Merge branch 'beta' into bulkTagRefactor

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

@@ -16,6 +16,8 @@ import org.apache.commons.lang3.StringUtils;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.Encoders;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import com.github.sisyphsu.dateparser.DateParserUtils;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
@@ -38,6 +40,127 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 
 	public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5;
 
+	public static <T extends Oaf> T cleanContext(T value, String contextId, String verifyParam) {
+		if (ModelSupport.isSubClass(value, Result.class)) {
+			final Result res = (Result) value;
+			if (shouldCleanContext(res, verifyParam)) {
+				res
+					.setContext(
+						res
+							.getContext()
+							.stream()
+							.filter(c -> !StringUtils.startsWith(c.getId().toLowerCase(), contextId))
+							.collect(Collectors.toList()));
+			}
+			return (T) res;
+		} else {
+			return value;
+		}
+	}
+
+	private static boolean shouldCleanContext(Result res, String verifyParam) {
+		boolean titleMatch = res
+			.getTitle()
+			.stream()
+			.filter(
+				t -> t
+					.getQualifier()
+					.getClassid()
+					.equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid()))
+			.anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()));
+
+		return titleMatch && Objects.nonNull(res.getContext());
+	}
+
+	public static <T extends Oaf> T cleanCountry(T value, String[] verifyParam, Set<String> hostedBy,
+		String collectedfrom, String country) {
+		if (ModelSupport.isSubClass(value, Result.class)) {
+			final Result res = (Result) value;
+			if (res.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) ||
+				!res.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) {
+				return (T) res;
+			}
+
+			List<StructuredProperty> ids = getPidsAndAltIds(res).collect(Collectors.toList());
+			if (ids
+				.stream()
+				.anyMatch(
+					p -> p
+						.getQualifier()
+						.getClassid()
+						.equals(PidType.doi.toString()) && pidInParam(p.getValue(), verifyParam))) {
+				res
+					.setCountry(
+						res
+							.getCountry()
+							.stream()
+							.filter(
+								c -> toTakeCountry(c, country))
+							.collect(Collectors.toList()));
+			}
+
+			return (T) res;
+		} else {
+			return value;
+		}
+	}
+
+	private static <T extends Result> Stream<StructuredProperty> getPidsAndAltIds(T r) {
+		final Stream<StructuredProperty> resultPids = Optional
+			.ofNullable(r.getPid())
+			.map(Collection::stream)
+			.orElse(Stream.empty());
+
+		final Stream<StructuredProperty> instancePids = Optional
+			.ofNullable(r.getInstance())
+			.map(
+				instance -> instance
+					.stream()
+					.flatMap(
+						i -> Optional
+							.ofNullable(i.getPid())
+							.map(Collection::stream)
+							.orElse(Stream.empty())))
+			.orElse(Stream.empty());
+
+		final Stream<StructuredProperty> instanceAltIds = Optional
+			.ofNullable(r.getInstance())
+			.map(
+				instance -> instance
+					.stream()
+					.flatMap(
+						i -> Optional
+							.ofNullable(i.getAlternateIdentifier())
+							.map(Collection::stream)
+							.orElse(Stream.empty())))
+			.orElse(Stream.empty());
+
+		return Stream
+			.concat(
+				Stream.concat(resultPids, instancePids),
+				instanceAltIds);
+	}
+
+	private static boolean pidInParam(String value, String[] verifyParam) {
+		for (String s : verifyParam)
+			if (value.startsWith(s))
+				return true;
+		return false;
+	}
+
+	private static boolean toTakeCountry(Country c, String country) {
+		// If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be
+		// inserted via propagation
+		if (!Optional.ofNullable(c.getDataInfo()).isPresent())
+			return true;
+		if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent())
+			return true;
+		return !(c
+			.getClassid()
+			.equalsIgnoreCase(country) &&
+			c.getDataInfo().getInferenceprovenance().equals("propagation"));
+	}
+
 	public static <T extends Oaf> T fixVocabularyNames(T value) {
 		if (value instanceof Datasource) {
 			// nothing to clean here

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java

@@ -9,7 +9,9 @@ import java.util.*;
 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.MapFunction;
+import org.apache.spark.api.java.function.MapGroupsFunction;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
@@ -70,28 +72,33 @@ public class PrepareResultCommunitySet {
 		String outputPath,
 		OrganizationMap organizationMap) {
 
-		Dataset<Relation> relation = readPath(spark, inputPath, Relation.class);
+		Dataset<Relation> relationAffiliation = readPath(spark, inputPath, Relation.class)
-		relation.createOrReplaceTempView("relation");
+			.filter(
+				(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
+					r.getRelClass().equalsIgnoreCase(ModelConstants.HAS_AUTHOR_INSTITUTION));
 
