[Country Propagation] changed the logic to get the collectedfrom at the result level. To fix issue when no instance is created for a result that should have the country associated. Change the code to use spark instead of hive to prepare the data needed for the propagation step. Added new tests for the intermediate steps and new verification for the propagation itself

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/CountrySbs.java

@@ -22,4 +22,11 @@ public class CountrySbs implements Serializable {
 	public void setClassname(String classname) {
 		this.classname = classname;
 	}
+
+	public static CountrySbs newInstance(String classid, String classname) {
+		CountrySbs csbs = new CountrySbs();
+		csbs.classid = classid;
+		csbs.classname = classname;
+		return csbs;
+	}
 }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountry.java

@@ -22,4 +22,11 @@ public class DatasourceCountry implements Serializable {
 	public void setCountry(CountrySbs country) {
 		this.country = country;
 	}
+
+	public static DatasourceCountry newInstance(String dataSourceId, CountrySbs country) {
+		DatasourceCountry dsc = new DatasourceCountry();
+		dsc.dataSourceId = dataSourceId;
+		dsc.country = country;
+		return dsc;
+	}
 }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/EntityEntityRel.java

@@ -0,0 +1,32 @@
+
+package eu.dnetlib.dhp.countrypropagation;
+
+import java.io.Serializable;
+
+public class EntityEntityRel implements Serializable {
+	private String entity1Id;
+	private String entity2Id;
+
+	public static EntityEntityRel newInstance(String source, String target) {
+		EntityEntityRel dso = new EntityEntityRel();
+		dso.entity1Id = source;
+		dso.entity2Id = target;
+		return dso;
+	}
+
+	public String getEntity1Id() {
+		return entity1Id;
+	}
+
+	public void setEntity1Id(String entity1Id) {
+		this.entity1Id = entity1Id;
+	}
+
+	public String getEntity2Id() {
+		return entity2Id;
+	}
+
+	public void setEntity2Id(String entity2Id) {
+		this.entity2Id = entity2Id;
+	}
+}

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java

@@ -2,14 +2,17 @@
 package eu.dnetlib.dhp.countrypropagation;
 
 import static eu.dnetlib.dhp.PropagationConstant.*;
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.util.Arrays;
 import java.util.List;
-import java.util.stream.Collectors;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.ForeachFunction;
+import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SaveMode;
@@ -21,7 +24,9 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.Datasource;
 import eu.dnetlib.dhp.schema.oaf.Organization;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
 import eu.dnetlib.dhp.schema.oaf.Relation;
+import scala.Tuple2;
 
 /**
  * For the association of the country to the datasource The association is computed only for datasource of specific type
@@ -54,9 +59,8 @@ public class PrepareDatasourceCountryAssociation {
 		log.info("outputPath {}: ", outputPath);
 
 		SparkConf conf = new SparkConf();
-		conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
 
-		runWithSparkHiveSession(
+		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
 			spark -> {
@@ -77,40 +81,46 @@ public class PrepareDatasourceCountryAssociation {
 		String inputPath,
 		String outputPath) {
 
-		final String whitelisted = whitelist
+		// filtering of the datasource taking only the non deleted by inference and those with the allowed types or
-			.stream()
+		// whose id is in whitelist
-			.map(id -> " d.id = '" + id + "'")
+		Dataset<Datasource> datasource = readPath(spark, inputPath + "/datasource", Datasource.class)
-			.collect(Collectors.joining(" OR "));
+			.filter(
+				(FilterFunction<Datasource>) ds -> !ds.getDataInfo().getDeletedbyinference() &&
+					(allowedtypes.contains(ds.getDatasourcetype().getClassid()) ||
+						whitelist.contains(ds.getId())));
 
-		final String allowed = allowedtypes
+		// filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass
-			.stream()
+		Dataset<Relation> relation = readPath(spark, inputPath + "/relation", Relation.class)
-			.map(type -> " d.datasourcetype.classid = '" + type + "'")
+			.filter(
-			.collect(Collectors.joining(" OR "));
+				(FilterFunction<Relation>) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) &&
+					!rel.getDataInfo().getDeletedbyinference());
 
