Merge branch 'master' into stable_ids

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

@@ -94,7 +94,13 @@ public class AuthorMerger {
 							if (r.getPid() == null) {
 								r.setPid(new ArrayList<>());
 							}
-							r.getPid().add(a._1());
+
+							// TERRIBLE HACK but for some reason when we create and Array with Arrays.asList,
+							// it creates of fixed size, and the add method raise UnsupportedOperationException at
+							// java.util.AbstractList.add
+							final List<StructuredProperty> tmp = new ArrayList<>(r.getPid());
+							tmp.add(a._1());
+							r.setPid(tmp);
 						}
 					}
 				});

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

@@ -39,15 +39,15 @@ public class ModelConstants {
 	public static final String IS_SUPPLEMENT_TO = "isSupplementTo";
 	public static final String IS_SUPPLEMENTED_BY = "isSupplementedBy";
 	public static final String PART = "part";
-	public static final String IS_PART_OF = "IsPartOf";
+	public static final String IS_PART_OF = "isPartOf";
-	public static final String HAS_PARTS = "HasParts";
+	public static final String HAS_PARTS = "hasParts";
 	public static final String RELATIONSHIP = "relationship";
 	public static final String CITATION = "citation";
 	public static final String CITES = "cites";
-	public static final String IS_CITED_BY = "IsCitedBy";
+	public static final String IS_CITED_BY = "isCitedBy";
 	public static final String REVIEW = "review";
 	public static final String REVIEWS = "reviews";
-	public static final String IS_REVIEWED_BY = "IsReviewedBy";
+	public static final String IS_REVIEWED_BY = "isReviewedBy";
 
 	public static final String RESULT_PROJECT = "resultProject";
 	public static final String OUTCOME = "outcome";

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

@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.actionmanager.project;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.Optional;
 
@@ -11,6 +12,7 @@ import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.*;
 import org.slf4j.Logger;
@@ -175,43 +177,54 @@ public class PrepareProgramme {
 				return csvProgramme;
 			});
 
-		prepareClassification(h2020Programmes);
+		// prepareClassification(h2020Programmes);
 
-		h2020Programmes
+		JavaSparkContext jsc = new JavaSparkContext(spark.sparkContext());
-			.map(csvProgramme -> OBJECT_MAPPER.writeValueAsString(csvProgramme))
+
+		JavaRDD<CSVProgramme> rdd = jsc.parallelize(prepareClassification(h2020Programmes), 1);
+		rdd
+			.map(csvProgramme -> {
+				String tmp = OBJECT_MAPPER.writeValueAsString(csvProgramme);
+				return tmp;
+			})
 			.saveAsTextFile(outputPath);
 
 	}
 
-	private static void prepareClassification(JavaRDD<CSVProgramme> h2020Programmes) {
+	private static List<CSVProgramme> prepareClassification(JavaRDD<CSVProgramme> h2020Programmes) {
 		Object[] codedescription = h2020Programmes
-			.map(value -> new Tuple2<>(value.getCode(), value.getTitle()))
+			.map(
+				value -> new Tuple2<>(value.getCode(),
+					new Tuple2<String, String>(value.getTitle(), value.getShortTitle())))
 			.collect()
 			.toArray();
 
 		for (int i = 0; i < codedescription.length - 1; i++) {
 			for (int j = i + 1; j < codedescription.length; j++) {
-				Tuple2<String, String> t2i = (Tuple2<String, String>) codedescription[i];
+				Tuple2<String, Tuple2<String, String>> t2i = (Tuple2<String, Tuple2<String, String>>) codedescription[i];
-				Tuple2<String, String> t2j = (Tuple2<String, String>) codedescription[j];
+				Tuple2<String, Tuple2<String, String>> t2j = (Tuple2<String, Tuple2<String, String>>) codedescription[j];
 				if (t2i._1().compareTo(t2j._1()) > 0) {
-					Tuple2<String, String> temp = t2i;
+					Tuple2<String, Tuple2<String, String>> temp = t2i;
 					codedescription[i] = t2j;
 					codedescription[j] = temp;
 				}
 			}
 		}
 