-		String query = "SELECT result_organization.source resultId, result_organization.target orgId, org_set merges "
+		Dataset<Relation> relationOrganization = readPath(spark, inputPath, Relation.class)
-			+ "FROM (SELECT source, target "
+			.filter(
-			+ "      FROM relation "
+				(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
-			+ "      WHERE datainfo.deletedbyinference = false "
+					r.getRelClass().equalsIgnoreCase(ModelConstants.MERGES));
-			+ "      AND lower(relClass) = '"
-			+ ModelConstants.HAS_AUTHOR_INSTITUTION.toLowerCase()
-			+ "') result_organization "
-			+ "LEFT JOIN (SELECT source, collect_set(target) org_set "
-			+ "      FROM relation "
-			+ "      WHERE datainfo.deletedbyinference = false "
-			+ "      AND lower(relClass) = '"
-			+ ModelConstants.MERGES.toLowerCase()
-			+ "' "
-			+ "      GROUP BY source) organization_organization "
-			+ "ON result_organization.target = organization_organization.source ";
 
-		Dataset<ResultOrganizations> result_organizationset = spark
+		Dataset<ResultOrganizations> result_organizationset = relationAffiliation
-			.sql(query)
+			.joinWith(
-			.as(Encoders.bean(ResultOrganizations.class));
+				relationOrganization,
+				relationAffiliation.col("target").equalTo(relationOrganization.col("source")),
+				"left")
+			.groupByKey((MapFunction<Tuple2<Relation, Relation>, String>) t2 -> t2._2().getSource(), Encoders.STRING())
+			.mapGroups((MapGroupsFunction<String, Tuple2<Relation, Relation>, ResultOrganizations>) (k, it) -> {
+				ResultOrganizations rOrgs = new ResultOrganizations();
+				rOrgs.setOrgId(k);
+				Tuple2<Relation, Relation> first = it.next();
+				rOrgs.setResultId(first._1().getSource());
+				ArrayList<String> merges = new ArrayList<>();
+				merges.add(first._2().getTarget());
+				it.forEachRemaining(t -> merges.add(t._2().getTarget()));
+				rOrgs.setMerges(merges);
+				return rOrgs;
+			}, Encoders.bean(ResultOrganizations.class));
 
 		result_organizationset
 			.map(mapResultCommunityFn(organizationMap), Encoders.bean(ResultCommunityList.class))

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

@@ -1,122 +0,0 @@
-
-package eu.dnetlib.dhp.oa.graph.clean;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.io.Serializable;
-import java.util.Optional;
-import java.util.stream.Collectors;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.spark.SparkConf;
-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;
-import org.apache.spark.sql.SparkSession;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Result;
-
-public class CleanContextSparkJob implements Serializable {
-	private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class);
-
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
-	public static void main(String[] args) throws Exception {
-
-		String jsonConfiguration = IOUtils
-			.toString(
-				CleanContextSparkJob.class
-					.getResourceAsStream(
-						"/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json"));
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
-		parser.parseArgument(args);
-
-		Boolean isSparkSessionManaged = Optional
-			.ofNullable(parser.get("isSparkSessionManaged"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
-
-		String inputPath = parser.get("inputPath");
-		log.info("inputPath: {}", inputPath);
-
-		String workingDir = parser.get("workingDir");
-		log.info("workingDir: {}", workingDir);
-
-		String contextId = parser.get("contextId");
-		log.info("contextId: {}", contextId);
-
-		String verifyParam = parser.get("verifyParam");
-		log.info("verifyParam: {}", verifyParam);
-
-		String graphTableClassName = parser.get("graphTableClassName");
-		log.info("graphTableClassName: {}", graphTableClassName);
-
-		Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
-
-		SparkConf conf = new SparkConf();
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-
-				cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingDir);
-			});
-	}
-
-	private static <T extends Result> void cleanContext(SparkSession spark, String contextId, String verifyParam,
-		String inputPath, Class<T> entityClazz, String workingDir) {
-		Dataset<T> res = spark
-			.read()
-			.textFile(inputPath)
-			.map(
-				(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
-				Encoders.bean(entityClazz));
-
-		res.map((MapFunction<T, T>) r -> {
-			if (!r
-				.getTitle()
-				.stream()
-				.filter(
-					t -> t
-						.getQualifier()
-						.getClassid()
-						.equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid()))
-				.anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) {
-				return r;
-			}
-			r
-				.setContext(
-					r
-						.getContext()
-						.stream()
-						.filter(
-							c -> !c.getId().split("::")[0]
-								.equalsIgnoreCase(contextId))
-						.collect(Collectors.toList()));
-			return r;
-		}, Encoders.bean(entityClazz))
-			.write()
-			.mode(SaveMode.Overwrite)
-			.option("compression", "gzip")
-			.json(workingDir);
-
-		spark
-			.read()
-			.textFile(workingDir)
-			.map(
-				(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
-				Encoders.bean(entityClazz))
-			.write()
-			.mode(SaveMode.Overwrite)
-			.option("compression", "gzip")
-			.json(inputPath);
-	}
-}