-		Dataset<Datasource> datasource = readPath(spark, inputPath + "/datasource", Datasource.class);
+		// filtering of the organization taking only the non deleted by inference and those with information about the
-		Dataset<Relation> relation = readPath(spark, inputPath + "/relation", Relation.class);
+		// country
-		Dataset<Organization> organization = readPath(spark, inputPath + "/organization", Organization.class);
+		Dataset<Organization> organization = readPath(spark, inputPath + "/organization", Organization.class)
+			.filter(
+				(FilterFunction<Organization>) o -> !o.getDataInfo().getDeletedbyinference() &&
+					o.getCountry().getClassid().length() > 0  &&
+						!o.getCountry().getClassid().equals(ModelConstants.UNKNOWN)) ;
 
-		datasource.createOrReplaceTempView("datasource");
+		// associated the datasource id with the id of the organization providing the datasource
-		relation.createOrReplaceTempView("relation");
+		Dataset<EntityEntityRel> dse = datasource
-		organization.createOrReplaceTempView("organization");
+			.joinWith(relation, datasource.col("id").equalTo(relation.col("source")))
+			.map(
+				(MapFunction<Tuple2<Datasource, Relation>, EntityEntityRel>) t2 -> EntityEntityRel
+					.newInstance(t2._2.getSource(), t2._2.getTarget()),
+				Encoders.bean(EntityEntityRel.class));
 
-		String query = "SELECT source dataSourceId, " +
+		// joins with the information stored in the organization dataset to associate the country to the datasource id
-			"named_struct('classid', country.classid, 'classname', country.classname) country " +
+		dse
-			"FROM datasource d " +
+			.joinWith(organization, dse.col("entity2Id").equalTo(organization.col("id")))
-			"JOIN relation rel " +
+			.map((MapFunction<Tuple2<EntityEntityRel, Organization>, DatasourceCountry>) t2 -> {
-			"ON d.id = rel.source " +
+				Qualifier country = t2._2.getCountry();
-			"JOIN organization o " +
+				return DatasourceCountry
-			"ON o.id = rel.target " +
+					.newInstance(
-			"WHERE rel.datainfo.deletedbyinference = false  " +
+						t2._1.getEntity1Id(),
-			"and lower(rel.relclass) = '" + ModelConstants.IS_PROVIDED_BY.toLowerCase() + "'" +
+						CountrySbs.newInstance(country.getClassid(), country.getClassname()));
-			"and o.datainfo.deletedbyinference = false  " +
+			}, Encoders.bean(DatasourceCountry.class))
-			"and length(o.country.classid) > 0 " +
-			"and (" + allowed + " or " + whitelisted + ")";
-
-		spark
-			.sql(query)
-			.as(Encoders.bean(DatasourceCountry.class))
 			.write()
 			.option("compression", "gzip")
 			.mode(SaveMode.Overwrite)

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java

@@ -3,14 +3,21 @@ package eu.dnetlib.dhp.countrypropagation;
 
 import static eu.dnetlib.dhp.PropagationConstant.*;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
 import java.util.Set;
 import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.api.java.function.MapGroupsFunction;
 import org.apache.spark.sql.*;
 import org.apache.spark.sql.Dataset;
 import org.slf4j.Logger;
@@ -23,14 +30,6 @@ import scala.Tuple2;
 public class PrepareResultCountrySet {
 	private static final Logger log = LoggerFactory.getLogger(PrepareResultCountrySet.class);
 
-	private static final String RESULT_COUNTRYSET_QUERY = "SELECT id resultId, collect_set(country) countrySet "
-		+ "FROM ( SELECT id, country "
-		+ "FROM datasource_country JOIN cfhb ON cf = dataSourceId "
-		+ "UNION ALL "
-		+ "SELECT id, country FROM datasource_country "
-		+ "JOIN cfhb ON hb = dataSourceId ) tmp "
-		+ "GROUP BY id";
-
 	public static void main(String[] args) throws Exception {
 		String jsonConfiguration = IOUtils
 			.toString(
@@ -45,6 +44,8 @@ public class PrepareResultCountrySet {
 		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
+		String workingPath = parser.get("workingPath");
+
 		String inputPath = parser.get("sourcePath");
 		log.info("inputPath: {}", inputPath);
 
