndefined": "true",
-            "params": {
-              "windowSize": "4"
-            }
+            "params": {}
           },
           {
             "field": "legalshortname",
-            "comparator": "jaroWinklerNormalizedName",
+            "comparator": "jaroWinklerLegalname",
             "weight": 0.1,
             "countIfUndefined": "false",
-            "params": {
-              "windowSize": 4
-            }
+            "params": {}
           }
         ],
         "threshold": 0.9,
@@ -144,126 +147,16 @@
       }
     },
     "model" : [
-      { "name" : "country", "type" : "String", "path" : "$.country.classid"},
-      { "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"},
-      { "name" : "legalname", "type" : "String", "path" : "$.legalname.value" },
+      { "name" : "country", "type" : "String", "path" : "$.country.classid", "infer" : "country", "inferenceFrom" : "$.legalname.value"},
+      { "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value", "infer" : "city_keyword"},
+      { "name" : "original_legalname", "type" : "String", "path" : "$.legalname.value" },
+      { "name" : "legalname", "type" : "String", "path" : "$.legalname.value", "infer" : "city_keyword"},
       { "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" },
       { "name" : "gridid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='grid')].value"},
+      { "name" : "rorid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='ROR')].value"},
       { "name" : "originalId", "type" : "String", "path" : "$.id" }
     ],
-    "blacklists" : {
-      "legalname" : []
-    },
-    "synonyms": {
-      "key::1": ["university","università", "universitas", "università studi","universitario","universitaria","université", "universite", "universitaire","universitaires","universidad","universitade","Universität","universitaet","Uniwersytet","университет","universiteit","πανεπιστήμιο","universitesi","universiteti", "universiti"],
-      "key::2": ["studies","studi","études","estudios","estudos","Studien","studia","исследования","studies","σπουδές"],
-      "key::3": ["advanced","superiore","supérieur","supérieure","supérieurs","supérieures","avancado","avancados","fortgeschrittene","fortgeschritten","zaawansowany","передовой","gevorderd","gevorderde","προχωρημένος","προχωρημένη","προχωρημένο","προχωρημένες","προχωρημένα","wyzsza"],
-      "key::4": ["institute","istituto","institut","instituto","instituto","Institut","instytut","институт","instituut","ινστιτούτο"],
-      "key::5": ["hospital","ospedale","hôpital","hospital","hospital","Krankenhaus","szpital","больница","ziekenhuis","νοσοκομείο"],
-      "key::6": ["research","ricerca","recherche","investigacion","pesquisa","Forschung","badania","исследования","onderzoek","έρευνα","erevna","erevnas"],
-      "key::7": ["college","collegio","colegio","faculdade","Hochschule","Szkoła Wyższa","Высшая школа","κολλέγιο"],
-      "key::8": ["foundation","fondazione","fondation","fundación","fundação","Stiftung","Fundacja","фонд","stichting","ίδρυμα","idryma"],
-      "key::9": ["center","centro","centre","centro","centro","zentrum","centrum","центр","centrum","κέντρο"],
-      "key::10": ["national","nazionale","national","nationale","nationaux","nationales","nacional","nacional","national","krajowy","национальный","nationaal","nationale","εθνικό"],
-      "key::11": ["association","associazione","association","asociación","associação","Verein","verband","stowarzyszenie","ассоциация","associatie"],
-      "key::12": ["society","societa","société","sociedad","sociedade","gesellschaft","społeczeństwo","общество","maatschappij","κοινωνία"],
-      "key::13": ["international","internazionale","international","internacional","internacional","international","międzynarodowy","Международный","internationaal","internationale","διεθνής","διεθνή","διεθνές"],
-      "key::14": ["community","comunita","communauté","comunidad","comunidade","Gemeinschaft","społeczność","сообщество","gemeenschap","κοινότητα"],
-      "key::15": ["school","scuola","école","escuela","escola","schule","Szkoła","школа","school","σχολείο"],
-      "key::16": ["education","educazione","éducation","educacion","Educação","Bildung","Edukacja","образование","opleiding","εκπαίδευση"],