-		Map<String, String> map = new HashMap<>();
+		Map<String, Tuple2<String, String>> map = new HashMap<>();
 		for (int j = 0; j < codedescription.length; j++) {
-			Tuple2<String, String> entry = (Tuple2<String, String>) codedescription[j];
+			Tuple2<String, Tuple2<String, String>> entry = (Tuple2<String, Tuple2<String, String>>) codedescription[j];
 			String ent = entry._1();
 			if (ent.contains("Euratom-")) {
 				ent = ent.replace("-Euratom-", ".Euratom.");
 			}
 			String[] tmp = ent.split("\\.");
 			if (tmp.length <= 2) {
-				map.put(entry._1(), entry._2());
+				if (StringUtils.isEmpty(entry._2()._2())) {
-
+					map.put(entry._1(), new Tuple2<String, String>(entry._2()._1(), entry._2()._1()));
+				} else {
+					map.put(entry._1(), entry._2());
+				}
 			} else {
 				if (ent.endsWith(".")) {
 					ent = ent.substring(0, ent.length() - 1);
@@ -224,14 +237,14 @@ public class PrepareProgramme {
 						key = key.substring(0, key.length() - 1);
 					}
 				}
-				String current = entry._2();
+				String current = entry._2()._1();
 				if (!ent.contains("Euratom")) {
 
 					String parent;
 					String tmp_key = tmp[0] + ".";
 					for (int i = 1; i < tmp.length - 1; i++) {
 						tmp_key += tmp[i] + ".";
-						parent = map.get(tmp_key).toLowerCase().trim();
+						parent = map.get(tmp_key)._1().toLowerCase().trim();
 						if (parent.contains("|")) {
 							parent = parent.substring(parent.lastIndexOf("|") + 1).trim();
 						}
@@ -246,18 +259,29 @@ public class PrepareProgramme {
 					}
 
 				}
-				map.put(ent + ".", map.get(key) + " | " + current);
+				String shortTitle = entry._2()._2();
+				if (StringUtils.isEmpty(shortTitle)) {
+					shortTitle = current;
+				}
+				Tuple2<String, String> newEntry = new Tuple2<>(map.get(key)._1() + " | " + current,
+					map.get(key)._2() + " | " + shortTitle);
+				map.put(ent + ".", newEntry);
 
 			}
 
 		}
-		h2020Programmes.foreach(csvProgramme -> {
+		return h2020Programmes.map(csvProgramme -> {
-			if (!csvProgramme.getCode().endsWith(".") && !csvProgramme.getCode().contains("Euratom")
+
-				&& !csvProgramme.getCode().equals("H2020-EC"))
+			String code = csvProgramme.getCode();
-				csvProgramme.setClassification(map.get(csvProgramme.getCode() + "."));
+			if (!code.endsWith(".") && !code.contains("Euratom")
-			else
+				&& !code.equals("H2020-EC"))
-				csvProgramme.setClassification(map.get(csvProgramme.getCode()));
+				code += ".";
-		});
+
+			csvProgramme.setClassification(map.get(code)._1());
+			csvProgramme.setClassification_short(map.get(code)._2());
+
+			return csvProgramme;
+		}).collect();
 	}
 
 	public static <R> Dataset<R> readPath(

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

@@ -9,7 +9,6 @@ import java.util.Objects;
 import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
@@ -138,7 +137,8 @@ public class SparkAtomicActionJob {
 						pm.setCode(csvProject.getProgramme());
 						h2020classification.setClassification(ocsvProgramme.get().getClassification());
 						h2020classification.setH2020Programme(pm);
-						setLevelsAndProgramme(h2020classification, ocsvProgramme.get().getClassification());
+						setLevelsandProgramme(h2020classification, ocsvProgramme.get().getClassification_short());
+						// setProgramme(h2020classification, ocsvProgramme.get().getClassification());
 						pp.setH2020classification(Arrays.asList(h2020classification));
 
 						return pp;
@@ -177,8 +177,8 @@ public class SparkAtomicActionJob {
 
 	}
 
-	private static void setLevelsAndProgramme(H2020Classification h2020Classification, String classification) {
+	private static void setLevelsandProgramme(H2020Classification h2020Classification, String classification_short) {
-		String[] tmp = classification.split(" \\| ");
+		String[] tmp = classification_short.split(" \\| ");
 		h2020Classification.setLevel1(tmp[0]);
 		if (tmp.length > 1) {
 			h2020Classification.setLevel2(tmp[1]);
@@ -189,6 +189,12 @@ public class SparkAtomicActionJob {
 		h2020Classification.getH2020Programme().setDescription(tmp[tmp.length - 1]);
 	}
 
