Merge pull request 'Changes in maven poms to build and test the project using Spark 3.4.x and scala 2.12' (#327) from spark34-integration into beta

Reviewed-on: #327

.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>

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/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)
+    if (master != null)
-      .getOrCreate()
+      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 = {
+    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(r.getResulttype.getClassid)
-      s.setTypology(Typology.publication)
-    else
-      s.setTypology(Typology.dataset)
 
     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/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
  *

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 = {

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/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/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-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/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

@@ -94,7 +94,8 @@ object MagUtility extends Serializable {
     )
     di
   }
-val datatypedict = Map(
+
+  val datatypedict = Map(
     "bool"     -> BooleanType,
     "int"      -> IntegerType,
     "uint"     -> IntegerType,
@@ -505,8 +506,6 @@ val datatypedict = Map(
       )
     )
 
-
-
     result.setOriginalId(pidList.map(s => s.getValue).asJava)
 
     result.setId(s"50|mag_________::${DHPUtils.md5(paper.paperId.get.toString)}")

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

@@ -35,8 +35,6 @@ class SparkMAGtoOAF(propertyPath: String, args: Array[String], log: Logger)
   def convertMAG(spark: SparkSession, magBasePath: String, mdStorePath: String): Unit = {
     import spark.implicits._
 
-
-
     spark.read
       .load(s"$magBasePath/mag_denormalized")
       .as[MAGPaper]

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
-import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
 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 java.io.{ByteArrayInputStream, InputStream}
-import scala.io.Source
+import java.nio.charset.Charset
-import scala.xml.pull.XMLEventReader
+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")
+    val targetPath = parser.get("targetPath")
-    log.info("mdstoreOutputVersion: {}", mdstoreOutputVersion)
+    log.info("targetPath: {}", targetPath)
-
-    val cleanedMdStoreVersion = MAPPER.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
-    val outputBasePath = cleanedMdStoreVersion.getHdfsPath
-    log.info("outputBasePath: {}", outputBasePath)
 
     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.*;
-import org.junit.jupiter.api.Assertions;
-import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

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/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

@@ -7,13 +7,10 @@ import org.apache.spark.sql.functions.col
 import org.junit.jupiter.api.Assertions._
 import org.junit.jupiter.api.Test
 
-
-
 class MAGMappingTest {
 
   val mapper = new ObjectMapper()
 
-
   def mappingTest(): Unit = {
 
     val spark = SparkSession
@@ -26,8 +23,6 @@ class MAGMappingTest {
     s.convertMAG(spark, "/Users/sandro/Downloads/", "/Users/sandro/Downloads/mag_OAF")
   }
 
-
-
   @Test
   def mappingMagType(): Unit = {
 

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
+    val inputFactory = XMLInputFactory.newInstance
-      .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
+    val xml = inputFactory.createXMLEventReader(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
-      .mkString
-    val xml = new XMLEventReader(Source.fromBytes(inputXML.getBytes()))
     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(
+    val inputFactory = XMLInputFactory.newInstance
-      Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
+
-    )
+    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(
+    val inputFactory = XMLInputFactory.newInstance
-      Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
+    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
+					SparkCompatUtils.encoderFor(StructType.fromDDL("id STRING, lastUsage STRING")));
-						.apply(StructType.fromDDL("id STRING, lastUsage STRING")));
 
 			if (StringUtils.isNotBlank(pivotHistoryDatabase)) {
 				pivotHistory = spark

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

@@ -61,7 +61,8 @@ public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Obje
 					subject.getQualifier().setClassname(vocabulary.getName());
 				}
 			} else {
-				final String provenanceActionClassId = Optional.ofNullable(subject.getDataInfo())
+				final String provenanceActionClassId = Optional
+					.ofNullable(subject.getDataInfo())
 					.map(DataInfo::getProvenanceaction)
 					.map(Qualifier::getClassid)
 					.orElse(null);

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}
+]

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

@@ -0,0 +1,166 @@
+{
+  "cites":{
+    "original":"Cites",
+    "inverse":"IsCitedBy"
+  },
+  "compiles":{
+    "original":"Compiles",
+    "inverse":"IsCompiledBy"
+  },
+  "continues":{
+    "original":"Continues",
+    "inverse":"IsContinuedBy"
+  },
+  "derives":{
+    "original":"IsSourceOf",
+    "inverse":"IsDerivedFrom"
+  },
+  "describes":{
+    "original":"Describes",
+    "inverse":"IsDescribedBy"
+  },
+  "documents":{
+    "original":"Documents",
+    "inverse":"IsDocumentedBy"
+  },
+  "hasmetadata":{
+    "original":"HasMetadata",
+    "inverse":"IsMetadataOf"
+  },
+  "hasassociationwith":{
+    "original":"HasAssociationWith",
+    "inverse":"HasAssociationWith"
+  },
+  "haspart":{
+    "original":"HasPart",
+    "inverse":"IsPartOf"
+  },
+  "hasversion":{
+    "original":"HasVersion",
+    "inverse":"IsVersionOf"
+  },
+  "iscitedby":{
+    "original":"IsCitedBy",
+    "inverse":"Cites"
+  },
+  "iscompiledby":{
+    "original":"IsCompiledBy",
+    "inverse":"Compiles"
+  },
+  "iscontinuedby":{
+    "original":"IsContinuedBy",
+    "inverse":"Continues"
+  },
+  "isderivedfrom":{
+    "original":"IsDerivedFrom",
+    "inverse":"IsSourceOf"
+  },
+  "isdescribedby":{
+    "original":"IsDescribedBy",
+    "inverse":"Describes"
+  },
+  "isdocumentedby":{
+    "original":"IsDocumentedBy",
+    "inverse":"Documents"
+  },
+  "isidenticalto":{
+    "original":"IsIdenticalTo",
+    "inverse":"IsIdenticalTo"
+  },
+  "ismetadatafor":{
+    "original":"IsMetadataFor",
+    "inverse":"IsMetadataOf"
+  },
+  "ismetadataof":{
+    "original":"IsMetadataOf",
+    "inverse":"IsMetadataFor"
+  },
+  "isnewversionof":{
+    "original":"IsNewVersionOf",
+    "inverse":"IsPreviousVersionOf"
+  },
+  "isobsoletedby":{
+    "original":"IsObsoletedBy",
+    "inverse":"Obsoletes"
+  },
+  "isoriginalformof":{
+    "original":"IsOriginalFormOf",
+    "inverse":"IsVariantFormOf"
+  },
+  "ispartof":{
+    "original":"IsPartOf",
+    "inverse":"HasPart"
+  },
+  "ispreviousversionof":{
+    "original":"IsPreviousVersionOf",
+    "inverse":"IsNewVersionOf"
+  },
+  "isreferencedby":{
+    "original":"IsReferencedBy",
+    "inverse":"References"
+  },
+  "isrelatedto":{
+    "original":"IsRelatedTo",
+    "inverse":"IsRelatedTo"
+  },
+  "isrequiredby":{
+    "original":"IsRequiredBy",
+    "inverse":"Requires"
+  },
+  "isreviewedby":{
+    "original":"IsReviewedBy",
+    "inverse":"Reviews"
+  },
+  "issourceof":{
+    "original":"IsSourceOf",
+    "inverse":"IsDerivedFrom"
+  },
+  "issupplementedby":{
+    "original":"IsSupplementedBy",
+    "inverse":"IsSupplementTo"
+  },
+  "issupplementto":{
+    "original":"IsSupplementTo",
+    "inverse":"IsSupplementedBy"
+  },
+  "isvariantformof":{
+    "original":"IsVariantFormOf",
+    "inverse":"IsOriginalFormOf"
+  },
+  "isversionof":{
+    "original":"IsVersionOf",
+    "inverse":"HasVersion"
+  },
+  "obsoletes":{
+    "original":"Obsoletes",
+    "inverse":"IsObsoletedBy"
+  },
+  "references":{
+    "original":"References",
+    "inverse":"IsReferencedBy"
+  },
+  "requires":{
+    "original":"Requires",
+    "inverse":"IsRequiredBy"
+  },
+  "related":{
+    "original":"IsRelatedTo",
+    "inverse":"IsRelatedTo"
+  },
+  "reviews":{
+    "original":"Reviews",
+    "inverse":"IsReviewedBy"
+  },
+  "unknown":{
+    "original":"Unknown",
+    "inverse":"Unknown"
+  },
+  "isamongtopnsimilardocuments": {
+    "original": "IsAmongTopNSimilarDocuments",
+    "inverse": "HasAmongTopNSimilarDocuments"
+  },
+  "hasamongtopnsimilardocuments": {
+    "original": "HasAmongTopNSimilarDocuments",
+    "inverse": "IsAmongTopNSimilarDocuments"
+  }
+}

dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/ScholexplorerUtils.scala

@@ -0,0 +1,258 @@
+package eu.dnetlib.dhp.sx.graph
+
+import com.fasterxml.jackson.databind.ObjectMapper
+import eu.dnetlib.dhp.schema.oaf.{KeyValue, Result, StructuredProperty}
+import eu.dnetlib.dhp.schema.sx.scholix.{
+  Scholix,
+  ScholixCollectedFrom,
+  ScholixEntityId,
+  ScholixIdentifier,
+  ScholixRelationship,
+  ScholixResource
+}
+import org.json4s
+import org.json4s.DefaultFormats
+import org.json4s.jackson.JsonMethods.parse
+
+import scala.collection.JavaConverters._
+import scala.io.Source
+
+case class RelationInfo(
+  source: String,
+  target: String,
+  relclass: String,
+  id: String,
+  collectedfrom: Seq[RelKeyValue]
+) {}
+case class RelKeyValue(key: String, value: String) {}
+
+object ScholexplorerUtils {
+
+  val OPENAIRE_IDENTIFIER_SCHEMA: String = "OpenAIRE Identifier"
+  val mapper = new ObjectMapper()
+
+  case class RelationVocabulary(original: String, inverse: String) {}
+
+  val relations: Map[String, RelationVocabulary] = {
+    val input = Source
+      .fromInputStream(
+        getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/relation/relations.json")
+      )
+      .mkString
+    implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
+
+    lazy val json: json4s.JValue = parse(input)
+
+    json.extract[Map[String, RelationVocabulary]]
+  }
+
+  def invRel(rel: String): String = {
+    val semanticRelation = relations.getOrElse(rel.toLowerCase, null)
+    if (semanticRelation != null)
+      semanticRelation.inverse
+    else
+      null
+  }
+
+  def generateDatasourceOpenAIREURLS(id: String): String = {
+    if (id != null && id.length > 12)
+      s"https://explore.openaire.eu/search/dataprovider?datasourceId=${id.substring(3)}"
+    else
+      null
+  }
+
+  def findURLForPID(
+    pidValue: List[StructuredProperty],
+    urls: List[String]
+  ): List[(StructuredProperty, String)] = {
+    pidValue.map { p =>
+      val pv = p.getValue
+
+      val r = urls.find(u => u.toLowerCase.contains(pv.toLowerCase))
+      (p, r.orNull)
+    }
+  }
+
+  def extractTypedIdentifierFromInstance(r: Result): List[ScholixIdentifier] = {
+    if (r.getInstance() == null || r.getInstance().isEmpty)
+      return List()
+    r.getInstance()
+      .asScala
+      .filter(i => i.getUrl != null && !i.getUrl.isEmpty)
+      .filter(i => i.getPid != null && i.getUrl != null)
+      .flatMap(i => findURLForPID(i.getPid.asScala.toList, i.getUrl.asScala.toList))
+      .map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2))
+      .distinct
+      .toList
+  }
+
+  def generateScholixResourceFromResult(result: Result): ScholixResource = {
+
+    if (result.getInstance() == null || result.getInstance().size() == 0)
+      return null
+
+    if (result.getPid == null || result.getPid.isEmpty)
+      return null
+
+    val r = new ScholixResource
+    r.setDnetIdentifier(result.getId)
+
+    val persistentIdentifiers: List[ScholixIdentifier] = extractTypedIdentifierFromInstance(result)
+    if (persistentIdentifiers.isEmpty)
+      return null
+
+    r.setIdentifier(persistentIdentifiers.asJava)
+
+    r.setObjectType(result.getResulttype.getClassid)
+
+    r.setObjectSubType(
+      result
+        .getInstance()
+        .asScala
+        .filter(i => i != null && i.getInstancetype != null)
+        .map(i => i.getInstancetype.getClassname)
+        .distinct
+        .head
+    )
+
+    if (result.getTitle != null && result.getTitle.asScala.nonEmpty) {
+      val titles: List[String] = result.getTitle.asScala.map(t => t.getValue).toList
+      if (titles.nonEmpty)
+        r.setTitle(titles.head)
+      else
+        return null
+    }
+    if (result.getAuthor != null && !result.getAuthor.isEmpty) {
+      val authors: List[ScholixEntityId] =
+        result.getAuthor.asScala
+          .map(a => {
+            val entity = new ScholixEntityId()
+            entity.setName(a.getFullname)
+            if (a.getPid != null && a.getPid.size() > 0)
+              entity.setIdentifiers(
+                a.getPid.asScala
+                  .map(sp => {
+                    val id = new ScholixIdentifier()
+                    id.setIdentifier(sp.getValue)
+                    id.setSchema(sp.getQualifier.getClassid)
+                    id
+                  })
+                  .take(3)
+                  .toList
+                  .asJava
+              )
+            entity
+          })
+          .toList
+      if (authors.nonEmpty)
+        r.setCreator(authors.asJava)
+
+    }
+
+    val dt: List[String] = result
+      .getInstance()
+      .asScala
+      .filter(i => i.getDateofacceptance != null)
+      .map(i => i.getDateofacceptance.getValue)
+      .toList
+    if (dt.nonEmpty)
+      r.setPublicationDate(dt.distinct.head)
+
+    r.setPublisher(
+      result
+        .getInstance()
+        .asScala
+        .map(i => i.getHostedby)
+        .filter(h => !"unknown".equalsIgnoreCase(h.getValue))
+        .map(h => {
+          val eid = new ScholixEntityId()
+          eid.setName(h.getValue)
+          val id = new ScholixIdentifier()
+          id.setIdentifier(h.getKey)
+          id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
+          id.setUrl(generateDatasourceOpenAIREURLS(h.getKey))
+          eid.setIdentifiers(List(id).asJava)
+          eid
+        })
+        .distinct
+        .asJava
+    )
+
+    r.setCollectedFrom(
+      result.getCollectedfrom.asScala
+        .map(cf => {
+          val scf = new ScholixCollectedFrom()
+          scf.setProvisionMode("collected")
+          scf.setCompletionStatus("complete")
+          val eid = new ScholixEntityId()
+          eid.setName(cf.getValue)
+          val id = new ScholixIdentifier()
+          id.setIdentifier(cf.getKey)
+          id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
+          id.setUrl(generateDatasourceOpenAIREURLS(cf.getKey))
+          eid.setIdentifiers(List(id).asJava)
+          scf.setProvider(eid)
+          scf
+        })
+        .asJava
+    )
+
+    r
+  }
+
+  def generateScholix(relation: RelationInfo, source: ScholixResource): Scholix = {
+    val s: Scholix = new Scholix
+    s.setSource(source)
+    if (relation.collectedfrom != null && relation.collectedfrom.nonEmpty)
+      s.setLinkprovider(
+        relation.collectedfrom
+          .map(cf => {
+            val eid = new ScholixEntityId()
+            eid.setName(cf.value)
+            val id = new ScholixIdentifier()
+            id.setIdentifier(cf.key)
+            id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
+            id.setUrl(generateDatasourceOpenAIREURLS(cf.key))
+            eid.setIdentifiers(List(id).asJava)
+            eid
+          })
+          .toList
+          .asJava
+      )
+    else {
+      val eid = new ScholixEntityId()
+      eid.setName("OpenAIRE")
+      val id = new ScholixIdentifier()
+      id.setIdentifier("10|infrastruct_::f66f1bd369679b5b077dcdf006089556")
+      id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
+      id.setUrl(generateDatasourceOpenAIREURLS(id.getIdentifier))
+      eid.setIdentifiers(List(id).asJava)
+      s.setLinkprovider(List(eid).asJava)
+    }
+    s.setIdentifier(relation.id)
+    val semanticRelation = relations.getOrElse(relation.relclass.toLowerCase, null)
+    if (semanticRelation == null)
+      return null
+    s.setRelationship(
+      new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse)
+    )
+    s.setPublicationDate(source.getPublicationDate)
+    s.setPublisher(source.getPublisher)
+    val mockTarget = new ScholixResource
+    mockTarget.setDnetIdentifier(relation.target)
+    s.setTarget(mockTarget)
+    s
+  }
+
+  def updateTarget(s: Scholix, t: ScholixResource): String = {
+
+    s.setTarget(t)
+    val spublishers: Seq[ScholixEntityId] =
+      if (s.getPublisher != null && !s.getPublisher.isEmpty) s.getPublisher.asScala else List()
+    val tpublishers: Seq[ScholixEntityId] =
+      if (t.getPublisher != null && !t.getPublisher.isEmpty) t.getPublisher.asScala else List()
+    val mergedPublishers = spublishers.union(tpublishers).distinct.take(10).toList
+    s.setPublisher(mergedPublishers.asJava)
+    mapper.writeValueAsString(s)
+  }
+}

dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateScholexplorerDump.scala

@@ -0,0 +1,141 @@
+package eu.dnetlib.dhp.sx.graph
+
+import eu.dnetlib.dhp.application.AbstractScalaApplication
+import eu.dnetlib.dhp.schema.oaf.{
+  KeyValue,
+  OtherResearchProduct,
+  Publication,
+  Relation,
+  Result,
+  Software,
+  Dataset => OafDataset
+}
+import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixResource}
+import org.apache.spark.sql.functions.{col, concat, expr, first, md5}
+import org.apache.spark.sql.types.StructType
+import org.apache.spark.sql._
+import org.slf4j.{Logger, LoggerFactory}
+
+class SparkCreateScholexplorerDump(propertyPath: String, args: Array[String], log: Logger)
+    extends AbstractScalaApplication(propertyPath, args, log: Logger) {
+
+  /** Here all the spark applications runs this method
+    * where the whole logic of the spark node is defined
+    */
+  override def run(): Unit = {
+    val sourcePath = parser.get("sourcePath")
+    log.info("sourcePath: {}", sourcePath)
+    val targetPath = parser.get("targetPath")
+    log.info("targetPath: {}", targetPath)
+    generateBidirectionalRelations(sourcePath, targetPath, spark)
+    generateScholixResource(sourcePath, targetPath, spark)
+    generateScholix(targetPath, spark)
+  }
+
+  def generateScholixResource(inputPath: String, outputPath: String, spark: SparkSession): Unit = {
+    val entityMap: Map[String, StructType] = Map(
+      "publication"          -> Encoders.bean(classOf[Publication]).schema,
+      "dataset"              -> Encoders.bean(classOf[OafDataset]).schema,
+      "software"             -> Encoders.bean(classOf[Software]).schema,
+      "otherresearchproduct" -> Encoders.bean(classOf[OtherResearchProduct]).schema
+    )
+
+    implicit val scholixResourceEncoder: Encoder[ScholixResource] = Encoders.bean(classOf[ScholixResource])
+    implicit val resultEncoder: Encoder[Result] = Encoders.bean(classOf[Result])
+
+    val resDs = spark.emptyDataset[ScholixResource]
+    val scholixResourceDS = entityMap.foldLeft[Dataset[ScholixResource]](resDs)((res, item) => {
+      println(s"adding ${item._1}")
+      res.union(
+        spark.read
+          .schema(item._2)
+          .json(s"$inputPath/${item._1}")
+          .as[Result]
+          .map(r => ScholexplorerUtils.generateScholixResourceFromResult(r))
+          .filter(s => s != null)
+      )
+    })
+    scholixResourceDS.write.mode(SaveMode.Overwrite).save(s"$outputPath/resource")
+  }
+
+  def generateBidirectionalRelations(inputPath: String, otuputPath: String, spark: SparkSession): Unit = {
+    val relSchema = Encoders.bean(classOf[Relation]).schema
+
+    val relDF = spark.read
+      .schema(relSchema)
+      .json(s"$inputPath/relation")
+      .where(
+        "datainfo.deletedbyinference is false and source like '50%' and target like '50%' " +
+        "and relClass <> 'merges' and relClass <> 'isMergedIn'"
+      )
+      .select("source", "target", "collectedfrom", "relClass")
+
+    def invRel: String => String = { s =>
+      ScholexplorerUtils.invRel(s)
+    }
+
+    import org.apache.spark.sql.functions.udf
+    val inverseRelationUDF = udf(invRel)
+    val inverseRelation = relDF.select(
+      col("target").alias("source"),
+      col("source").alias("target"),
+      col("collectedfrom"),
+      inverseRelationUDF(col("relClass")).alias("relClass")
+    )
+
+    val bidRel = inverseRelation
+      .union(relDF)
+      .withColumn("id", md5(concat(col("source"), col("relClass"), col("target"))))
+      .withColumn("cf", expr("transform(collectedfrom, x -> struct(x.key, x.value))"))
+      .drop("collectedfrom")
+      .withColumnRenamed("cf", "collectedfrom")
+      .groupBy(col("id"))
+      .agg(
+        first("source").alias("source"),
+        first("target").alias("target"),
+        first("relClass").alias("relClass"),
+        first("collectedfrom").alias("collectedfrom")
+      )
+
+    bidRel.write.mode(SaveMode.Overwrite).save(s"$otuputPath/relation")
+
+  }
+
+  def generateScholix(outputPath: String, spark: SparkSession): Unit = {
+    implicit val scholixResourceEncoder: Encoder[ScholixResource] = Encoders.bean(classOf[ScholixResource])
+    implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo(classOf[Scholix])
+
+    import spark.implicits._
+    val relations = spark.read.load(s"$outputPath/relation").as[RelationInfo]
+    val resource = spark.read.load(s"$outputPath/resource").as[ScholixResource]
+
+    val scholix_one_verse = relations
+      .joinWith(resource, relations("source") === resource("dnetIdentifier"), "inner")
+      .map(res => ScholexplorerUtils.generateScholix(res._1, res._2))
+      .map(s => (s.getIdentifier, s))(Encoders.tuple(Encoders.STRING, Encoders.kryo(classOf[Scholix])))