-      "key::17": ["academy","accademia","académie","academia","academia","Akademie","akademie","академия","academie","ακαδημία"],
-      "key::18": ["public","pubblico","public","publique","publics","publiques","publico","publico","Öffentlichkeit","publiczny","публичный","publiek","publieke","δημόσιος","δημόσια","δημόσιο"],
-      "key::19": ["museum","museo","musée","mueso","museu","museum","muzeum","музей","museum","μουσείο"],
-      "key::20": ["group","gruppo","groupe","grupo","grupo","gruppe","grupa","группа","groep","ομάδα","όμιλος"],
-      "key::21": ["department","dipartimento","département","departamento","departamento","abteilung","departament","отдел","afdeling","τμήμα"],
-      "key::22": ["council","consiglio","conseil","Consejo","conselho","gesellschaft","rada","совет","raad","συμβούλιο"],
-      "key::23": ["library","biblioteca","bibliothèque","biblioteca","biblioteca","Bibliothek","biblioteka","библиотека","bibliotheek","βιβλιοθήκη"],
-      "key::24": ["ministry","ministero","ministère","ministerio","ministério","Ministerium","ministerstwo","министерство","ministerie","υπουργείο"],
-      "key::25": ["services","servizi","services","servicios","Serviços","Dienstleistungen","usługi","услуги","diensten","υπηρεσίες"],
-      "key::26": ["central","centrale","central","centrale","centrales","central","central","zentral","centralny","цетральный","centraal","κεντρικός","κεντρική","κεντρικό","κεντρικά"],
-      "key::27": ["general","generale","général","générale","généraux","générales","general","geral","general","Allgemeines","general","общий","algemeen","algemene","γενικός","γενική","γενικό","γενικά"],
-      "key::28": ["applied","applicati","appliqué","appliquée","appliqués","appliquées","aplicado","aplicada","angewendet","stosowany","прикладной","toegepast","toegepaste","εφαρμοσμένος","εφαρμοσμένη","εφαρμοσμένο","εφαρμοσμένα"],
-      "key::29": ["european","europee","europea","européen","européenne","européens","européennes","europeo","europeu","europäisch","europejski","европейский","Europees","Europese","ευρωπαϊκός","ευρωπαϊκή","ευρωπαϊκό","ευρωπαϊκά"],
-      "key::30": ["agency","agenzia","agence","agencia","agencia","agentur","agencja","агенция","agentschap","πρακτορείο"],
-      "key::31": ["laboratory","laboratorio","laboratoire","laboratorio","laboratorio","labor","laboratorium","лаборатория","laboratorium","εργαστήριο"],
-      "key::32": ["industry","industria","industrie","индустрия","industrie","βιομηχανία"],
-      "key::33": ["industrial","industriale","industriel","industrielle","industriels","industrielles","индустриальный","industrieel","βιομηχανικός","βιομηχανική","βιομηχανικό","βιομηχανικά","βιομηχανικές"],
-      "key::34": ["consortium","consorzio","consortium","консорциум","consortium","κοινοπραξία"],
-      "key::35": ["organization","organizzazione","organisation","organización","organização","organizacja","организация","organisatie","οργανισμός"],
-      "key::36": ["authority","autorità","autorité","авторитет","autoriteit"],
-      "key::37": ["federation","federazione","fédération","федерация","federatie","ομοσπονδία"],
-      "key::38": ["observatory","osservatorio","observatoire","обсерватория","observatorium","αστεροσκοπείο"],
-      "key::39": ["bureau","ufficio","bureau","офис","bureau","γραφείο"],
-      "key::40": ["company","impresa","compagnie","société","компания","bedrijf","εταιρία"],
-      "key::41": ["polytechnic","politecnico","polytechnique","политехника","polytechnisch","πολυτεχνείο","universita politecnica","polytechnic university","universidad politecnica","universitat politecnica","politechnika","politechniki","university technology","university science technology"],
-      "key::42": ["coalition","coalizione","coalition","коалиция","coalitie","συνασπισμός"],
-      "key::43": ["initiative","iniziativa","initiative","инициатива","initiatief","πρωτοβουλία"],
-      "key::44": ["academic","accademico","académique","universitaire","акадеческий academisch","ακαδημαϊκός","ακαδημαϊκή","ακαδημαϊκό","ακαδημαϊκές","ακαδημαϊκοί"],
-      "key::45": ["institution","istituzione","institution","институциональный","instelling","ινστιτούτο"],
-      "key::46": ["division","divisione","division","отделение","divisie","τμήμα"],
-      "key::47": ["committee","comitato","comité","комитет","commissie","επιτροπή"],
-      "key::48": ["promotion","promozione","продвижение","proothisis","forderung"],