+//	private static void setProgramme(H2020Classification h2020Classification, String classification) {
+//		String[] tmp = classification.split(" \\| ");
+//
+//		h2020Classification.getH2020Programme().setDescription(tmp[tmp.length - 1]);
+//	}
+
 	public static <R> Dataset<R> readPath(
 		SparkSession spark, String inputPath, Class<R> clazz) {
 		return spark

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

@@ -22,6 +22,15 @@ public class CSVProgramme implements Serializable {
 	private String shortTitle;
 	private String language;
 	private String classification;
+	private String classification_short;
+
+	public String getClassification_short() {
+		return classification_short;
+	}
+
+	public void setClassification_short(String classification_short) {
+		this.classification_short = classification_short;
+	}
 
 	public String getClassification() {
 		return classification;

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java

@@ -9,12 +9,14 @@ import java.util.List;
 import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
 import eu.dnetlib.dhp.actionmanager.project.httpconnector.CollectorServiceException;
 import eu.dnetlib.dhp.actionmanager.project.httpconnector.HttpConnector;
 import eu.dnetlib.dhp.actionmanager.project.utils.EXCELParser;
 
+@Disabled
 public class EXCELParserTest {
 
 	private static Path workingDir;

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareH2020ProgrammeTest.java

@@ -92,6 +92,8 @@ public class PrepareH2020ProgrammeTest {
 
 		Assertions.assertEquals(0, verificationDataset.filter("classification = ''").count());
 
+		// tmp.foreach(csvProgramme -> System.out.println(OBJECT_MAPPER.writeValueAsString(csvProgramme)));
+
 		Assertions
 			.assertEquals(
 				"Societal challenges | Smart, Green And Integrated Transport | CLEANSKY2 | IADP Fast Rotorcraft",

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java

@@ -78,7 +78,7 @@ public class SparkUpdateProjectTest {
 					"-programmePath",
 					getClass()
 						.getResource(
-							"/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_classification_whole.json.gz")
+							"/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_whole.json.gz")
 						.getPath(),
 					"-projectPath",
 					getClass().getResource("/eu/dnetlib/dhp/actionmanager/project/prepared_projects.json").getPath(),
@@ -124,7 +124,7 @@ public class SparkUpdateProjectTest {
 					.getString(0));
 		Assertions
 			.assertEquals(
-				"Societal challenges",
+				"Societal Challenges",
 				execverification
 					.filter("id = '40|corda__h2020::2c7298913008865ba784e5c1350a0aa5'")
 					.select("classification.level1")
@@ -133,7 +133,7 @@ public class SparkUpdateProjectTest {
 					.getString(0));
 		Assertions
 			.assertEquals(
-				"Smart, Green And Integrated Transport",
+				"Transport",
 				execverification
 					.filter("id = '40|corda__h2020::2c7298913008865ba784e5c1350a0aa5'")
 					.select("classification.level2")
@@ -188,7 +188,7 @@ public class SparkUpdateProjectTest {
 					.getString(0));
 		Assertions
 			.assertEquals(
-				"Nurturing excellence by means of cross-border and cross-sector mobility",
+				"MSCA Mobility",
 				execverification
 					.filter("id = '40|corda__h2020::1a1f235fdd06ef14790baec159aa1202'")
 					.select("classification.h2020Programme.description")
@@ -197,7 +197,7 @@ public class SparkUpdateProjectTest {
 					.getString(0));
 		Assertions
 			.assertEquals(
-				"Excellent science",
+				"Excellent Science",
 				execverification
 					.filter("id = '40|corda__h2020::1a1f235fdd06ef14790baec159aa1202'")
 					.select("classification.level1")
@@ -206,7 +206,7 @@ public class SparkUpdateProjectTest {
 					.getString(0));
 		Assertions
 			.assertEquals(
-				"Marie Skłodowska-Curie Actions",
+				"Marie-Sklodowska-Curie Actions",
 				execverification
 					.filter("id = '40|corda__h2020::1a1f235fdd06ef14790baec159aa1202'")
 					.select("classification.level2")
@@ -215,7 +215,7 @@ public class SparkUpdateProjectTest {
 					.getString(0));
 		Assertions
 			.assertEquals(
-				"Nurturing excellence by means of cross-border and cross-sector mobility",
+				"MSCA Mobility",
 				execverification
 					.filter("id = '40|corda__h2020::1a1f235fdd06ef14790baec159aa1202'")
 					.select("classification.level3")