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

@@ -3,12 +3,16 @@ package eu.dnetlib.dhp.oa.graph.clean;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
-import java.util.Optional;
+import java.util.*;
+import java.util.stream.Stream;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
 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.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SaveMode;
@@ -17,15 +21,22 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.Sets;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.common.action.model.MasterDuplicate;
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
 import eu.dnetlib.dhp.schema.oaf.Oaf;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import scala.Tuple2;
 
 public class CleanGraphSparkJob {
 
@@ -33,8 +44,13 @@ public class CleanGraphSparkJob {
 
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-	public static void main(String[] args) throws Exception {
+	private ArgumentApplicationParser parser;
 
+	public CleanGraphSparkJob(ArgumentApplicationParser parser) {
+		this.parser = parser;
+	}
+
+	public static void main(String[] args) throws Exception {
 		String jsonConfiguration = IOUtils
 			.toString(
 				CleanGraphSparkJob.class
@@ -49,30 +65,70 @@ public class CleanGraphSparkJob {
 			.orElse(Boolean.TRUE);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
+		String isLookupUrl = parser.get("isLookupUrl");
+		log.info("isLookupUrl: {}", isLookupUrl);
+
+		ISLookUpService isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
+
+		new CleanGraphSparkJob(parser).run(isSparkSessionManaged, isLookup);
+	}
+
+	public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService)
+		throws ISLookUpException, ClassNotFoundException {
+
 		String inputPath = parser.get("inputPath");
 		log.info("inputPath: {}", inputPath);
 
 		String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
-		String isLookupUrl = parser.get("isLookupUrl");
-		log.info("isLookupUrl: {}", isLookupUrl);
-
 		String graphTableClassName = parser.get("graphTableClassName");
 		log.info("graphTableClassName: {}", graphTableClassName);
 
+		String contextId = parser.get("contextId");
+		log.info("contextId: {}", contextId);
+
+		String verifyParam = parser.get("verifyParam");
+		log.info("verifyParam: {}", verifyParam);
+
+		String datasourcePath = parser.get("hostedBy");
+		log.info("datasourcePath: {}", datasourcePath);
+
+		String country = parser.get("country");
+		log.info("country: {}", country);
+
+		String[] verifyCountryParam = Optional
+			.ofNullable(parser.get("verifyCountryParam"))
+			.map(s -> s.split(";"))
+			.orElse(new String[] {});
+		log.info("verifyCountryParam: {}", verifyCountryParam);
+
+		String collectedfrom = parser.get("collectedfrom");
+		log.info("collectedfrom: {}", collectedfrom);
+
+		String dsMasterDuplicatePath = parser.get("masterDuplicatePath");
+		log.info("masterDuplicatePath: {}", dsMasterDuplicatePath);
+
+		Boolean deepClean = Optional
+			.ofNullable(parser.get("deepClean"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.FALSE);
+		log.info("deepClean: {}", deepClean);
+
 		Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
 
-		final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
+		final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService);
-		final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService);
 
 		SparkConf conf = new SparkConf();
+		conf.setAppName(CleanGraphSparkJob.class.getSimpleName() + "#" + entityClazz.getSimpleName());
 		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
 			spark -> {
 				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
-				cleanGraphTable(spark, vocs, inputPath, entityClazz, outputPath);
+				cleanGraphTable(
+					spark, vocs, inputPath, entityClazz, outputPath, contextId, verifyParam, datasourcePath, country,
+					verifyCountryParam, collectedfrom, dsMasterDuplicatePath, deepClean);
 			});
 	}
 
@@ -81,21 +137,88 @@ public class CleanGraphSparkJob {
 		VocabularyGroup vocs,
 		String inputPath,
 		Class<T> clazz,
-		String outputPath) {
+		String outputPath, String contextId, String verifyParam, String datasourcePath, String country,
+		String[] verifyCountryParam, String collectedfrom, String dsMasterDuplicatePath,
+		Boolean deepClean) {
 
 		final CleaningRuleMap mapping = CleaningRuleMap.create(vocs);
 