-      "key::49": ["medical","medicine","clinical","medicina","clinici","médico","medicina","clínica","médico","medicina","clínica","medizinisch","Medizin","klinisch","medisch","geneeskunde","klinisch","ιατρικός","ιατρική","ιατρικό","ιατρικά","κλινικός","κλινική","κλινικό","κλινικά","tıbbi","tıp","klinik","orvosi","orvostudomány","klinikai","zdravniški","medicinski","klinični","meditsiini","kliinik","kliiniline"],
-      "key::50": ["technology","technological","tecnologia","tecnologie","tecnología","tecnológico","tecnologia","tecnológico","Technologie","technologisch","technologie","technologisch","τεχνολογία","τεχνολογικός","τεχνολογική","τεχνολογικό","teknoloji","teknolojik","technológia","technológiai","tehnologija","tehnološki","tehnoloogia","tehnoloogiline","technologii","technical","texniki","teknik"],
-      "key::51": ["science","scientific","scienza","scientifiche","scienze","ciencia","científico","ciência","científico","Wissenschaft","wissenschaftlich","wetenschap","wetenschappelijk","επιστήμη","επιστημονικός","επιστημονική","επιστημονικό","επιστημονικά","bilim","bilimsel","tudomány","tudományos","znanost","znanstveni","teadus","teaduslik",""],
-      "key::52": ["engineering","ingegneria","ingeniería","engenharia","Ingenieurwissenschaft","ingenieurswetenschappen","bouwkunde","μηχανικός","μηχανική","μηχανικό","mühendislik","mérnöki","Inženirstvo","inseneeria","inseneri",""],
-      "key::53": ["management","gestione","gestionale","gestionali","gestión","administración","gestão","administração","Verwaltung","management","διαχείριση","yönetim","menedzsment","vodstvo","upravljanje","management","juhtkond","juhtimine","haldus",""],
-      "key::54": ["energy","energia","energía","energia","Energie","energie","ενέργεια","enerji","energia","energija","energia",""],
-      "key::55": ["agricultural","agriculture","agricoltura","agricole","agrícola","agricultura","agrícola","agricultura","landwirtschaftlich","Landwirtschaft","landbouwkundig","landbouw","αγροτικός","αγροτική","αγροτικό","γεωργικός","γεωργική","γεωργικό","γεωργία","tarımsal","tarım","mezőgazdasági","mezőgazdaság","poljedelski","poljedelstvo","põllumajandus","põllumajanduslik",""],
-      "key::56": ["information","informazione","información","informação","Information","informatie","πληροφορία","bilgi","információ","informacija","informatsioon","informatycznych",""],
-      "key::57": ["social","sociali","social","social","Sozial","sociaal","maatschappelijk","κοινωνικός","κοινωνική","κοινωνικό","κοινωνικά","sosyal","szociális","družbeni","sotsiaal","sotsiaalne",""],
-      "key::58": ["environmental","ambiente","medioambiental","ambiente","medioambiente","meioambiente","Umwelt","milieu","milieuwetenschap","milieukunde","περιβαλλοντικός","περιβαλλοντική","περιβαλλοντικό","περιβαλλοντικά","çevre","környezeti","okoliški","keskonna",""],
-      "key::59": ["business","economia","economiche","economica","negocio","empresa","negócio","Unternehmen","bedrijf","bedrijfskunde","επιχείρηση","iş","üzleti","posel","ettevõte/äri",""],
-      "key::60": ["pharmaceuticals","pharmacy","farmacia","farmaceutica","farmacéutica","farmacia","farmacêutica","farmácia","Pharmazeutika","Arzneimittelkunde","farmaceutica","geneesmiddelen","apotheek","φαρμακευτικός","φαρμακευτική","φαρμακευτικό","φαρμακευτικά","φαρμακείο","ilaç","eczane","gyógyszerészeti","gyógyszertár","farmacevtika","lekarništvo","farmaatsia","farmatseutiline",""],
-      "key::61": ["healthcare","health services","salute","atenciónmédica","cuidadodelasalud","cuidadoscomasaúde","Gesundheitswesen","gezondheidszorg","ιατροφαρμακευτικήπερίθαλψη","sağlıkhizmeti","egészségügy","zdravstvo","tervishoid","tervishoiu",""],
-      "key::62": ["history","storia","historia","história","Geschichte","geschiedenis","geschiedkunde","ιστορία","tarih","történelem","zgodovina","ajalugu",""],
-      "key::63": ["materials","materiali","materia","materiales","materiais","materialen","υλικά","τεκμήρια","malzemeler","anyagok","materiali","materjalid","vahendid",""],
-      "key::64": ["economics","economia","economiche","economica","economía","economia","Wirtschaft","economie","οικονομικά","οικονομικέςεπιστήμες","ekonomi","közgazdaságtan","gospodarstvo","ekonomija","majanduslik","majandus",""],