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java

@@ -6,8 +6,11 @@ import org.apache.commons.logging.LogFactory;
 import org.apache.http.conn.ssl.SSLConnectionSocketFactory;
 import org.apache.http.ssl.SSLContextBuilder;
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
+
+@Disabled
 public class HttpConnectorTest {
 
 	private static final Log log = LogFactory.getLog(HttpConnectorTest.class);

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

@@ -1,13 +1,15 @@
 package eu.dnetlib.doiboost
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset, Organization}
+import eu.dnetlib.dhp.oa.merge.AuthorMerger
+import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset}
 import eu.dnetlib.doiboost.mag.ConversionUtil
 import org.apache.commons.io.IOUtils
 import org.apache.spark.SparkConf
 import org.apache.spark.sql.functions.col
 import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
 import org.slf4j.{Logger, LoggerFactory}
+
 import scala.collection.JavaConverters._
 
 object SparkGenerateDoiBoost {
@@ -49,6 +51,7 @@ object SparkGenerateDoiBoost {
         val otherPub = item._2._2
         if (otherPub != null) {
           crossrefPub.mergeFrom(otherPub)
+          crossrefPub.setAuthor(AuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor))
         }
       }
       crossrefPub

dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/QueryTest.scala

@@ -38,6 +38,8 @@ class QueryTest {
   def myQuery(spark:SparkSession, sc:SparkContext): Unit = {
     implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
 
+
+
     val mapper = new ObjectMapper()
     mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
 

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

@@ -4,7 +4,6 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation}
 import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIUnknown}
 import eu.dnetlib.dhp.sx.ebi.EBIAggregator
-import eu.dnetlib.dhp.sx.ebi.model.{PMArticle, PMAuthor, PMJournal}
 import org.apache.commons.io.IOUtils
 import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
 import org.slf4j.LoggerFactory
@@ -18,38 +17,38 @@ object SparkSplitOafTODLIEntities {
 
   }
 
-  def main(args: Array[String]): Unit = {
-    val parser = new ArgumentApplicationParser(IOUtils.toString(SparkSplitOafTODLIEntities.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json")))
-    val logger = LoggerFactory.getLogger(SparkSplitOafTODLIEntities.getClass)
-    parser.parseArgument(args)
 
-    val workingPath: String = parser.get("workingPath")
+  def extract_dataset(spark:SparkSession, workingPath:String) :Unit = {
-    logger.info(s"Working dir path = $workingPath")
+
+    implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
+    implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo[DLIDataset]
+
+    val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf].repartition(4000)
+
+    val ebi_dataset:Dataset[DLIDataset] = spark.read.load(s"$workingPath/ebi/baseline_dataset_ebi").as[DLIDataset].repartition(1000)
+
+
+    OAFDataset
+      .filter(s => s != null && s.isInstanceOf[DLIDataset])
+      .map(s =>s.asInstanceOf[DLIDataset])
+      .union(ebi_dataset)
+      .map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, datEncoder))
+      .groupByKey(_._1)(Encoders.STRING)
+      .agg(EBIAggregator.getDLIDatasetAggregator().toColumn)
+      .map(p => p._2)
+      .repartition(2000)
+      .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/dataset")
+
+  }
+
+  def extract_publication(spark:SparkSession, workingPath:String) :Unit = {
 
     implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
     implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo[DLIPublication]
-    implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo[DLIDataset]
-    implicit val unkEncoder: Encoder[DLIUnknown] = Encoders.kryo[DLIUnknown]
-    implicit val relEncoder: Encoder[Relation] = Encoders.kryo[Relation]
-
-
-
-    val spark:SparkSession  = SparkSession
-      .builder()
-      .appName(SparkSplitOafTODLIEntities.getClass.getSimpleName)
-      .config("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
-      .master(parser.get("master"))
-      .getOrCreate()
-
-
-
 
     val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf]
 
-    val ebi_dataset:Dataset[DLIDataset] = spark.read.load(s"$workingPath/ebi/baseline_dataset_ebi").as[DLIDataset]
+    val ebi_publication:Dataset[DLIPublication] = spark.read.load(s"$workingPath/ebi/baseline_publication_ebi").as[DLIPublication].repartition(1000)
-    val ebi_publication:Dataset[DLIPublication] = spark.read.load(s"$workingPath/ebi/baseline_publication_ebi").as[DLIPublication]
-    val ebi_relation:Dataset[Relation] = spark.read.load(s"$workingPath/ebi/baseline_relation_ebi").as[Relation]
-
 