+
+    val resourceTarget = relations
+      .joinWith(resource, relations("target") === resource("dnetIdentifier"), "inner")
+      .map(res => (res._1.id, res._2))(Encoders.tuple(Encoders.STRING, Encoders.kryo(classOf[ScholixResource])))
+
+    scholix_one_verse
+      .joinWith(resourceTarget, scholix_one_verse("_1") === resourceTarget("_1"), "inner")
+      .map(k => ScholexplorerUtils.updateTarget(k._1._2, k._2._2))
+      .write
+      .mode(SaveMode.Overwrite)
+      .option("compression", "gzip")
+      .text(s"$outputPath/scholix")
+  }
+}
+
+object SparkCreateScholexplorerDump {
+  val logger: Logger = LoggerFactory.getLogger(SparkCreateScholexplorerDump.getClass)
+
+  def main(args: Array[String]): Unit = {
+    new SparkCreateScholexplorerDump(
+      log = logger,
+      args = args,
+      propertyPath = "/eu/dnetlib/dhp/sx/create_scholix_dump_params.json"
+    ).initialize().run()
+  }
+}

dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGenerationTest.scala

@@ -0,0 +1,26 @@
+package eu.dnetlib.dhp.sx.graph.scholix
+
+import eu.dnetlib.dhp.schema.sx.scholix.ScholixResource
+import eu.dnetlib.dhp.sx.graph.SparkCreateScholexplorerDump
+import org.apache.spark.SparkConf
+import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
+import org.junit.jupiter.api.Test
+import org.objenesis.strategy.StdInstantiatorStrategy
+
+class ScholixGenerationTest {
+
+  @Test
+  def generateScholix(): Unit = {
+
+    val spark: SparkSession = SparkSession.builder().master("local[*]").getOrCreate()
+    val app = new SparkCreateScholexplorerDump(null, null, null)
+//   app.generateScholixResource("/home/sandro/Downloads/scholix_sample/", "/home/sandro/Downloads/scholix/", spark)
+//    app.generateBidirectionalRelations(
+//      "/home/sandro/Downloads/scholix_sample/",
+//      "/home/sandro/Downloads/scholix/",
+//      spark
+//    )
+    app.generateScholix("/home/sandro/Downloads/scholix/", spark)
+
+  }
+}

dhp-workflows/dhp-graph-provision/pom.xml

@@ -18,7 +18,7 @@
                 <executions>
                     <execution>
                         <id>scala-compile-first</id>
-                        <phase>initialize</phase>
+                        <phase>process-resources</phase>
                         <goals>
                             <goal>add-source</goal>
                             <goal>compile</goal>
@@ -59,12 +59,6 @@
         <dependency>
             <groupId>com.jayway.jsonpath</groupId>
             <artifactId>json-path</artifactId>
-            <exclusions>
-                <exclusion>
-                    <groupId>org.slf4j</groupId>
-                    <artifactId>slf4j-api</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <dependency>
             <groupId>dom4j</groupId>
@@ -160,6 +154,26 @@
                     <groupId>org.apache.zookeeper</groupId>
                     <artifactId>zookeeper</artifactId>
                 </exclusion>
+                <exclusion>
+                    <artifactId>ant</artifactId>
+                    <groupId>org.apache.ant</groupId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>antlr4-runtime</artifactId>
+                    <groupId>org.antlr</groupId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>woodstox-core</artifactId>
+                    <groupId>com.fasterxml.woodstox</groupId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>log4j</artifactId>
+                    <groupId>*</groupId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.apache.logging.log4j</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
         <dependency>
@@ -206,5 +220,90 @@
 
     </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/sparksolr-3</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/sparksolr-4</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/sparksolr-4</source>
+                                    </sources>
+                                </configuration>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+    </profiles>
 
 </project>

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

@@ -25,6 +25,7 @@ import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
 import eu.dnetlib.dhp.oa.provision.model.TupleWrapper;
 import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
 import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory;
+import eu.dnetlib.dhp.sparksolr.DHPSolrSupport;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@@ -129,7 +130,7 @@ public class XmlIndexingJob extends AbstractSolrRecordTransformJob {
 			.javaRDD()
 			.map(
 				t -> new StreamingInputDocumentFactory().parseDocument(t.getXml(), t.getJson()));
-		SolrSupport.indexDocs(zkHost, collection, batchSize, docs.rdd());
+		DHPSolrSupport.indexDocs(zkHost, collection, batchSize, docs.rdd());
 	}
 