-      "key::65": ["therapeutics","terapeutica","terapéutica","terapêutica","therapie","θεραπευτική","tedavibilimi","gyógykezelés","terapevtika","terapeutiline","ravi",""],
-      "key::66": ["oncology","oncologia","oncologico","oncología","oncologia","Onkologie","oncologie","ογκολογία","onkoloji","onkológia","onkologija","onkoloogia",""],
-      "key::67": ["natural","naturali","naturale","natural","natural","natürlich","natuurlijk","φυσικός","φυσική","φυσικό","φυσικά","doğal","természetes","naraven","loodus",""],
-      "key::68": ["educational","educazione","pedagogia","educacional","educativo","educacional","pädagogisch","educatief","εκπαιδευτικός","εκπαιδευτική","εκπαιδευτικό","εκπαιδευτικά","eğitimsel","oktatási","izobraževalen","haridus","hariduslik",""],
-      "key::69": ["biomedical","biomedica","biomédico","biomédico","biomedizinisch","biomedisch","βιοιατρικός","βιοιατρική","βιοιατρικό","βιοιατρικά","biyomedikal","orvosbiológiai","biomedicinski","biomeditsiiniline",""],
-      "key::70": ["veterinary","veterinaria","veterinarie","veterinaria","veterinária","tierärtzlich","veterinair","veeartsenijlkunde","κτηνιατρικός","κτηνιατρική","κτηνιατρικό","κτηνιατρικά","veteriner","állatorvosi","veterinar","veterinarski","veterinaaria",""],
-      "key::71": ["chemistry","chimica","química","química","Chemie","chemie","scheikunde","χημεία","kimya","kémia","kemija","keemia",""],
-      "key::72": ["security","sicurezza","seguridad","segurança","Sicherheit","veiligheid","ασφάλεια","güvenlik","biztonsági","varnost","turvalisus","julgeolek",""],
-      "key::73": ["biotechnology","biotecnologia","biotecnologie","biotecnología","biotecnologia","Biotechnologie","biotechnologie","βιοτεχνολογία","biyoteknoloji","biotechnológia","biotehnologija","biotehnoloogia",""],
-      "key::74": ["military","militare","militari","militar","militar","Militär","militair","leger","στρατιωτικός","στρατιωτική","στρατιωτικό","στρατιωτικά","askeri","katonai","vojaški","vojni","militaar","wojskowa",""],
-      "key::75": ["theological","teologia","teologico","teológico","tecnológica","theologisch","theologisch","θεολογικός","θεολογική","θεολογικό","θεολογικά","teolojik","technológiai","teološki","teoloogia","usuteadus","teoloogiline",""],
-      "key::76": ["electronics","elettronica","electrónica","eletrônicos","Elektronik","elektronica","ηλεκτρονική","elektronik","elektronika","elektronika","elektroonika",""],
-      "key::77": ["forestry","forestale","forestali","silvicultura","forestal","floresta","Forstwirtschaft","bosbouw","δασοκομία","δασολογία","ormancılık","erdészet","gozdarstvo","metsandus",""],
-      "key::78": ["maritime","marittima","marittime","marittimo","marítimo","marítimo","maritiem","ναυτικός","ναυτική","ναυτικό","ναυτικά","ναυτιλιακός","ναυτιλιακή","ναυτιλιακό","ναυτιλιακά","θαλάσσιος","θαλάσσια","θαλάσσιο","denizcilik","tengeri","morski","mere","merendus",""],
-      "key::79": ["sports","sport","deportes","esportes","Sport","sport","sportwetenschappen","άθληση","γυμναστικήδραστηριότητα","spor","sport","šport","sport","spordi",""],
-      "key::80": ["surgery","chirurgia","chirurgiche","cirugía","cirurgia","Chirurgie","chirurgie","heelkunde","εγχείρηση","επέμβαση","χειρουργικήεπέμβαση","cerrahi","sebészet","kirurgija","kirurgia",""],
-      "key::81": ["cultural","culturale","culturali","cultura","cultural","cultural","kulturell","cultureel","πολιτιστικός","πολιτιστική","πολιτιστικό","πολιτισμικός","πολιτισμική","πολιτισμικό","kültürel","kultúrális","kulturni","kultuuri","kultuuriline",""],
-      "key::82": ["computerscience","informatica","ordenador","computadora","informática","computación","cienciasdelacomputación","ciênciadacomputação","Computer","computer","υπολογιστής","ηλεκτρονικόςυπολογιστής","bilgisayar","számítógép","računalnik","arvuti",""],
-      "key::83": ["finance","financial","finanza","finanziarie","finanza","financiero","finanças","financeiro","Finanzen","finanziell","financiën","financieel","χρηματοοικονομικά","χρηματοδότηση","finanse","finansal","pénzügy","pénzügyi","finance","finančni","finants","finantsiline",""],
-      "key::84": ["communication","comunicazione","comuniciación","comunicação","Kommunikation","communication","επικοινωνία","iletişim","kommunikáció","komuniciranje","kommunikatsioon",""],