 
     OAFDataset
@@ -60,20 +59,17 @@ object SparkSplitOafTODLIEntities {
       .groupByKey(_._1)(Encoders.STRING)
       .agg(EBIAggregator.getDLIPublicationAggregator().toColumn)
       .map(p => p._2)
-      .repartition(1000)
+      .repartition(2000)
       .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/publication")
 
-    OAFDataset
+  }
-      .filter(s => s != null && s.isInstanceOf[DLIDataset])
-      .map(s =>s.asInstanceOf[DLIDataset])
-      .union(ebi_dataset)
-      .map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, datEncoder))
-      .groupByKey(_._1)(Encoders.STRING)
-      .agg(EBIAggregator.getDLIDatasetAggregator().toColumn)
-      .map(p => p._2)
-      .repartition(1000)
-      .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/dataset")
 
+  def extract_unknown(spark:SparkSession, workingPath:String) :Unit = {
+
+    implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
+    implicit val unkEncoder: Encoder[DLIUnknown] = Encoders.kryo[DLIUnknown]
+
+    val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf]
 
     OAFDataset
       .filter(s => s != null && s.isInstanceOf[DLIUnknown])
@@ -82,9 +78,18 @@ object SparkSplitOafTODLIEntities {
       .groupByKey(_._1)(Encoders.STRING)
       .agg(EBIAggregator.getDLIUnknownAggregator().toColumn)
       .map(p => p._2)
-      .repartition(1000)
       .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/unknown")
 
+  }
+
+
+  def extract_relations(spark:SparkSession, workingPath:String) :Unit = {
+
+    implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
+    implicit val relEncoder: Encoder[Relation] = Encoders.kryo[Relation]
+
+    val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf]
+    val ebi_relation:Dataset[Relation] = spark.read.load(s"$workingPath/ebi/baseline_relation_ebi").as[Relation].repartition(2000)
 
     OAFDataset
       .filter(s => s != null && s.isInstanceOf[Relation])
@@ -94,9 +99,35 @@ object SparkSplitOafTODLIEntities {
       .groupByKey(_._1)(Encoders.STRING)
       .agg(EBIAggregator.getRelationAggregator().toColumn)
       .map(p => p._2)
-      .repartition(1000)
+      .repartition(4000)
       .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/relation")
 
+  }
+
+
+  def main(args: Array[String]): Unit = {
+    val parser = new ArgumentApplicationParser(IOUtils.toString(SparkSplitOafTODLIEntities.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json")))
+    val logger = LoggerFactory.getLogger(SparkSplitOafTODLIEntities.getClass)
+    parser.parseArgument(args)
+
+    val workingPath: String = parser.get("workingPath")
+    val entity:String = parser.get("entity")
+    logger.info(s"Working dir path = $workingPath")
+
+    val spark:SparkSession  = SparkSession
+      .builder()
+      .appName(SparkSplitOafTODLIEntities.getClass.getSimpleName)
+      .config("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
+      .master(parser.get("master"))
+      .getOrCreate()
+
+
+    entity match {
+      case "publication" => extract_publication(spark, workingPath)
+      case "dataset" => extract_dataset(spark,workingPath)
+      case "relation" => extract_relations(spark, workingPath)
+      case "unknown" => extract_unknown(spark, workingPath)
+    }
 
 
 

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

@@ -1,4 +1,5 @@
 [
   {"paramName":"mt",  "paramLongName":"master",       "paramDescription": "should be local or yarn",  "paramRequired": true},
-  {"paramName":"w",   "paramLongName":"workingPath",  "paramDescription": "the work dir path",        "paramRequired": true}
+  {"paramName":"w",   "paramLongName":"workingPath",  "paramDescription": "the work dir path",        "paramRequired": true},
+  {"paramName":"e",   "paramLongName":"entity",       "paramDescription": "the work dir path",        "paramRequired": true}
 ]

