merge branch with master

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

@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.common.api;
 
 import java.io.*;
 import java.io.IOException;
+import java.util.concurrent.TimeUnit;
 
 import com.google.gson.Gson;
 
@@ -92,7 +93,11 @@ public class ZenodoAPIClient implements Serializable {
 	 * @return the response code
 	 */
 	public int uploadIS(InputStream is, String file_name, long len) throws IOException {
-		OkHttpClient httpClient = new OkHttpClient();
+		OkHttpClient httpClient = new OkHttpClient
+				.Builder()
+				.connectTimeout(600, TimeUnit.SECONDS)
+				.readTimeout(600, TimeUnit.SECONDS)
+				.writeTimeout(600, TimeUnit.SECONDS).build();
 
 		Request request = new Request.Builder()
 			.url(bucket + "/" + file_name)

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/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/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/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)