-      "key::85": ["justice","giustizia","justicia","justiça","Recht","Justiz","justitie","gerechtigheid","δικαιοσύνη","υπουργείοδικαιοσύνης","δίκαιο","adalet","igazságügy","pravo","õigus",""],
-      "key::86": ["aerospace","aerospaziale","aerospaziali","aeroespacio","aeroespaço","Luftfahrt","luchtvaart","ruimtevaart","αεροπορικός","αεροπορική","αεροπορικό","αεροναυπηγικός","αεροναυπηγική","αεροναυπηγικό","αεροναυπηγικά","havacılıkveuzay","légtér","zrakoplovstvo","atmosfäär","kosmos",""],
-      "key::87": ["dermatology","dermatologia","dermatología","dermatologia","Dermatologie","dermatologie","δρματολογία","dermatoloji","bőrgyógyászat","dermatológia","dermatologija","dermatoloogia",""],
-      "key::88": ["architecture","architettura","arquitectura","arquitetura","Architektur","architectuur","αρχιτεκτονική","mimarlık","építészet","arhitektura","arhitektuur",""],
-      "key::89": ["mathematics","matematica","matematiche","matemáticas","matemáticas","Mathematik","wiskunde","mathematica","μαθηματικά","matematik","matematika","matematika","matemaatika",""],
-      "key::90": ["language","lingue","linguistica","linguistiche","lenguaje","idioma","língua","idioma","Sprache","taal","taalkunde","γλώσσα","dil","nyelv","jezik","keel",""],
-      "key::91": ["neuroscience","neuroscienza","neurociencia","neurociência","Neurowissenschaft","neurowetenschappen","νευροεπιστήμη","nörobilim","idegtudomány","nevroznanost","neuroteadused",""],
-      "key::92": ["automation","automazione","automatización","automação","Automatisierung","automatisering","αυτοματοποίηση","otomasyon","automatizálás","avtomatizacija","automatiseeritud",""],
-      "key::93": ["pediatric","pediatria","pediatriche","pediatrico","pediátrico","pediatría","pediátrico","pediatria","pädiatrisch","pediatrische","παιδιατρική","pediatrik","gyermekgyógyászat","pediatrija","pediaatria",""],
-      "key::94": ["photonics","fotonica","fotoniche","fotónica","fotônica","Photonik","fotonica","φωτονική","fotonik","fotonika","fotonika","fotoonika",""],
-      "key::95": ["mechanics", "mechanical", "meccanica","meccaniche","mecánica","mecânica","Mechanik","Maschinenbau","mechanica","werktuigkunde","μηχανικής","mekanik","gépészet","mehanika","mehaanika",""],
-      "key::96": ["psychiatrics","psichiatria","psichiatrica","psichiatriche","psiquiatría","psiquiatria","Psychiatrie","psychiatrie","ψυχιατρική","psikiyatrik","pszihiátria","psihiatrija","psühhaatria",""],
-      "key::97": ["psychology","fisiologia","psicología","psicologia","Psychologie","psychologie","ψυχολογία","psikoloji","pszihológia","psihologija","psühholoogia",""],
-      "key::98": ["automotive","industriaautomobilistica","industriadelautomóvil","automotriz","industriaautomotriz","automotivo","Automobilindustrie","autoindustrie","αυτοκίνητος","αυτοκίνητη","αυτοκίνητο","αυτοκινούμενος","αυτοκινούμενη","αυτοκινούμενο","αυτοκινητιστικός","αυτοκινητιστική","αυτοκινητιστικό","otomotiv","autóipari","samogiben","avtomobilskaindustrija","auto-",""],
-      "key::99": ["neurology","neurologia","neurologiche","neurología","neurologia","Neurologie","neurologie","zenuwleer","νευρολογία","nöroloji","neurológia","ideggyógyászat","nevrologija","neuroloogia",""],
-      "key::100": ["geology","geologia","geologiche","geología","geologia","Geologie","geologie","aardkunde","γεωλογία","jeoloji","geológia","földtudomány","geologija","geoloogia",""],
-      "key::101": ["microbiology","microbiologia","micro-biologia","microbiologiche","microbiología","microbiologia","Mikrobiologie","microbiologie","μικροβιολογία","mikrobiyoloji","mikrobiológia","mikrobiologija","mikrobioloogia",""],
-      "key::102": ["informatics","informatica","informática","informática","informatica",""],
-      "key::103": ["forschungsgemeinschaft","comunita ricerca","research community","research foundation","research association"],
-      "key::104": ["commerce","ticaret","ticarət","commercio","trade","handel","comercio"],
-      "key::105" : ["state", "stato", "etade", "estado", "statale", "etat", "zustand", "estado"],
-      "key::106" : ["seminary", "seminario", "seminaire", "seminar"],
-      "key::107" : ["agricultural forestry", "af", "a f"],
-      "key::108" : ["agricultural mechanical", "am", "a m"],
-      "key::109" : ["catholic", "catholique", "katholische", "catolica", "cattolica", "catolico"]
-    }
+    "blacklists" : {},
+    "synonyms": {}
   }
 }