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml

@@ -14,30 +14,103 @@
         </property>
     </parameters>
 
-    <start to="ExtractDLIEntities"/>
+    <start to="ExtractDLIPublication"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
-    <action name="ExtractDLIEntities">
+    <action name="ExtractDLIPublication">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <master>yarn-cluster</master>
             <mode>cluster</mode>
-            <name>Extract DLI Entities</name>
+            <name>Extract DLI Entities (Publication)</name>
             <class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
             <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
             <spark-opts>
                 --executor-memory ${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=5000
                 ${sparkExtraOPT}
             </spark-opts>
             <arg>-mt</arg> <arg>yarn-cluster</arg>
             <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>-e</arg><arg>publication</arg>
+        </spark>
+        <ok to="ExtractDLIDataset"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="ExtractDLIDataset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Extract DLI Entities (Dataset)</name>
+            <class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory ${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=5000
+                ${sparkExtraOPT}
+            </spark-opts>
+            <arg>-mt</arg> <arg>yarn-cluster</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>-e</arg><arg>dataset</arg>
+        </spark>
+        <ok to="ExtractDLIUnknown"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="ExtractDLIUnknown">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Extract DLI Entities (Unknown)</name>
+            <class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory ${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=5000
+                ${sparkExtraOPT}
+            </spark-opts>
+            <arg>-mt</arg> <arg>yarn-cluster</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>-e</arg><arg>unknown</arg>
+        </spark>
+        <ok to="ExtractDLIRelation"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="ExtractDLIRelation">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Extract DLI Entities (Relation)</name>
+            <class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory ${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=5000
+                ${sparkExtraOPT}
+            </spark-opts>
+            <arg>-mt</arg> <arg>yarn-cluster</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>-e</arg><arg>relation</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerAggregationTest.scala

@@ -30,7 +30,7 @@ class SparkScholexplorerAggregationTest {
 
 
     implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo[DLIPublication]
-    val spark: SparkSession = SparkSession.builder().appName("Test").master("local[*]").getOrCreate()
+    val spark: SparkSession = SparkSession.builder().appName("Test").master("local[*]").config("spark.driver.bindAddress", "127.0.0.1").getOrCreate()
 
 
     val ds: Dataset[DLIPublication] = spark.createDataset(spark.sparkContext.parallelize(s)).as[DLIPublication]

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

@@ -62,6 +62,10 @@
             <artifactId>dhp-schemas</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.apache.httpcomponents</groupId>
+            <artifactId>httpmime</artifactId>
+        </dependency>
 
         <dependency>
             <groupId>org.elasticsearch</groupId>

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/zenodo/MakeTar.java

@@ -0,0 +1,111 @@
+
+package eu.dnetlib.dhp.export.zenodo;
+
+import java.io.*;
+
+import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
+import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+
+public class MakeTar implements Serializable {
+
+	private static final Logger log = LoggerFactory.getLogger(MakeTar.class);
+
+	public static void main(String[] args) throws Exception {
+		String jsonConfiguration = IOUtils
+			.toString(
+				MakeTar.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/export/input_maketar_parameters.json"));
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+		parser.parseArgument(args);
+
+		final String outputPath = parser.get("targetPath");
+		log.info("hdfsPath: {}", outputPath);
+
+		final String hdfsNameNode = parser.get("nameNode");
+		log.info("nameNode: {}", hdfsNameNode);
+
+		final String inputPath = parser.get("sourcePath");
+		log.info("input path : {}", inputPath);
+
+		Configuration conf = new Configuration();
+		conf.set("fs.defaultFS", hdfsNameNode);
+
+		FileSystem fileSystem = FileSystem.get(conf);
+
+		makeTArArchive(fileSystem, inputPath, outputPath);
+
+	}
+
+	public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath) throws IOException {
+
+		RemoteIterator<LocatedFileStatus> dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath));
+
+		while (dir_iterator.hasNext()) {
+			LocatedFileStatus fileStatus = dir_iterator.next();
+
+			Path p = fileStatus.getPath();
+			String p_string = p.toString();
+			String entity = p_string.substring(p_string.lastIndexOf("/") + 1);
+
+			write(fileSystem, p_string, outputPath + "/" + entity + ".tar", entity);
+		}
+
+	}
+
+	private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name)
+		throws IOException {
+
+		Path hdfsWritePath = new Path(outputPath);
+		FSDataOutputStream fsDataOutputStream = null;
+		if (fileSystem.exists(hdfsWritePath)) {
+			fileSystem.delete(hdfsWritePath, true);
+
+		}
+		fsDataOutputStream = fileSystem.create(hdfsWritePath);
+
+		TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
+
+		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
+			.listFiles(
+				new Path(inputPath), true);
+
+		while (fileStatusListIterator.hasNext()) {
+			LocatedFileStatus fileStatus = fileStatusListIterator.next();
+
+			Path p = fileStatus.getPath();
+			String p_string = p.toString();
+			if (!p_string.endsWith("_SUCCESS")) {
+				String name = p_string.substring(p_string.lastIndexOf("/") + 1);
+				TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name + ".json.gz");
+				entry.setSize(fileStatus.getLen());
+				ar.putArchiveEntry(entry);
+
+				InputStream is = fileSystem.open(fileStatus.getPath());
+
+				BufferedInputStream bis = new BufferedInputStream(is);
+
+				int count;
+				byte data[] = new byte[1024];
+				while ((count = bis.read(data, 0, data.length)) != -1) {
+					ar.write(data, 0, count);
+				}
+				bis.close();
+				ar.closeArchiveEntry();
+
+			}
+
+		}
+
+		ar.close();
+	}
+
+}