 }

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

@@ -5,14 +5,11 @@ import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.removePrefix;
 import static eu.dnetlib.dhp.oa.provision.utils.XmlSerializationUtils.escapeXml;
 
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
-import javax.swing.text.html.Option;
-
 import org.apache.commons.lang3.StringUtils;
 import org.stringtemplate.v4.ST;
 

dhp-workflows/dhp-graph-provision/src/main/sparksolr-3/eu/dnetlib/dhp/sparksolr/DHPSolrSupport.java

@@ -0,0 +1,12 @@
+package eu.dnetlib.dhp.sparksolr;
+
+import com.lucidworks.spark.util.SolrSupport;
+import org.apache.solr.common.SolrInputDocument;
+import org.apache.spark.rdd.RDD;
+
+public class DHPSolrSupport {
+
+    static public void indexDocs(String zkhost, String collection, int batchSize, RDD<SolrInputDocument> docs) {
+        SolrSupport.indexDocs(zkhost, collection, batchSize, docs);
+    }
+}

dhp-workflows/dhp-graph-provision/src/main/sparksolr-4/eu/dnetlib/dhp/sparksolr/DHPSolrSupport.java

@@ -0,0 +1,12 @@
+package eu.dnetlib.dhp.sparksolr;
+
+import com.lucidworks.spark.util.SolrSupport;
+import org.apache.solr.common.SolrInputDocument;
+import org.apache.spark.rdd.RDD;
+
+public class DHPSolrSupport {
+
+    static public void indexDocs(String zkhost, String collection, int batchSize, RDD<SolrInputDocument> docs) {
+        SolrSupport.indexDocs(zkhost, collection, batchSize, com.lucidworks.spark.BatchSizeType.NUM_DOCS, docs);
+    }
+}

dhp-workflows/dhp-stats-actionsets/pom.xml

@@ -16,11 +16,11 @@
 
         <dependency>
             <groupId>org.apache.spark</groupId>
-            <artifactId>spark-core_2.11</artifactId>
+            <artifactId>spark-core_${scala.binary.version}</artifactId>
         </dependency>
         <dependency>
             <groupId>org.apache.spark</groupId>
-            <artifactId>spark-sql_2.11</artifactId>
+            <artifactId>spark-sql_${scala.binary.version}</artifactId>
         </dependency>
 
         <dependency>

dhp-workflows/dhp-stats-hist-snaps/pom.xml

@@ -10,11 +10,11 @@
     <dependencies>
         <dependency>
             <groupId>org.apache.spark</groupId>
-            <artifactId>spark-core_2.11</artifactId>
+            <artifactId>spark-core_${scala.binary.version}</artifactId>
         </dependency>
         <dependency>
             <groupId>org.apache.spark</groupId>
-            <artifactId>spark-sql_2.11</artifactId>
+            <artifactId>spark-sql_${scala.binary.version}</artifactId>
         </dependency>
     </dependencies>
 	<build>

dhp-workflows/dhp-stats-monitor-irish/pom.xml

@@ -10,11 +10,11 @@
     <dependencies>
         <dependency>
             <groupId>org.apache.spark</groupId>
-            <artifactId>spark-core_2.11</artifactId>
+            <artifactId>spark-core_${scala.binary.version}</artifactId>
         </dependency>
         <dependency>
             <groupId>org.apache.spark</groupId>
-            <artifactId>spark-sql_2.11</artifactId>
+            <artifactId>spark-sql_${scala.binary.version}</artifactId>
         </dependency>
     </dependencies>
 	<build>

dhp-workflows/dhp-stats-monitor-update/pom.xml

@@ -10,11 +10,11 @@
     <dependencies>
         <dependency>
             <groupId>org.apache.spark</groupId>
-            <artifactId>spark-core_2.11</artifactId>
+            <artifactId>spark-core_${scala.binary.version}</artifactId>
         </dependency>
         <dependency>
             <groupId>org.apache.spark</groupId>
-            <artifactId>spark-sql_2.11</artifactId>
+            <artifactId>spark-sql_${scala.binary.version}</artifactId>
         </dependency>
     </dependencies>
 	<build>

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

@@ -17,6 +17,7 @@ import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaPairRDD;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.*;
 import org.apache.spark.sql.Dataset;
@@ -117,7 +118,7 @@ public class PrepareSWHActionsets {
 			.map(
 				(MapFunction<String, Software>) t -> OBJECT_MAPPER.readValue(t, Software.class),
 				Encoders.bean(Software.class))
-			.filter(t -> t.getCodeRepositoryUrl() != null)
+			.filter((FilterFunction<Software>) t -> t.getCodeRepositoryUrl() != null)
 			.select(col("id"), col("codeRepositoryUrl.value").as("repoUrl"));
 	}
 

dhp-workflows/dhp-usage-raw-data-update/pom.xml

@@ -39,8 +39,8 @@
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <cdh.hive.version>0.13.1-cdh5.2.1</cdh.hive.version>
+        <cdh.hive.version>1.1.0-cdh5.16.2</cdh.hive.version>
-        <cdh.hadoop.version>2.5.0-cdh5.2.1</cdh.hadoop.version>
+        <cdh.hadoop.version>2.6.0-cdh5.16.2</cdh.hadoop.version>
     </properties>
 
     <dependencies>
@@ -72,6 +72,12 @@
             <groupId>org.apache.hadoop</groupId>
             <artifactId>hadoop-common</artifactId>
             <version>${cdh.hadoop.version}</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>jdk.tools</groupId>
+                    <artifactId>jdk.tools</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>eu.dnetlib.dhp</groupId>

dhp-workflows/dhp-usage-stats-build/pom.xml

@@ -39,8 +39,8 @@
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <cdh.hive.version>0.13.1-cdh5.2.1</cdh.hive.version>
+        <cdh.hive.version>1.1.0-cdh5.16.2</cdh.hive.version>
-        <cdh.hadoop.version>2.5.0-cdh5.2.1</cdh.hadoop.version>
+        <cdh.hadoop.version>2.6.0-cdh5.16.2</cdh.hadoop.version>
 	</properties>
     
     <dependencies>
@@ -67,11 +67,23 @@
 			<groupId>org.apache.hive</groupId>
 			<artifactId>hive-jdbc</artifactId>
 			<version>${cdh.hive.version}</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>jdk.tools</groupId>
+                    <artifactId>jdk.tools</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
 		<dependency>
   			<groupId>org.apache.hadoop</groupId>
   			<artifactId>hadoop-common</artifactId>
   			<version>${cdh.hadoop.version}</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>jdk.tools</groupId>
+                    <artifactId>jdk.tools</artifactId>
+                </exclusion>
+            </exclusions>
 		</dependency>        
         <dependency>
             <groupId>eu.dnetlib.dhp</groupId>

pom.xml

@@ -13,7 +13,8 @@
             <distribution>repo</distribution>
             <comments>This program is free software: you can redistribute it and/or modify it under the terms of the
                 GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the
-				License, or (at your option) any later version.</comments>
+                License, or (at your option) any later version.
+            </comments>
         </license>
     </licenses>
 