-		readTableFromPath(spark, inputPath, clazz)
+		final Dataset<T> cleaned_basic = readTableFromPath(spark, inputPath, clazz)
 			.map((MapFunction<T, T>) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz))
 			.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
 			.map((MapFunction<T, T>) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz))
-			.filter((FilterFunction<T>) GraphCleaningFunctions::filter)
+			.filter((FilterFunction<T>) GraphCleaningFunctions::filter);
+
+		// read the master-duplicate tuples
+		Dataset<MasterDuplicate> md = spark
+			.read()
+			.textFile(dsMasterDuplicatePath)
+			.map(as(MasterDuplicate.class), Encoders.bean(MasterDuplicate.class));
+
+		// prepare the resolved CF|HB references with the corresponding EMPTY master ID
+		Dataset<IdCfHbMapping> resolved = spark
+			.read()
+			.textFile(inputPath)
+			.map(as(clazz), Encoders.bean(clazz))
+			.flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class));
+
+		if (Boolean.FALSE.equals(deepClean)) {
+
+			if (Boolean.TRUE.equals(ModelSupport.isSubClass(clazz, Result.class))) {
+				save(fixCFHB(clazz, cleaned_basic, md, resolved), outputPath);
+			} else {
+				save(cleaned_basic, outputPath);
+			}
+		} else if (Boolean.TRUE.equals(ModelSupport.isSubClass(clazz, Result.class))) {
+
+			// load the hostedby mapping
+			Set<String> hostedBy = Sets
+				.newHashSet(
+					spark
+						.read()
+						.textFile(datasourcePath)
+						.collectAsList());
+
+			// perform the deep cleaning steps
+			final Dataset<T> cleaned_deep = fixCFHB(clazz, cleaned_basic, md, resolved)
+				.map(
+					(MapFunction<T, T>) value -> GraphCleaningFunctions.cleanContext(value, contextId, verifyParam),
+					Encoders.bean(clazz))
+				.map(
+					(MapFunction<T, T>) value -> GraphCleaningFunctions
+						.cleanCountry(value, verifyCountryParam, hostedBy, collectedfrom, country),
+					Encoders.bean(clazz));
+
+			save(cleaned_deep, outputPath);
+		} else {
+			save(cleaned_basic, outputPath);
+		}
+	}
+
+	private static <T extends Oaf> void save(final Dataset<T> dataset, final String outputPath) {
+		dataset
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
 			.json(outputPath);
 	}
 
+	private static <T extends Oaf> Dataset<T> fixCFHB(Class<T> clazz, Dataset<T> results, Dataset<MasterDuplicate> md,
+		Dataset<IdCfHbMapping> resolved) {
+
+		// set the EMPTY master ID/NAME
+		Dataset<IdCfHbMapping> resolvedDs = resolved
+			.joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId")))
+			.map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class))
+			.filter((FilterFunction<IdCfHbMapping>) m -> Objects.nonNull(m.getMasterId()));
+
+		return results
+			.joinWith(resolvedDs, results.col("id").equalTo(resolvedDs.col("resultId")), "left")
+			.groupByKey(
+				(MapFunction<Tuple2<T, IdCfHbMapping>, String>) t -> ((Result) t._1()).getId(), Encoders.STRING())
+			.mapGroups(getMapGroupsFunction(), Encoders.bean(clazz));
+	}
+
 	private static <T extends Oaf> Dataset<T> readTableFromPath(
 		SparkSession spark, String inputEntityPath, Class<T> clazz) {
 