@@ -60,9 +61,9 @@ public class PrepareResultCountrySet {
 		Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
 
 		SparkConf conf = new SparkConf();
-		conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
+		//conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
 
-		runWithSparkHiveSession(
+		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
 			spark -> {
@@ -72,6 +73,7 @@ public class PrepareResultCountrySet {
 					inputPath,
 					outputPath,
 					datasourcecountrypath,
+					workingPath,
 					resultClazz);
 			});
 	}
@@ -81,43 +83,63 @@ public class PrepareResultCountrySet {
 		String inputPath,
 		String outputPath,
 		String datasourcecountrypath,
+		String workingPath,
 		Class<R> resultClazz) {
 
-		Dataset<R> result = readPath(spark, inputPath, resultClazz);
+		// selects all the results non deleted by inference and non invisible
-		result.createOrReplaceTempView("result");
+		Dataset<R> result = readPath(spark, inputPath, resultClazz)
+			.filter(
+				(FilterFunction<R>) r -> !r.getDataInfo().getDeletedbyinference() &&
+					!r.getDataInfo().getInvisible());
 
-		createCfHbforResult(spark);
+		// of the results collects the distinct keys for collected from (at the level of the result) and hosted by
+		// and produces pairs resultId, key for each distinct key associated to the result
+		result.flatMap((FlatMapFunction<R, EntityEntityRel>) r -> {
+			Set<String> cfhb = r.getCollectedfrom().stream().map(cf -> cf.getKey()).collect(Collectors.toSet());
+			cfhb.addAll(r.getInstance().stream().map(i -> i.getHostedby().getKey()).collect(Collectors.toSet()));
+			return cfhb
+				.stream()
+				.map(value -> EntityEntityRel.newInstance(r.getId(), value))
+				.collect(Collectors.toList())
+				.iterator();
+		}, Encoders.bean(EntityEntityRel.class))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
+			.json(workingPath + "/resultCfHb");
 
 		Dataset<DatasourceCountry> datasource_country = readPath(spark, datasourcecountrypath, DatasourceCountry.class);
 
-		datasource_country.createOrReplaceTempView("datasource_country");
+		Dataset<EntityEntityRel> cfhb = readPath(spark, workingPath + "/resultCfHb", EntityEntityRel.class);
-
-		spark
-			.sql(RESULT_COUNTRYSET_QUERY)
-			.as(Encoders.bean(ResultCountrySet.class))
-			.toJavaRDD()
-			.mapToPair(value -> new Tuple2<>(value.getResultId(), value))
-			.reduceByKey((a, b) -> {
-				ArrayList<CountrySbs> countryList = a.getCountrySet();
-				Set<String> countryCodes = countryList
-					.stream()
-					.map(CountrySbs::getClassid)
-					.collect(Collectors.toSet());
-				b
-					.getCountrySet()
-					.stream()
-					.forEach(c -> {
-						if (!countryCodes.contains(c.getClassid())) {
-							countryList.add(c);
-							countryCodes.add(c.getClassid());
-						}
 
+		datasource_country
+			.joinWith(
+				cfhb, cfhb
+					.col("entity2Id")
+					.equalTo(datasource_country.col("datasourceId")))
+			.groupByKey(
+				(MapFunction<Tuple2<DatasourceCountry, EntityEntityRel>, String>) t2 -> t2._2().getEntity1Id(),
+				Encoders.STRING())
+			.mapGroups(
+				(MapGroupsFunction<String, Tuple2<DatasourceCountry, EntityEntityRel>, ResultCountrySet>) (k, it) -> {
+					ResultCountrySet rcs = new ResultCountrySet();
+					rcs.setResultId(k);
+					Set<CountrySbs> set = new HashSet<>();
+					Set<String> countryCodes = new HashSet<>();
+					DatasourceCountry first = it.next()._1();
+					countryCodes.add(first.getCountry().getClassid());
+					set.add(first.getCountry());
+					it.forEachRemaining(t2 -> {
+						if (!countryCodes.contains(t2._1().getCountry().getClassid()))
+							set.add(t2._1().getCountry());
 					});
-				a.setCountrySet(countryList);
+					rcs.setCountrySet(new ArrayList<>(set));
-				return a;
+					return rcs;
-			})
+				}, Encoders.bean(ResultCountrySet.class))
-			.map(couple -> OBJECT_MAPPER.writeValueAsString(couple._2()))
+			.write()
-			.saveAsTextFile(outputPath, GzipCodec.class);
+			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
+			.json(outputPath);
 	}
 