@@ -22,6 +23,7 @@
         <module>dhp-pace-core</module>
         <module>dhp-common</module>
         <module>dhp-workflows</module>
+        <module>dhp-shade-package</module>
     </modules>
 
     <issueManagement>
@@ -47,6 +49,19 @@
     </pluginRepositories>
 
     <repositories>
+
+        <repository>
+            <id>Openaire-third-parties-snaphot</id>
+            <name>Openaire third parties Snapshot</name>
+            <url>https://maven.d4science.org/nexus/content/repositories/Openaire-third-parties-snaphot/</url>
+            <releases>
+                <enabled>false</enabled>
+            </releases>
+            <snapshots>
+                <enabled>true</enabled>
+            </snapshots>
+        </repository>
+
         <repository>
             <id>dnet45-releases</id>
             <name>D-Net 45 releases</name>
@@ -125,6 +140,13 @@
     </repositories>
 
     <dependencies>
+        <!-- Quick FIX not to remove lombok everywhere -->
+        <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>
@@ -152,7 +174,7 @@
         <dependencies>
             <dependency>
                 <groupId>eu.dnetlib.dhp</groupId>
-				<artifactId>${dhp-schemas.artifact}</artifactId>
+                <artifactId>dhp-schemas</artifactId>
                 <version>${dhp-schemas.version}</version>
             </dependency>
             <dependency>
@@ -206,33 +228,76 @@
 
             <dependency>
                 <groupId>org.slf4j</groupId>
-				<artifactId>jcl-over-slf4j</artifactId>
+                <artifactId>slf4j-api</artifactId>
-				<version>1.7.25</version>
+                <version>${org.slf4j.version}</version>
                 <scope>provided</scope>
             </dependency>
 
+            <dependency>
+                <groupId>org.slf4j</groupId>
+                <artifactId>slf4j-log4j12</artifactId>
+                <version>${org.slf4j.version}</version>
+                <scope>provided</scope>
+            </dependency>
+
+            <dependency>
+                <groupId>org.slf4j</groupId>
+                <artifactId>jcl-over-slf4j</artifactId>
+                <version>${org.slf4j.version}</version>
+                <scope>provided</scope>
+            </dependency>
+
+            <dependency>
+                <groupId>org.apache.logging.log4j</groupId>
+                <artifactId>log4j-slf4j2-impl</artifactId>
+                <version>${log4j.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.logging.log4j</groupId>
+                <artifactId>log4j-api</artifactId>
+                <version>${log4j.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.logging.log4j</groupId>
+                <artifactId>log4j-core</artifactId>
+                <version>${log4j.version}</version>
+            </dependency>
+            <dependency>
+                <!-- API bridge between log4j 1 and 2 -->
+                <groupId>org.apache.logging.log4j</groupId>
+                <artifactId>log4j-1.2-api</artifactId>
+                <version>${log4j.version}</version>
+            </dependency>
+
             <dependency>
                 <groupId>org.apache.commons</groupId>
                 <artifactId>commons-lang3</artifactId>
                 <version>${dhp.commons.lang.version}</version>
             </dependency>
 
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-beanutils</artifactId>
+                <version>${commons-beanutils.version}</version>
+            </dependency>
+
+
             <dependency>
                 <groupId>commons-validator</groupId>
                 <artifactId>commons-validator</artifactId>
-				<version>1.7</version>
+                <version>${commons-validator.version}</version>
             </dependency>
 
             <dependency>
                 <groupId>com.github.sisyphsu</groupId>
                 <artifactId>dateparser</artifactId>
-				<version>1.0.7</version>
+                <version>${dateparser.version}</version>
             </dependency>
 
             <dependency>
                 <groupId>me.xuender</groupId>
                 <artifactId>unidecode</artifactId>
-				<version>0.0.7</version>
+                <version>${unidecode.version}</version>
             </dependency>
 
             <dependency>
@@ -245,13 +310,13 @@
             <dependency>
                 <groupId>commons-codec</groupId>
                 <artifactId>commons-codec</artifactId>
-				<version>1.9</version>
+                <version>${commons-codec.version}</version>
             </dependency>
 
             <dependency>
                 <groupId>commons-io</groupId>
                 <artifactId>commons-io</artifactId>
-				<version>2.4</version>
+                <version>${commons-io.version}</version>
             </dependency>
 
             <dependency>
@@ -345,7 +410,7 @@
             <dependency>
                 <groupId>org.apache.zookeeper</groupId>
                 <artifactId>zookeeper</artifactId>
-				<version>3.4.11</version>
+                <version>${zookeeper.version}</version>
             </dependency>
 
             <dependency>
@@ -415,6 +480,7 @@
                 <artifactId>cxf-rt-transports-http</artifactId>
                 <version>3.1.5</version>
             </dependency>
+
             <dependency>
                 <groupId>javax.persistence</groupId>
                 <artifactId>javax.persistence-api</artifactId>
@@ -504,16 +570,11 @@
                 <artifactId>commons-compress</artifactId>
                 <version>${common.compress.version}</version>
             </dependency>
-
-			<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-csv -->
             <dependency>
                 <groupId>org.apache.commons</groupId>
                 <artifactId>commons-csv</artifactId>
                 <version>${common.csv.version}</version>
             </dependency>
-
-
-			<!-- https://mvnrepository.com/artifact/org.apache.poi/poi-ooxml -->
             <dependency>
                 <groupId>org.apache.poi</groupId>
                 <artifactId>poi-ooxml</artifactId>
@@ -568,14 +629,12 @@
                 <scope>provided</scope>
             </dependency>
 
-
             <dependency>
                 <groupId>org.apache.commons</groupId>
                 <artifactId>commons-math3</artifactId>
                 <version>3.6.1</version>
             </dependency>
 
-
             <dependency>
                 <groupId>com.google.code.gson</groupId>
                 <artifactId>gson</artifactId>
@@ -596,7 +655,7 @@
             <dependency>
                 <groupId>org.reflections</groupId>
                 <artifactId>reflections</artifactId>
-				<version>0.9.10</version>
+                <version>${reflections.version}</version>
             </dependency>
 
             <dependency>
@@ -610,6 +669,12 @@
                 <artifactId>icu4j</artifactId>
                 <version>70.1</version>
             </dependency>
+
+            <dependency>
+                <groupId>org.javassist</groupId>
+                <artifactId>javassist</artifactId>
+                <version>${javassist.version}</version>
+            </dependency>
         </dependencies>
     </dependencyManagement>
 