@@ -103,9 +226,104 @@ public class CleanGraphSparkJob {
 		return spark
 			.read()
 			.textFile(inputEntityPath)
+			.map(as(clazz), Encoders.bean(clazz));
+	}
+
+	private static <R> MapFunction<String, R> as(Class<R> clazz) {
+		return s -> OBJECT_MAPPER.readValue(s, clazz);
+	}
+
+	private static <T extends Oaf> FlatMapFunction<T, IdCfHbMapping> flattenCfHbFn() {
+		return r -> Stream
+			.concat(
+				Optional
+					.ofNullable(r.getCollectedfrom())
+					.map(cf -> cf.stream().map(KeyValue::getKey))
+					.orElse(Stream.empty()),
+				Stream
+					.concat(
+						Optional
+							.ofNullable(((Result) r).getInstance())
 							.map(
-				(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz),
+								instances -> instances
-				Encoders.bean(clazz));
+									.stream()
+									.map(i -> Optional.ofNullable(i.getHostedby()).map(KeyValue::getKey).orElse("")))
+							.orElse(Stream.empty())
+							.filter(StringUtils::isNotBlank),
+						Optional
+							.ofNullable(((Result) r).getInstance())
+							.map(
+								instances -> instances
+									.stream()
+									.map(
+										i -> Optional
+											.ofNullable(i.getCollectedfrom())
+											.map(KeyValue::getKey)
+											.orElse("")))
+							.orElse(Stream.empty())
+							.filter(StringUtils::isNotBlank)))
+			.distinct()
+			.filter(StringUtils::isNotBlank)
+			.map(cfHb -> asIdCfHbMapping(((Result) r).getId(), cfHb))
+			.iterator();
+	}
+
+	private static MapFunction<Tuple2<IdCfHbMapping, MasterDuplicate>, IdCfHbMapping> asIdCfHbMapping() {
+		return t -> {
+			final IdCfHbMapping mapping = t._1();
+			Optional
+				.ofNullable(t._2())
+				.ifPresent(t2 -> {
+					mapping.setMasterId(t2.getMasterId());
+					mapping.setMasterName(t2.getMasterName());
+
+				});
+			return mapping;
+		};
+	}
+
+	private static IdCfHbMapping asIdCfHbMapping(String resultId, String cfHb) {
+		IdCfHbMapping m = new IdCfHbMapping(resultId);
+		m.setCfhb(cfHb);
+		return m;
+	}
+
+	private static <T extends Oaf> MapGroupsFunction<String, Tuple2<T, IdCfHbMapping>, T> getMapGroupsFunction() {
+		return new MapGroupsFunction<String, Tuple2<T, IdCfHbMapping>, T>() {
+			@Override
+			public T call(String key, Iterator<Tuple2<T, IdCfHbMapping>> values) {
+				final Tuple2<T, IdCfHbMapping> first = values.next();
+				final T res = first._1();
+
+				updateResult(res, first._2());
+				values.forEachRemaining(t -> updateResult(res, t._2()));
+				return res;
+			}
+
+			private void updateResult(T res, IdCfHbMapping m) {
+				if (Objects.nonNull(m)) {
+					filter(res.getCollectedfrom()).forEach(kv -> updateKeyValue(kv, m));
+					((Result) res).getInstance().forEach(i -> {
+						updateKeyValue(i.getHostedby(), m);
+						updateKeyValue(i.getCollectedfrom(), m);
+					});
+				}
+			}
+
+			private Stream<KeyValue> filter(List<KeyValue> kvs) {
+				return kvs
+					.stream()
+					.filter(kv -> StringUtils.isNotBlank(kv.getKey()) && StringUtils.isNotBlank(kv.getValue()));
+			}
+
+			private void updateKeyValue(final KeyValue kv, final IdCfHbMapping a) {
+				if (Objects.nonNull(kv) && Objects.nonNull(kv.getKey()) && kv.getKey().equals(a.getCfhb())) {
+					kv.setKey(a.getMasterId());
+					kv.setValue(a.getMasterName());
+				}
+			}
+
+		};
 	}
 
 }

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

@@ -1,10 +1,9 @@
 
-package eu.dnetlib.dhp.oa.graph.clean.country;
+package eu.dnetlib.dhp.oa.graph.clean;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
-import java.util.List;
 import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
@@ -21,7 +20,6 @@ import org.slf4j.LoggerFactory;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.*;
 import scala.Tuple2;

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

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.oa.graph.clean.cfhb;
+package eu.dnetlib.dhp.oa.graph.clean;
 
 import java.io.Serializable;
 