 }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java

@@ -56,12 +56,6 @@ public class SparkCountryPropagationJob {
 		final String resultClassName = parser.get("resultTableName");
 		log.info("resultTableName: {}", resultClassName);
 
-		final Boolean saveGraph = Optional
-			.ofNullable(parser.get("saveGraph"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-		log.info("saveGraph: {}", saveGraph);
-
 		Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
 
 		SparkConf conf = new SparkConf();
@@ -75,8 +69,7 @@ public class SparkCountryPropagationJob {
 					sourcePath,
 					preparedInfoPath,
 					outputPath,
-					resultClazz,
+					resultClazz);
-					saveGraph);
 			});
 	}
 
@@ -85,27 +78,26 @@ public class SparkCountryPropagationJob {
 		String sourcePath,
 		String preparedInfoPath,
 		String outputPath,
-		Class<R> resultClazz,
+		Class<R> resultClazz) {
-		boolean saveGraph) {
 
-		if (saveGraph) {
-			log.info("Reading Graph table from: {}", sourcePath);
-			Dataset<R> res = readPath(spark, sourcePath, resultClazz);
 
-			log.info("Reading prepared info: {}", preparedInfoPath);
+		log.info("Reading Graph table from: {}", sourcePath);
-			Dataset<ResultCountrySet> prepared = spark
+		Dataset<R> res = readPath(spark, sourcePath, resultClazz);
-				.read()
+
-				.json(preparedInfoPath)
+		log.info("Reading prepared info: {}", preparedInfoPath);
-				.as(Encoders.bean(ResultCountrySet.class));
+		Dataset<ResultCountrySet> prepared = spark
+			.read()
+			.json(preparedInfoPath)
+			.as(Encoders.bean(ResultCountrySet.class));
+
+		res
+			.joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer")
+			.map(getCountryMergeFn(), Encoders.bean(resultClazz))
+			.write()
+			.option("compression", "gzip")
+			.mode(SaveMode.Overwrite)
+			.json(outputPath);
 
-			res
-				.joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer")
-				.map(getCountryMergeFn(), Encoders.bean(resultClazz))
-				.write()
-				.option("compression", "gzip")
-				.mode(SaveMode.Overwrite)
-				.json(outputPath);
-		}
 	}
 
 	private static <R extends Result> MapFunction<Tuple2<R, ResultCountrySet>, R> getCountryMergeFn() {

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json

@@ -11,12 +11,6 @@
     "paramDescription": "the hive metastore uris",
     "paramRequired": false
   },
-  {
-    "paramName":"sg",
-    "paramLongName":"saveGraph",
-    "paramDescription": "true if the new version of the graph must be saved",
-    "paramRequired": false
-  },
   {
     "paramName":"tn",
     "paramLongName":"resultTableName",

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareassoc_parameters.json

@@ -5,12 +5,6 @@
     "paramDescription": "the path of the sequencial file to read",
     "paramRequired": true
   },
-  {
-    "paramName":"h",
-    "paramLongName":"hive_metastore_uris",
-    "paramDescription": "the hive metastore uris",
-    "paramRequired": true
-  },
   {
     "paramName": "out",
     "paramLongName": "outputPath",

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareresultcountry_parameters.json