@@ -677,6 +742,7 @@
                     <version>3.0.0-M4</version>
                     <configuration>
                         <redirectTestOutputToFile>true</redirectTestOutputToFile>
+                        <trimStackTrace>false</trimStackTrace>
                     </configuration>
                 </plugin>
                 <plugin>
@@ -746,7 +812,7 @@
             <plugin>
                 <groupId>net.revelc.code</groupId>
                 <artifactId>impsort-maven-plugin</artifactId>
-				<version>1.4.1</version>
+                <version>1.6.2</version>
                 <configuration>
                     <groups>java.,javax.,org.,com.</groups>
                     <staticGroups>java,*</staticGroups>
@@ -767,7 +833,9 @@
                 <groupId>org.antipathy</groupId>
                 <artifactId>mvn-scalafmt_${scala.binary.version}</artifactId>
                 <configuration>
-					<configLocation>https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf</configLocation>
+                    <configLocation>
+                        https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf
+                    </configLocation>
                     <skipTestSources>false</skipTestSources>
                     <skipSources>false</skipSources>
                     <sourceDirectories>
@@ -798,7 +866,7 @@
             <plugin>
                 <groupId>org.jacoco</groupId>
                 <artifactId>jacoco-maven-plugin</artifactId>
-				<version>0.7.9</version>
+                <version>0.8.10</version>
                 <configuration>
                     <excludes>
                         <exclude>**/schemas/*</exclude>
@@ -866,90 +934,174 @@
         <dhp.site.stage.path>sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop</dhp.site.stage.path>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-		<maven.compiler.plugin.version>3.6.0</maven.compiler.plugin.version>
         <maven.compiler.source>1.8</maven.compiler.source>
         <maven.compiler.target>1.8</maven.compiler.target>
-		<maven.failsave.plugin.version>2.22.2</maven.failsave.plugin.version>
+
-		<properties.maven.plugin.version>2.0.1</properties.maven.plugin.version>
+        <!-- scala version -->
-		<dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
-		<dhp.hadoop.version>2.6.0-${dhp.cdh.version}</dhp.hadoop.version>
-		<dhp.oozie.version>4.1.0-${dhp.cdh.version}</dhp.oozie.version>
-		<dhp-schemas.artifact>dhp-schemas</dhp-schemas.artifact>
-		<sparksolr.version>3.6.0</sparksolr.version>
-		<dhp.spark.version>2.4.0.cloudera2</dhp.spark.version>
-		<dhp.jackson.version>2.9.6</dhp.jackson.version>
-		<dhp.commons.lang.version>3.5</dhp.commons.lang.version>
-		<dhp.site.skip>true</dhp.site.skip>
-		<dhp.guava.version>11.0.2</dhp.guava.version>
         <scala.version>2.11.12</scala.version>
         <scala.binary.version>2.11</scala.binary.version>
-		<scala-xml.version>1.3.0</scala-xml.version>
+
-		<junit-jupiter.version>5.6.1</junit-jupiter.version>
+        <!-- plugin versions -->
-		<mockito-core.version>3.3.3</mockito-core.version>
+        <maven.compiler.plugin.version>3.6.0</maven.compiler.plugin.version>
-		<mongodb.driver.version>3.4.2</mongodb.driver.version>
+        <maven.failsave.plugin.version>2.22.2</maven.failsave.plugin.version>
-		<vtd.version>[2.12,3.0)</vtd.version>
+        <properties.maven.plugin.version>2.0.1</properties.maven.plugin.version>
+        <net.alchim31.maven.version>4.0.1</net.alchim31.maven.version>
+
+        <!-- dependency versions -->
+        <apache.poi.version>4.1.2</apache.poi.version>
+        <cnr-rmi-api.version>[2.6.1]</cnr-rmi-api.version>
+        <common.compress.version>1.20</common.compress.version>
+        <common.csv.version>1.8</common.csv.version>
+        <common.text.version>1.8</common.text.version>
+        <commons-beanutils.version>1.9.4</commons-beanutils.version>
+        <commons-codec.version>1.9</commons-codec.version>
+        <commons.collections.version>3.2.1</commons.collections.version>
+        <commons-io.version>2.4</commons-io.version>
+        <commons.logging.version>1.1.3</commons.logging.version>
+        <commons-validator.version>1.7</commons-validator.version>
+        <dateparser.version>1.0.7</dateparser.version>
         <dhp-schemas.version>[6.1.2]</dhp-schemas.version>
+        <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
+        <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
+        <dhp.guava.version>11.0.2</dhp.guava.version>
+        <dhp.hadoop.version>2.6.0-${dhp.cdh.version}</dhp.hadoop.version>
+        <dhp.jackson.version>2.9.6</dhp.jackson.version>
+        <dhp.oozie.version>4.1.0-${dhp.cdh.version}</dhp.oozie.version>
+        <dhp.site.skip>true</dhp.site.skip>
+        <dhp.spark.version>2.4.0.cloudera2</dhp.spark.version>
         <dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
         <dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
         <dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
-		<cnr-rmi-api.version>[2.6.1]</cnr-rmi-api.version>
+        <google.gson.version>2.2.2</google.gson.version>
-		<solr.version>7.5.0</solr.version>
+        <log4j.version>1.2.17</log4j.version>
-		<okhttp.version>4.7.2</okhttp.version>
+        <javassist.version>3.19.0-GA</javassist.version>
-		<common.compress.version>1.20</common.compress.version>
         <json4s.version>3.5.3</json4s.version>
         <jsonschemagenerator.version>4.13.0</jsonschemagenerator.version>
-		<common.csv.version>1.8</common.csv.version>
+        <junit-jupiter.version>5.6.1</junit-jupiter.version>
-		<apache.poi.version>4.1.2</apache.poi.version>
+        <mockito-core.version>3.3.3</mockito-core.version>
-		<common.text.version>1.8</common.text.version>
+        <mongodb.driver.version>3.4.2</mongodb.driver.version>
+        <okhttp.version>4.7.2</okhttp.version>
         <org.apache.httpcomponents.version>4.5.3</org.apache.httpcomponents.version>
-		<net.alchim31.maven.version>4.0.1</net.alchim31.maven.version>
+        <org.slf4j.version>1.7.25</org.slf4j.version>
-		<google.gson.version>2.2.2</google.gson.version>
+        <reflections.version>0.9.10</reflections.version>
-		<commons.logging.version>1.1.3</commons.logging.version>
+        <scala-xml.version>1.3.0</scala-xml.version>
-		<commons.collections.version>3.2.1</commons.collections.version>
+        <solr.version>7.5.0</solr.version>
+        <sparksolr.version>3.6.0</sparksolr.version>
+        <unidecode.version>0.0.7</unidecode.version>
+        <vtd.version>[2.12,3.0)</vtd.version>
+        <zookeeper.version>3.4.6</zookeeper.version>
     </properties>
 