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

@@ -1,227 +0,0 @@
-
-package eu.dnetlib.dhp.oa.graph.clean.cfhb;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.util.Iterator;
-import java.util.List;
-import java.util.Objects;
-import java.util.Optional;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
-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.expressions.Aggregator;
-import org.jetbrains.annotations.NotNull;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.common.action.model.MasterDuplicate;
-import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob;
-import eu.dnetlib.dhp.schema.oaf.Instance;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
-import eu.dnetlib.dhp.schema.oaf.Result;
-import eu.dnetlib.dhp.utils.DHPUtils;
-import scala.Tuple2;
-
-public class CleanCfHbSparkJob {
-
-	private static final Logger log = LoggerFactory.getLogger(CleanCfHbSparkJob.class);
-
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
-	public static void main(String[] args) throws Exception {
-
-		String jsonConfiguration = IOUtils
-			.toString(
-				CleanCountrySparkJob.class
-					.getResourceAsStream(
-						"/eu/dnetlib/dhp/oa/graph/input_clean_cfhb_parameters.json"));
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
-		parser.parseArgument(args);
-
-		Boolean isSparkSessionManaged = Optional
-			.ofNullable(parser.get("isSparkSessionManaged"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
-
-		String inputPath = parser.get("inputPath");
-		log.info("inputPath: {}", inputPath);
-
-		String resolvedPath = parser.get("resolvedPath");
-		log.info("resolvedPath: {}", resolvedPath);
-
-		String outputPath = parser.get("outputPath");
-		log.info("outputPath: {}", outputPath);
-
-		String dsMasterDuplicatePath = parser.get("masterDuplicatePath");
-		log.info("masterDuplicatePath: {}", dsMasterDuplicatePath);
-
-		String graphTableClassName = parser.get("graphTableClassName");
-		log.info("graphTableClassName: {}", graphTableClassName);
-
-		Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
-
-		SparkConf conf = new SparkConf();
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
-				HdfsSupport.remove(resolvedPath, spark.sparkContext().hadoopConfiguration());
-				cleanCfHb(
-					spark, inputPath, entityClazz, resolvedPath, dsMasterDuplicatePath, outputPath);
-			});
-	}
-
-	private static <T extends Result> void cleanCfHb(SparkSession spark, String inputPath, Class<T> entityClazz,
-		String resolvedPath, String masterDuplicatePath, String outputPath) {
-
-		// read the master-duplicate tuples
-		Dataset<MasterDuplicate> md = spark
-			.read()
-			.textFile(masterDuplicatePath)
-			.map(as(MasterDuplicate.class), Encoders.bean(MasterDuplicate.class));
-
-		// prepare the resolved CF|HB references with the corresponding EMPTY master ID
-		Dataset<IdCfHbMapping> resolved = spark
-			.read()
-			.textFile(inputPath)
-			.map(as(entityClazz), Encoders.bean(entityClazz))
-			.flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class));
-
-		// set the EMPTY master ID/NAME and save it
-		resolved
-			.joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId")))
-			.map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class))
-			.filter((FilterFunction<IdCfHbMapping>) m -> Objects.nonNull(m.getMasterId()))
-			.write()
-			.mode(SaveMode.Overwrite)
-			.json(resolvedPath);
-
-		// read again the resolved CF|HB mapping
-		Dataset<IdCfHbMapping> resolvedDS = spark
-			.read()
-			.textFile(resolvedPath)
-			.map(as(IdCfHbMapping.class), Encoders.bean(IdCfHbMapping.class));
-
-		// read the result table
-		Dataset<T> res = spark
-			.read()
-			.textFile(inputPath)
-			.map(as(entityClazz), Encoders.bean(entityClazz));
-
-		// Join the results with the resolved CF|HB mapping, apply the mapping and save it
-		res
-			.joinWith(resolvedDS, res.col("id").equalTo(resolvedDS.col("resultId")), "left")
-			.groupByKey((MapFunction<Tuple2<T, IdCfHbMapping>, String>) t -> t._1().getId(), Encoders.STRING())
-			.mapGroups(getMapGroupsFunction(), Encoders.bean(entityClazz))
-			.write()
-			.mode(SaveMode.Overwrite)
-			.option("compression", "gzip")
-			.json(outputPath);
-	}
-
-	private static MapFunction<Tuple2<IdCfHbMapping, MasterDuplicate>, IdCfHbMapping> asIdCfHbMapping() {
-		return t -> {
-			final IdCfHbMapping mapping = t._1();
-			Optional
-				.ofNullable(t._2())
-				.ifPresent(t2 -> {
-					mapping.setMasterId(t2.getMasterId());
-					mapping.setMasterName(t2.getMasterName());
-
-				});
-			return mapping;
-		};
-	}
-
-	private static <T extends Result> FlatMapFunction<T, IdCfHbMapping> flattenCfHbFn() {
-		return r -> Stream
-			.concat(
-				Optional
-					.ofNullable(r.getCollectedfrom())
-					.map(cf -> cf.stream().map(KeyValue::getKey))
-					.orElse(Stream.empty()),
-				Stream
-					.concat(
-						Optional
-							.ofNullable(r.getInstance())
-							.map(
-								instances -> instances
-									.stream()
-									.map(i -> Optional.ofNullable(i.getHostedby()).map(KeyValue::getKey).orElse("")))
-							.orElse(Stream.empty())
-							.filter(StringUtils::isNotBlank),
-						Optional
-							.ofNullable(r.getInstance())
-							.map(
-								instances -> instances
-									.stream()
-									.map(
-										i -> Optional
-											.ofNullable(i.getCollectedfrom())
-											.map(KeyValue::getKey)
-											.orElse("")))
-							.orElse(Stream.empty())
-							.filter(StringUtils::isNotBlank)))
-			.distinct()
-			.filter(StringUtils::isNotBlank)
-			.map(cfHb -> asIdCfHbMapping(r.getId(), cfHb))
-			.iterator();
-	}
-
-	private static <T extends Result> MapGroupsFunction<String, Tuple2<T, IdCfHbMapping>, T> getMapGroupsFunction() {
-		return new MapGroupsFunction<String, Tuple2<T, IdCfHbMapping>, T>() {
-			@Override
-			public T call(String key, Iterator<Tuple2<T, IdCfHbMapping>> values) {
-				final Tuple2<T, IdCfHbMapping> first = values.next();
-				final T res = first._1();
-
-				updateResult(res, first._2());
-				values.forEachRemaining(t -> updateResult(res, t._2()));
-				return res;
-			}
-
-			private void updateResult(T res, IdCfHbMapping m) {
-				if (Objects.nonNull(m)) {
-					res.getCollectedfrom().forEach(kv -> updateKeyValue(kv, m));
-					res.getInstance().forEach(i -> {
-						updateKeyValue(i.getHostedby(), m);
-						updateKeyValue(i.getCollectedfrom(), m);
-					});
-				}
-			}
-
-			private void updateKeyValue(final KeyValue kv, final IdCfHbMapping a) {
-				if (kv.getKey().equals(a.getCfhb())) {
-					kv.setKey(a.getMasterId());
-					kv.setValue(a.getMasterName());
-				}
-			}
-
-		};
-	}
-
-	private static IdCfHbMapping asIdCfHbMapping(String resultId, String cfHb) {
-		IdCfHbMapping m = new IdCfHbMapping(resultId);
-		m.setCfhb(cfHb);
-		return m;
-	}
-
-	private static <R> MapFunction<String, R> as(Class<R> clazz) {
-		return s -> OBJECT_MAPPER.readValue(s, clazz);
-	}
-}