@@ -12,9 +12,9 @@
     "paramRequired": true
   },
   {
-    "paramName":"h",
+    "paramName":"w",
-    "paramLongName":"hive_metastore_uris",
+    "paramLongName":"workingPath",
-    "paramDescription": "the hive metastore uris",
+    "paramDescription": "the working path",
     "paramRequired": true
   },
   {

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java

@@ -7,6 +7,7 @@ import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
 
+import eu.dnetlib.dhp.schema.oaf.Publication;
 import org.apache.commons.io.FileUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
@@ -69,17 +70,16 @@ public class CountryPropagationJobTest {
 	@Test
 	void testCountryPropagationSoftware() throws Exception {
 		final String sourcePath = getClass()
-			.getResource("/eu/dnetlib/dhp/countrypropagation/sample/software")
+			.getResource("/eu/dnetlib/dhp/countrypropagation/graph/software")
 			.getPath();
 		final String preparedInfoPath = getClass()
-			.getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo")
+			.getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo/software")
 			.getPath();
 		SparkCountryPropagationJob
 			.main(
 				new String[] {
 					"--isSparkSessionManaged", Boolean.FALSE.toString(),
 					"--sourcePath", sourcePath,
-					"-saveGraph", "true",
 					"-resultTableName", Software.class.getCanonicalName(),
 					"-outputPath", workingDir.toString() + "/software",
 					"-preparedInfoPath", preparedInfoPath
@@ -91,8 +91,6 @@ public class CountryPropagationJobTest {
 			.textFile(workingDir.toString() + "/software")
 			.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
 
-		// tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s));
-
 		Assertions.assertEquals(10, tmp.count());
 
 		Dataset<Software> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Software.class));
@@ -259,4 +257,69 @@ public class CountryPropagationJobTest {
 				7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count());
 	}
 
+	@Test
+	void testCountryPropagationPublication() throws Exception {
+		final String sourcePath = getClass()
+				.getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication")
+				.getPath();
+		final String preparedInfoPath = getClass()
+				.getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication")
+				.getPath();
+		SparkCountryPropagationJob
+				.main(
+						new String[] {
+								"--isSparkSessionManaged", Boolean.FALSE.toString(),
+								"--sourcePath", sourcePath,
+								"-resultTableName", Publication.class.getCanonicalName(),
+								"-outputPath", workingDir.toString() + "/publication",
+								"-preparedInfoPath", preparedInfoPath
+						});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Publication> tmp = sc
+				.textFile(workingDir.toString() + "/publication")
+				.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
+
+		Assertions.assertEquals(12, tmp.count());
+
+		Assertions.assertEquals(5, tmp.filter(r -> r.getCountry().size() > 0).count());
+
+		tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemeid())));
+		tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemename())));
+		tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertFalse(c.getDataInfo().getDeletedbyinference())));
+		tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertFalse(c.getDataInfo().getInvisible())));
+		tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertTrue(c.getDataInfo().getInferred())));
+		tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("0.85", c.getDataInfo().getTrust())));
+		tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("propagation", c.getDataInfo().getInferenceprovenance())));
+		tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("country:instrepos", c.getDataInfo().getProvenanceaction().getClassid())));
+		tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemeid())));
+		tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemename())));
+
+		List<Country> countries = tmp.filter(r -> r.getId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072")).collect().get(0).getCountry();
+		Assertions.assertEquals(1, countries.size());
+		Assertions.assertEquals("NL",countries.get(0).getClassid());
+		Assertions.assertEquals("Netherlands",countries.get(0).getClassname());
+
+		countries = tmp.filter(r -> r.getId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b")).collect().get(0).getCountry();
+		Assertions.assertEquals(1, countries.size());
+		Assertions.assertEquals("NL",countries.get(0).getClassid());
+		Assertions.assertEquals("Netherlands",countries.get(0).getClassname());
+
+		countries = tmp.filter(r -> r.getId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6")).collect().get(0).getCountry();
+		Assertions.assertEquals(2, countries.size());
+		Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
+		Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
+
+		countries = tmp.filter(r -> r.getId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df")).collect().get(0).getCountry();
+		Assertions.assertEquals(2, countries.size());
+		Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
+		Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands")));
+		
+		countries = tmp.filter(r -> r.getId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088")).collect().get(0).getCountry();
+		Assertions.assertEquals(2, countries.size());
+		Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
+		Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
+	}
+
 }