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/zenodo/SendToZenodoHDFS.java

@@ -0,0 +1,80 @@
+
+package eu.dnetlib.dhp.export.zenodo;
+
+import java.io.Serializable;
+import java.util.Optional;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.*;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.api.MissingConceptDoiException;
+import eu.dnetlib.dhp.common.api.ZenodoAPIClient;
+
+public class SendToZenodoHDFS implements Serializable {
+
+	private static final Log log = LogFactory.getLog(SendToZenodoHDFS.class);
+
+	public static void main(final String[] args) throws Exception, MissingConceptDoiException {
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					SendToZenodoHDFS.class
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/export/upload_zenodo.json")));
+
+		parser.parseArgument(args);
+
+		final String hdfsPath = parser.get("hdfsPath");
+		final String hdfsNameNode = parser.get("nameNode");
+		final String access_token = parser.get("accessToken");
+		final String connection_url = parser.get("connectionUrl");
+		final String metadata = parser.get("metadata");
+		final Boolean newDeposition = Boolean.valueOf(parser.get("newDeposition"));
+		final String concept_rec_id = Optional
+			.ofNullable(parser.get("conceptRecordId"))
+			.orElse(null);
+
+		Configuration conf = new Configuration();
+		conf.set("fs.defaultFS", hdfsNameNode);
+
+		FileSystem fileSystem = FileSystem.get(conf);
+
+		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
+			.listFiles(
+				new Path(hdfsPath), true);
+		ZenodoAPIClient zenodoApiClient = new ZenodoAPIClient(connection_url, access_token);
+		if (newDeposition) {
+			zenodoApiClient.newDeposition();
+		} else {
+			if (concept_rec_id == null) {
+				throw new MissingConceptDoiException("No concept record id has been provided");
+			}
+			zenodoApiClient.newVersion(concept_rec_id);
+		}
+
+		while (fileStatusListIterator.hasNext()) {
+			LocatedFileStatus fileStatus = fileStatusListIterator.next();
+
+			Path p = fileStatus.getPath();
+			String p_string = p.toString();
+			if (!p_string.endsWith("_SUCCESS")) {
+				// String tmp = p_string.substring(0, p_string.lastIndexOf("/"));
+				String name = p_string.substring(p_string.lastIndexOf("/") + 1);
+				log.info("Sending information for community: " + name);
+				FSDataInputStream inputStream = fileSystem.open(p);
+				zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen());
+
+			}
+
+		}
+
+		zenodoApiClient.sendMretadata(metadata);
+		zenodoApiClient.publish();
+
+	}
+
+}

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/input_maketar_parameters.json

@@ -0,0 +1,20 @@
+[
+  {
+    "paramName": "n",
+    "paramLongName": "nameNode",
+    "paramDescription": "the Name Node",
+    "paramRequired": true
+  },
+  {
+    "paramName": "s",
+    "paramLongName": "sourcePath",
+    "paramDescription": "the source path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "t",
+    "paramLongName": "targetPath",
+    "paramDescription": "the target path",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/upload_zenodo.json

@@ -0,0 +1,45 @@
+
+[
+  {
+    "paramName":"nd",
+    "paramLongName":"newDeposition",
+    "paramDescription": "if it is a new deposition (true) or a new version (false)",
+    "paramRequired": true
+  },
+  {
+    "paramName":"cri",
+    "paramLongName":"conceptRecordId",
+    "paramDescription": "The id of the concept record for a new version",
+    "paramRequired": false
+  },
+  {
+    "paramName":"hdfsp",
+    "paramLongName":"hdfsPath",
+    "paramDescription": "the path of the folder tofind files to send to Zenodo",
+    "paramRequired": true
+  },
+  {
+    "paramName": "nn",
+    "paramLongName": "nameNode",
+    "paramDescription": "the name node",
+    "paramRequired": true
+  },
+  {
+    "paramName": "at",
+    "paramLongName": "accessToken",
+    "paramDescription": "the access token for the deposition",
+    "paramRequired": false
+  },
+  {
+    "paramName":"cu",
+    "paramLongName":"connectionUrl",
+    "paramDescription": "the url to connect to deposit",
+    "paramRequired": false
+  },
+  {
+    "paramName":"m",
+    "paramLongName":"metadata",
+    "paramDescription": "metadata associated to the deposition",
+    "paramRequired": false
+  }
+]