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

@@ -1,211 +0,0 @@
-
-package eu.dnetlib.dhp.oa.graph.clean.country;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.io.Serializable;
-import java.util.Collection;
-import java.util.List;
-import java.util.Optional;
-import java.util.function.Function;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-
-import javax.swing.text.html.Option;
-
-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.MapFunction;
-import org.apache.spark.sql.Dataset;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SaveMode;
-import org.apache.spark.sql.SparkSession;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * @author miriam.baglioni
- * @Date 20/07/22
- */
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob;
-import eu.dnetlib.dhp.schema.oaf.Country;
-import eu.dnetlib.dhp.schema.oaf.Instance;
-import eu.dnetlib.dhp.schema.oaf.Result;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
-import eu.dnetlib.dhp.schema.oaf.utils.PidType;
-
-public class CleanCountrySparkJob implements Serializable {
-	private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class);
-
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
-	public static void main(String[] args) throws Exception {
-
-		String jsonConfiguration = IOUtils
-			.toString(
-				CleanCountrySparkJob.class
-					.getResourceAsStream(
-						"/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json"));
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
-		parser.parseArgument(args);
-
-		Boolean isSparkSessionManaged = Optional
-			.ofNullable(parser.get("isSparkSessionManaged"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
-
-		String inputPath = parser.get("inputPath");
-		log.info("inputPath: {}", inputPath);
-
-		String workingDir = parser.get("workingDir");
-		log.info("workingDir: {}", workingDir);
-
-		String datasourcePath = parser.get("hostedBy");
-		log.info("datasourcePath: {}", datasourcePath);
-
-		String country = parser.get("country");
-		log.info("country: {}", country);
-
-		String[] verifyParam = parser.get("verifyParam").split(";");
-		log.info("verifyParam: {}", verifyParam);
-
-		String collectedfrom = parser.get("collectedfrom");
-		log.info("collectedfrom: {}", collectedfrom);
-
-		String graphTableClassName = parser.get("graphTableClassName");
-		log.info("graphTableClassName: {}", graphTableClassName);
-
-		Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
-
-		SparkConf conf = new SparkConf();
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-
-				cleanCountry(
-					spark, country, verifyParam, inputPath, entityClazz, workingDir, collectedfrom, datasourcePath);
-			});
-	}
-
-	private static <T extends Result> void cleanCountry(SparkSession spark, String country, String[] verifyParam,
-		String inputPath, Class<T> entityClazz, String workingDir, String collectedfrom, String datasourcePath) {
-
-		List<String> hostedBy = spark
-			.read()
-			.textFile(datasourcePath)
-			.collectAsList();
-
-		Dataset<T> res = spark
-			.read()
-			.textFile(inputPath)
-			.map(
-				(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
-				Encoders.bean(entityClazz));
-
-		res.map((MapFunction<T, T>) r -> {
-			if (r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) ||
-				!r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) {
-				return r;
-			}
-
-			List<StructuredProperty> ids = getPidsAndAltIds(r).collect(Collectors.toList());
-			if (ids
-				.stream()
-				.anyMatch(
-					p -> p
-						.getQualifier()
-						.getClassid()
-						.equals(PidType.doi.toString()) && pidInParam(p.getValue(), verifyParam))) {
-				r
-					.setCountry(
-						r
-							.getCountry()
-							.stream()
-							.filter(
-								c -> toTakeCountry(c, country))
-							.collect(Collectors.toList()));
-
-			}
-
-			return r;
-		}, Encoders.bean(entityClazz))
-			.write()
-			.mode(SaveMode.Overwrite)
-			.option("compression", "gzip")
-			.json(workingDir);
-
-		spark
-			.read()
-			.textFile(workingDir)
-			.map(
-				(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
-				Encoders.bean(entityClazz))
-			.write()
-			.mode(SaveMode.Overwrite)
-			.option("compression", "gzip")
-			.json(inputPath);
-	}
-
-	private static <T extends Result> Stream<StructuredProperty> getPidsAndAltIds(T r) {
-		final Stream<StructuredProperty> resultPids = Optional
-			.ofNullable(r.getPid())
-			.map(Collection::stream)
-			.orElse(Stream.empty());
-
-		final Stream<StructuredProperty> instancePids = Optional
-			.ofNullable(r.getInstance())
-			.map(
-				instance -> instance
-					.stream()
-					.flatMap(
-						i -> Optional
-							.ofNullable(i.getPid())
-							.map(Collection::stream)
-							.orElse(Stream.empty())))
-			.orElse(Stream.empty());
-
-		final Stream<StructuredProperty> instanceAltIds = Optional
-			.ofNullable(r.getInstance())
-			.map(
-				instance -> instance
-					.stream()
-					.flatMap(
-						i -> Optional
-							.ofNullable(i.getAlternateIdentifier())
-							.map(Collection::stream)
-							.orElse(Stream.empty())))
-			.orElse(Stream.empty());
-
-		return Stream
-			.concat(
-				Stream.concat(resultPids, instancePids),
-				instanceAltIds);
-	}
-
-	private static boolean pidInParam(String value, String[] verifyParam) {
-		for (String s : verifyParam)
-			if (value.startsWith(s))
-				return true;
-		return false;
-	}
-
-	private static boolean toTakeCountry(Country c, String country) {
-		// If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be
-		// inserted via propagation
-		if (!Optional.ofNullable(c.getDataInfo()).isPresent())
-			return true;
-		if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent())
-			return true;
-		return !(c
-			.getClassid()
-			.equalsIgnoreCase(country) &&
-			c.getDataInfo().getInferenceprovenance().equals("propagation"));
-	}
-
-}