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java

@@ -0,0 +1,111 @@
+package eu.dnetlib.dhp.countrypropagation;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+
+public class DatasourceCountryPreparationTest {
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    private static SparkSession spark;
+
+    private static Path workingDir;
+
+    @BeforeAll
+    public static void beforeAll() throws IOException {
+        workingDir = Files.createTempDirectory(DatasourceCountryPreparationTest.class.getSimpleName());
+
+        SparkConf conf = new SparkConf();
+        conf.setAppName(DatasourceCountryPreparationTest.class.getSimpleName());
+
+        conf.setMaster("local[*]");
+        conf.set("spark.driver.host", "localhost");
+        conf.set("hive.metastore.local", "true");
+        conf.set("spark.ui.enabled", "false");
+        conf.set("spark.sql.warehouse.dir", workingDir.toString());
+        conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+        spark = SparkSession
+                .builder()
+                .appName(DatasourceCountryPreparationTest.class.getSimpleName())
+                .config(conf)
+                .getOrCreate();
+    }
+
+    @AfterAll
+    public static void afterAll() throws IOException {
+        FileUtils.deleteDirectory(workingDir.toFile());
+        spark.stop();
+    }
+
+    @Test
+    void testPrepareDatasourceCountry() throws Exception {
+        final String sourcePath = getClass()
+                .getResource("/eu/dnetlib/dhp/countrypropagation/graph")
+                .getPath();
+
+        PrepareDatasourceCountryAssociation
+                .main(
+                        new String[] {
+                                "--isSparkSessionManaged", Boolean.FALSE.toString(),
+                                "--sourcePath", sourcePath,
+                                "--outputPath", workingDir.toString() + "/datasourceCountry",
+                                "--allowedtypes","pubsrepository::institutional" ,
+                                "--whitelist","10|openaire____::3795d6478e30e2c9f787d427ff160944;10|opendoar____::16e6a3326dd7d868cbc926602a61e4d0;10|eurocrisdris::fe4903425d9040f680d8610d9079ea14;10|openaire____::5b76240cc27a58c6f7ceef7d8c36660e;10|openaire____::172bbccecf8fca44ab6a6653e84cb92a;10|openaire____::149c6590f8a06b46314eed77bfca693f;10|eurocrisdris::a6026877c1a174d60f81fd71f62df1c1;10|openaire____::4692342f0992d91f9e705c26959f09e0;10|openaire____::8d529dbb05ec0284662b391789e8ae2a;10|openaire____::345c9d171ef3c5d706d08041d506428c;10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0;10|opendoar____::7a614fd06c325499f1680b9896beedeb;10|opendoar____::1ee3dfcd8a0645a25a35977997223d22;10|opendoar____::d296c101daa88a51f6ca8cfc1ac79b50;10|opendoar____::798ed7d4ee7138d49b8828958048130a;10|openaire____::c9d2209ecc4d45ba7b4ca7597acb88a2;10|eurocrisdris::c49e0fe4b9ba7b7fab717d1f0f0a674d;10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539;10|eurocrisdris::432ca599953ff50cd4eeffe22faf3e48"
+                        });
+
+        final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+        JavaRDD<DatasourceCountry> tmp = sc
+                .textFile(workingDir.toString() + "/datasourceCountry")
+                .map(item -> OBJECT_MAPPER.readValue(item, DatasourceCountry.class));
+
+        Assertions.assertEquals(3, tmp.count());
+        Assertions.assertEquals(1, tmp.filter(dsc -> dsc.getDataSourceId()
+                .equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")).count());
+        Assertions.assertEquals(1, tmp.filter(dsc -> dsc.getDataSourceId()
+                .equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")).count());
+        Assertions.assertEquals(1, tmp.filter(dsc -> dsc.getDataSourceId()
+                .equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")).count());
+
+        Assertions.assertEquals("NL", tmp.filter(dsc -> dsc.getDataSourceId()
+                .equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")).collect()
+                .get(0).getCountry().getClassid());
+        Assertions.assertEquals("Netherlands", tmp.filter(dsc -> dsc.getDataSourceId()
+                        .equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")).collect()
+                .get(0).getCountry().getClassname());
+
+        Assertions.assertEquals("IT", tmp.filter(dsc -> dsc.getDataSourceId()
+                        .equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")).collect()
+                .get(0).getCountry().getClassid());
+        Assertions.assertEquals("Italy", tmp.filter(dsc -> dsc.getDataSourceId()
+                        .equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")).collect()
+                .get(0).getCountry().getClassname());
+
+        Assertions.assertEquals("FR", tmp.filter(dsc -> dsc.getDataSourceId()
+                        .equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")).collect()
+                .get(0).getCountry().getClassid());
+        Assertions.assertEquals("France", tmp.filter(dsc -> dsc.getDataSourceId()
+                        .equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")).collect()
+                .get(0).getCountry().getClassname());
+
+        tmp.foreach(e -> System.out.println(OBJECT_MAPPER.writeValueAsString(e)));
+
+    }
+}