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

@@ -172,7 +172,7 @@ public class SparkBulkTagJob {
 			.option("compression", "gzip")
 			.json(outputPath + "project");
 
-		readPath(spark, outputPath + "project", Datasource.class)
+		readPath(spark, outputPath + "project", Project.class)
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")

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

@@ -50,7 +50,7 @@ public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Obje
 	 * @param subject
 	 */
 	private static void cleanSubjectForVocabulary(String vocabularyId, VocabularyGroup vocabularies,
-												  Subject subject) {
+		Subject subject) {
 
 		vocabularies.find(vocabularyId).ifPresent(vocabulary -> {
 			if (ModelConstants.DNET_SUBJECT_KEYWORD.equalsIgnoreCase(subject.getQualifier().getClassid())) {
@@ -61,13 +61,14 @@ public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Obje
 					subject.getQualifier().setClassname(vocabulary.getName());
 				}
 			} else {
-				final String provenanceActionClassId = Optional.ofNullable(subject.getDataInfo())
-						.map(DataInfo::getProvenanceaction)
-						.map(Qualifier::getClassid)
-						.orElse(null);
+				final String provenanceActionClassId = Optional
+					.ofNullable(subject.getDataInfo())
+					.map(DataInfo::getProvenanceaction)
+					.map(Qualifier::getClassid)
+					.orElse(null);
 
 				if (vocabularyId.equals(subject.getQualifier().getClassid()) &&
-						!"subject:fos".equals(provenanceActionClassId)) {
+					!"subject:fos".equals(provenanceActionClassId)) {
 
 					Qualifier syn = vocabulary.getSynonymAsQualifier(subject.getValue());
 					VocabularyTerm term = vocabulary.getTerm(subject.getValue());