     <!-- Build with scala 12 and Spark 3.4 -->
     <profiles>
         <profile>
-			<id>scala-2.12</id>
+            <id>spark-34</id>
             <properties>
                 <scala.binary.version>2.12</scala.binary.version>
                 <scala.version>2.12.18</scala.version>
-				<!-- scala-xml.version>2.1.0</scala-xml.version -->
+                <scala-xml.version>1.3.0</scala-xml.version>
 
-
+                <!-- plugin versions -->
-				<sparksolr.version>4.0.2</sparksolr.version>
-				<dhp.spark.version>3.4.1</dhp.spark.version>
-				<dhp.jackson.version>2.14.2</dhp.jackson.version>
-				<dhp.commons.lang.version>3.12.0</dhp.commons.lang.version>
-				<json4s.version>3.7.0-M11</json4s.version>
                 <net.alchim31.maven.version>4.8.1</net.alchim31.maven.version>
 
-				<!--
+                <!-- dependencies -->
-				<dhp-schemas.artifact>dhp-schemas_${scala.binary.version}</dhp-schemas.artifact>
+                <common.compress.version>1.22</common.compress.version>
-				<dhp-schemas.version>3.17.2-SNAPSHOT</dhp-schemas.version>
+                <common.csv.version>1.8</common.csv.version>
-				 -->
+                <common.text.version>1.10.0</common.text.version>
+                <commons-beanutils.version>1.9.4</commons-beanutils.version>
+                <commons-codec.version>1.15</commons-codec.version>
+                <commons.collections.version>3.2.2</commons.collections.version>
+                <commons-io.version>2.11.0</commons-io.version>
+                <commons.logging.version>1.1.3</commons.logging.version>
+                <commons-validator.version>1.7</commons-validator.version>
+
+                <dhp.guava.version>14.0.1</dhp.guava.version>
+                <solr.version>8.11.0</solr.version>
+                <sparksolr.version>4.0.4</sparksolr.version>
+                <dhp.spark.version>3.4.2.openaire</dhp.spark.version>
+                <dhp.jackson.version>2.14.2</dhp.jackson.version>
+                <dhp.commons.lang.version>3.12.0</dhp.commons.lang.version>
+                <log4j.version>2.19.0</log4j.version>
+                <json4s.version>3.7.0-M11</json4s.version>
+                <javassist.version>3.25.0-GA</javassist.version>
+                <okhttp.version>4.10.0</okhttp.version>
+                <org.slf4j.version>2.0.6</org.slf4j.version>
+                <reflections.version>0.10.2</reflections.version>
+                <zookeeper.version>3.6.3</zookeeper.version>
             </properties>
         </profile>
 
-		<!-- Activate ARM-compatible snappy dependency on new Silicon Macs -->
         <profile>
-			<id>arm-silicon-mac</id>
+            <id>spark-35</id>
+            <properties>
+                <scala.binary.version>2.12</scala.binary.version>
+                <scala.version>2.12.18</scala.version>
+                <scala-xml.version>1.3.0</scala-xml.version>
+
+                <!-- plugin versions -->
+                <net.alchim31.maven.version>4.8.1</net.alchim31.maven.version>
+
+                <!-- dependencies -->
+                <common.compress.version>1.23.0</common.compress.version>
+                <common.csv.version>1.8</common.csv.version>
+                <common.text.version>1.10.0</common.text.version>
+                <commons-beanutils.version>1.9.4</commons-beanutils.version>
+                <commons-codec.version>1.16.0</commons-codec.version>
+                <commons.collections.version>3.2.2</commons.collections.version>
+                <commons-io.version>2.13.0</commons-io.version>
+                <commons.logging.version>1.1.3</commons.logging.version>
+                <commons-validator.version>1.7</commons-validator.version>
+
+                <dhp.guava.version>14.0.1</dhp.guava.version>
+                <solr.version>8.11.0</solr.version>
+                <sparksolr.version>4.0.4</sparksolr.version>
+                <dhp.spark.version>3.5.1.openaire-SNAPSHOT</dhp.spark.version>
+                <dhp.jackson.version>2.15.2</dhp.jackson.version>
+                <dhp.commons.lang.version>3.12.0</dhp.commons.lang.version>
+                <log4j.version>2.20.0</log4j.version>
+                <json4s.version>3.7.0-M11</json4s.version>
+                <javassist.version>3.25.0-GA</javassist.version>
+                <okhttp.version>4.10.0</okhttp.version>
+                <org.slf4j.version>2.0.7</org.slf4j.version>
+                <reflections.version>0.10.2</reflections.version>
+                <zookeeper.version>3.6.3</zookeeper.version>
+            </properties>
+        </profile>
+
+        <profile>
+            <id>java11</id>
             <activation>
-				<os>
+                <jdk>[11</jdk>
-					<arch>aarch64</arch>
-					<family>mac</family>
-				</os>
             </activation>
-			<dependencyManagement>
+            <build>
-				<dependencies>
+                <pluginManagement>
-					<dependency>
+                    <plugins>
-						<groupId>org.xerial.snappy</groupId>
+                        <plugin>
-						<artifactId>snappy-java</artifactId>
+                            <groupId>org.apache.maven.plugins</groupId>
-						<version>1.1.8.4</version>
+                            <artifactId>maven-surefire-plugin</artifactId>
-					</dependency>
+                            <version>3.0.0-M4</version>
-				</dependencies>
+                            <configuration>
-			</dependencyManagement>
+                                <!-- only for java 11+ to run spark in tests -->
+                                <argLine>--add-opens=java.base/java.lang=ALL-UNNAMED
+                                    --add-opens=java.base/java.lang.invoke=ALL-UNNAMED
+                                    --add-opens=java.base/java.lang.reflect=ALL-UNNAMED
+                                    --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED
+                                    --add-opens=java.base/java.nio=ALL-UNNAMED
+                                    --add-opens=java.base/java.util=ALL-UNNAMED
+                                    --add-opens=java.base/java.util.concurrent=ALL-UNNAMED
+                                    --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED
+                                    --add-opens=java.base/sun.nio.ch=ALL-UNNAMED
+                                    --add-opens=java.base/sun.nio.cs=ALL-UNNAMED
+                                    --add-opens=java.base/sun.security.action=ALL-UNNAMED
+                                    --add-opens=java.base/sun.util.calendar=ALL-UNNAMED
+                                </argLine>
+                                <redirectTestOutputToFile>true</redirectTestOutputToFile>
+                                <trimStackTrace>false</trimStackTrace>
+                            </configuration>
+                        </plugin>
+                    </plugins>
+                </pluginManagement>
+            </build>
         </profile>
 	</profiles>
 </project>