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/ResultCountryPreparationTest.java

@@ -0,0 +1,115 @@
+package eu.dnetlib.dhp.countrypropagation;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.schema.oaf.Publication;
+import org.apache.commons.io.FileUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import static eu.dnetlib.dhp.PropagationConstant.isSparkSessionManaged;
+
+public class ResultCountryPreparationTest {
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    private static SparkSession spark;
+
+    private static Path workingDir;
+
+    @BeforeAll
+    public static void beforeAll() throws IOException {
+        workingDir = Files.createTempDirectory(ResultCountryPreparationTest.class.getSimpleName());
+
+        SparkConf conf = new SparkConf();
+        conf.setAppName(ResultCountryPreparationTest.class.getSimpleName());
+
+        conf.setMaster("local[*]");
+        conf.set("spark.driver.host", "localhost");
+        conf.set("hive.metastore.local", "true");
+        conf.set("spark.ui.enabled", "false");
+        conf.set("spark.sql.warehouse.dir", workingDir.toString());
+        conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+        spark = SparkSession
+                .builder()
+                .appName(ResultCountryPreparationTest.class.getSimpleName())
+                .config(conf)
+                .getOrCreate();
+    }
+
+    @AfterAll
+    public static void afterAll() throws IOException {
+        FileUtils.deleteDirectory(workingDir.toFile());
+        spark.stop();
+    }
+
+    @Test
+    void testPrepareResultCountry() throws Exception {
+        final String sourcePath = getClass()
+                .getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication")
+                .getPath();
+
+        final String preparedInfoPath = getClass()
+                .getResource("/eu/dnetlib/dhp/countrypropagation/datasourcecountry")
+                .getPath();
+
+
+        PrepareResultCountrySet
+                .main(
+                        new String[] {
+                                "--isSparkSessionManaged", Boolean.FALSE.toString(),
+                                "--workingPath", workingDir.toString() + "/working",
+                                "--sourcePath", sourcePath,
+                                "--outputPath", workingDir.toString() + "/resultCountry",
+                                "--preparedInfoPath", preparedInfoPath,
+                                "--resultTableName", Publication.class.getCanonicalName()
+                        });
+
+        final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+        JavaRDD<ResultCountrySet> tmp = sc
+                .textFile(workingDir.toString() + "/resultCountry")
+                .map(item -> OBJECT_MAPPER.readValue(item, ResultCountrySet.class));
+
+
+        Assertions.assertEquals(5, tmp.count());
+
+        ResultCountrySet rc = tmp.filter(r -> r.getResultId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072")).collect().get(0);
+        Assertions.assertEquals(1, rc.getCountrySet().size());
+        Assertions.assertEquals("NL",rc.getCountrySet().get(0).getClassid());
+        Assertions.assertEquals("Netherlands",rc.getCountrySet().get(0).getClassname());
+
+        rc = tmp.filter(r -> r.getResultId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b")).collect().get(0);
+        Assertions.assertEquals(1, rc.getCountrySet().size());
+        Assertions.assertEquals("NL",rc.getCountrySet().get(0).getClassid());
+        Assertions.assertEquals("Netherlands",rc.getCountrySet().get(0).getClassname());
+
+        rc = tmp.filter(r -> r.getResultId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6")).collect().get(0);
+        Assertions.assertEquals(2, rc.getCountrySet().size());
+        Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
+        Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
+
+        rc = tmp.filter(r -> r.getResultId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df")).collect().get(0);
+        Assertions.assertEquals(2, rc.getCountrySet().size());
+        Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
+        Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands")));
+
+
+        rc = tmp.filter(r -> r.getResultId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088")).collect().get(0);
+        Assertions.assertEquals(2, rc.getCountrySet().size());
+        Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
+        Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
+
+
+    }
+}

dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/datasourcecountry/datasourcecountry

@@ -0,0 +1,3 @@
+{"dataSourceId":"10|eurocrisdris::fe4903425d9040f680d8610d9079ea14","country":{"classid":"NL","classname":"Netherlands"}}
+{"dataSourceId":"10|opendoar____::f0dd4a99fba6075a9494772b58f95280","country":{"classid":"IT","classname":"Italy"}}
+{"dataSourceId":"10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539","country":{"classid":"FR","classname":"France"}}

dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/datasource/datasource.json

@@ -0,0 +1,11 @@
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+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0ef8dfab3927cb4d69df0d3113f05a42","subRelType":"affiliation","target":"20|pending_org_::a50fdd7f7e77b74ea2b16823151c391a","validated":false}
+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","subRelType":"affiliation","target":"50|dedup_wf_001::0f488ad00253126c14a21abe6b2d406c","validated":false}
+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0f488ad00253126c14a21abe6b2d406c","subRelType":"affiliation","target":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","validated":false}
+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","subRelType":"affiliation","target":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","validated":false}
+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","subRelType":"affiliation","target":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","validated":false}

dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication/resultCountrySet

@@ -0,0 +1,5 @@
+{"resultId":"50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b","countrySet":[{"classid":"NL","classname":"Netherlands"}]}
+{"resultId":"50|355e65625b88::54a1c76f520bb2c8da27d12e42891088","countrySet":[{"classid":"IT","classname":"Italy"},{"classid":"FR","classname":"France"}]}
+{"resultId":"50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072","countrySet":[{"classid":"NL","classname":"Netherlands"}]}
+{"resultId":"50|355e65625b88::74009c567c81b4aa55c813db658734df","countrySet":[{"classid":"NL","classname":"Netherlands"},{"classid":"IT","classname":"Italy"}]}
+{"resultId":"50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6","countrySet":[{"classid":"IT","classname":"Italy"},{"classid":"FR","classname":"France"}]}

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java

@@ -8,7 +8,6 @@ import java.io.IOException;
 import java.io.StringReader;
 import java.util.List;
 
-import eu.dnetlib.dhp.schema.oaf.Datasource;
 import org.apache.commons.io.IOUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
@@ -24,6 +23,7 @@ import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
 import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
 import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
 import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
+import eu.dnetlib.dhp.schema.oaf.Datasource;
 import eu.dnetlib.dhp.schema.oaf.Project;
 import eu.dnetlib.dhp.schema.oaf.Publication;
 import eu.dnetlib.dhp.schema.oaf.Relation;
@@ -146,10 +146,10 @@ public class XmlRecordFactoryTest {
 		final ContextMapper contextMapper = new ContextMapper();
 
 		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
-				XmlConverterJob.schemaLocation);
+			XmlConverterJob.schemaLocation);
 
 		final Datasource d = OBJECT_MAPPER
-				.readValue(IOUtils.toString(getClass().getResourceAsStream("datasource.json")), Datasource.class);
+			.readValue(IOUtils.toString(getClass().getResourceAsStream("datasource.json")), Datasource.class);
 
 		final String xml = xmlRecordFactory.build(new JoinedEntity<>(d));