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

@@ -398,6 +398,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
 			o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info));
 			o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info));
 			o.setCountry(prepareQualifierSplitting(rs.getString("country")));
+			o.setOrganizationType(Organization.OrganizationType.valueOf(rs.getString("typology")));
 			o.setDataInfo(info);
 			o.setLastupdatetimestamp(lastUpdateTimestamp);
 

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

@@ -156,6 +156,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -190,6 +191,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -224,6 +226,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -258,6 +261,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -292,6 +296,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -326,6 +331,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -360,6 +366,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -394,6 +401,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

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

@@ -116,17 +116,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --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}
+                --conf spark.sql.shuffle.partitions=10000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/publication</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>8000</arg>
+            <arg>--numPartitions</arg><arg>10000</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>
@@ -143,17 +145,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=4000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/dataset</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>4000</arg>
+            <arg>--numPartitions</arg><arg>8000</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>
@@ -170,11 +174,13 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --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}
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/otherresearchproduct</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
@@ -197,17 +203,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --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}
+                --conf spark.sql.shuffle.partitions=1000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/software</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>300</arg>
+            <arg>--numPartitions</arg><arg>1000</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>
@@ -224,17 +232,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=200
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/datasource</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>100</arg>
+            <arg>--numPartitions</arg><arg>200</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>
@@ -251,17 +261,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --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}
+                --conf spark.sql.shuffle.partitions=1000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/organization</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>400</arg>
+            <arg>--numPartitions</arg><arg>1000</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>
@@ -278,17 +290,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=1000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/project</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>100</arg>
+            <arg>--numPartitions</arg><arg>1000</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>
@@ -305,17 +319,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --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}
+                --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/relation</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>10000</arg>
+            <arg>--numPartitions</arg><arg>15000</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>

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

@@ -45,6 +45,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.shuffle.partitions=15000
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -79,6 +80,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.shuffle.partitions=10000
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}

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

@@ -28,7 +28,8 @@ SELECT
     (array_remove(array_cat(ARRAY[o.ec_internationalorganization], array_agg(od.ec_internationalorganization)), NULL))[1]              AS ecinternationalorganization,
     (array_remove(array_cat(ARRAY[o.ec_enterprise], array_agg(od.ec_enterprise)), NULL))[1]                      AS ecenterprise,
     (array_remove(array_cat(ARRAY[o.ec_smevalidated], array_agg(od.ec_smevalidated)), NULL))[1]                    AS ecsmevalidated,
-    (array_remove(array_cat(ARRAY[o.ec_nutscode], array_agg(od.ec_nutscode)), NULL))[1]                       AS ecnutscode
+    (array_remove(array_cat(ARRAY[o.ec_nutscode], array_agg(od.ec_nutscode)), NULL))[1]                       AS ecnutscode,
+    org_types.name                                                                                              AS typology
 FROM organizations o
 	LEFT OUTER JOIN acronyms a    ON (a.id = o.id)
 	LEFT OUTER JOIN urls u        ON (u.id = o.id)
@@ -37,6 +38,7 @@ FROM organizations o
 	LEFT OUTER JOIN oa_duplicates d ON (o.id = d.local_id AND d.reltype != 'is_different')
     LEFT OUTER JOIN organizations od ON (d.oa_original_id = od.id)
     LEFT OUTER JOIN other_ids idup  ON (od.id = idup.id)
+    LEFT OUTER JOIN org_types ON (org_types.val = o.type)
 WHERE
     o.status = 'approved' OR o.status = 'suggested'
 GROUP BY
@@ -44,4 +46,5 @@ GROUP BY
 	o.name,
 	o.creation_date,
 	o.modification_date,
-	o.country;
+	o.country,
+	org_types.name;

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/create_scholix_dump_params.json

@@ -0,0 +1,5 @@
+[
+  {"paramName":"mt",  "paramLongName":"master",     "paramDescription": "should be local or yarn",  "paramRequired": false},
+  {"paramName":"s",   "paramLongName":"sourcePath", "paramDescription": "the source Path",           "paramRequired": true},
+  {"paramName":"t",   "paramLongName":"targetPath", "paramDescription": "the path of the scholix dump", "paramRequired": true}
+]