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/sx/zenodo/oozie_app/config-default.xml

@@ -0,0 +1,48 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+    <property>
+        <name>oozie.wf.rerun.failnodes</name>
+        <value>false</value>
+    </property>
+    <property>
+        <name>hive_metastore_uris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>spark2YarnHistoryServerAddress</name>
+        <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
+    </property>
+    <property>
+        <name>spark2EventLogDir</name>
+        <value>/user/spark/spark2ApplicationHistory</value>
+    </property>
+    <property>
+        <name>spark2ExtraListeners</name>
+        <value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
+    </property>
+    <property>
+        <name>spark2SqlQueryExecutionListeners</name>
+        <value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
+    </property>
+
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+
+</configuration>

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/sx/zenodo/oozie_app/workflow.xml

@@ -0,0 +1,53 @@
+<workflow-app name="Send Dump to Zenodo" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>sourcePath</name>
+            <description>the source path</description>
+        </property>
+        <property>
+            <name>targetPath</name>
+            <description>the target path</description>
+        </property>
+        <property>
+            <name>metadata</name>
+            <description>the metadata</description>
+        </property>
+    </parameters>
+
+    <start to="send_zenodo"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="MakeTar">
+        <java>
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <main-class>eu.dnetlib.dhp.export.zenodo.MakeTar</main-class>
+            <arg>-t</arg><arg>${targetPath}</arg>
+            <arg>-n</arg><arg>${nameNode}</arg>
+            <arg>-s</arg><arg>${sourcePath}</arg>
+        </java>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+
+    <action name="send_zenodo">
+        <java>
+            <main-class>eu.dnetlib.dhp.export.zenodo.SendToZenodoHDFS</main-class>
+            <arg>--hdfsPath</arg><arg>/user/dnet.scholexplorer/scholix/provision/scholix.tar/scholix-2020-10-16.tar</arg>
+            <arg>--nameNode</arg><arg>${nameNode}</arg>
+            <arg>--accessToken</arg><arg>b6ddrY6b77WxcDEevn9gqVE5sL5sDNjdUijt75W3o7cQo5vpFFI48dMiu8Gv</arg>
+            <arg>--connectionUrl</arg><arg>https://zenodo.org/api/deposit/depositions</arg>
+            <arg>--metadata</arg><arg>${metadata}</arg>
+            <arg>--conceptRecordId</arg><arg>1200252</arg>
+            <arg>--newDeposition</arg><arg>false</arg>
+        </java>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>

dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala

@@ -3,14 +3,15 @@ package eu.dnetlib.dhp.export
 import java.time.LocalDateTime
 import java.time.format.DateTimeFormatter
 
+import eu.dnetlib.dhp.provision.scholix.Scholix
+import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary
 import eu.dnetlib.dhp.schema.oaf.Relation
 import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication}
-
 import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
 import org.junit.jupiter.api.Test
 
 import scala.io.Source
-
+import scala.collection.JavaConverters._
 class ExportDLITOOAFTest {
 
   val mapper = new ObjectMapper()
@@ -22,12 +23,27 @@ class ExportDLITOOAFTest {
   }
 
 
+  def extractDatasources(s:Scholix):List[String]= {
+    s.getTarget.getCollectedFrom.asScala.map(c => c.getProvider.getName)(collection.breakOut)
+  }
+
+
+  def extractDatasources(s:ScholixSummary):List[String] = {
+
+    s.getDatasources.asScala.map(c => c.getDatasourceName)(collection.breakOut)
+
+
+  }
+
+
   @Test
   def testMappingRele():Unit = {
 
     val r:Relation = new Relation
     r.setSource("60|fbff1d424e045eecf24151a5fe3aa738")
     r.setTarget("50|dedup_wf_001::ec409f09e63347d4e834087fe1483877")
+    r.setRelType("IsReferencedBy")
+
 
     val r1 =DLIToOAF.convertDLIRelation(r)
     println(r1.getSource, r1.getTarget)