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

@@ -83,12 +83,57 @@
         </property>
     </parameters>
 
-    <start to="fork_clean_graph"/>
+    <start to="prepare_info"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
+    <fork name="prepare_info">
+        <path start="select_datasourceId_from_country"/>
+        <path start="get_ds_master_duplicate"/>
+    </fork>
+
+    <action name="select_datasourceId_from_country">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Select datasource ID from country</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.GetDatasourceFromCountry</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=10000
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${graphInputPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--country</arg><arg>${country}</arg>
+        </spark>
+        <ok to="wait_prepare"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="get_ds_master_duplicate">
+        <java>
+            <main-class>eu.dnetlib.dhp.oa.graph.clean.MasterDuplicateAction</main-class>
+            <arg>--postgresUrl</arg><arg>${postgresURL}</arg>
+            <arg>--postgresUser</arg><arg>${postgresUser}</arg>
+            <arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
+            <arg>--hdfsPath</arg><arg>${workingDir}/masterduplicate</arg>
+            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
+        </java>
+        <ok to="wait_prepare"/>
+        <error to="Kill"/>
+    </action>
+
+    <join name="wait_prepare" to="fork_clean_graph"/>
+
     <fork name="fork_clean_graph">
         <path start="clean_publication"/>
         <path start="clean_dataset"/>
@@ -115,12 +160,20 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/publication</arg>
             <arg>--outputPath</arg><arg>${graphOutputPath}/publication</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
+            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
+            <arg>--deepClean</arg><arg>${shouldClean}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -141,12 +194,20 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/dataset</arg>
             <arg>--outputPath</arg><arg>${graphOutputPath}/dataset</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
+            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
+            <arg>--deepClean</arg><arg>${shouldClean}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -167,12 +228,20 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.sql.shuffle.partitions=5000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/otherresearchproduct</arg>
             <arg>--outputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
+            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
+            <arg>--deepClean</arg><arg>${shouldClean}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -193,12 +262,20 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.sql.shuffle.partitions=2000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/software</arg>
             <arg>--outputPath</arg><arg>${graphOutputPath}/software</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
+            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
+            <arg>--deepClean</arg><arg>${shouldClean}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -219,12 +296,20 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.sql.shuffle.partitions=1000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/datasource</arg>
             <arg>--outputPath</arg><arg>${graphOutputPath}/datasource</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
+            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
+            <arg>--deepClean</arg><arg>${shouldClean}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -245,12 +330,20 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.sql.shuffle.partitions=1000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/organization</arg>
             <arg>--outputPath</arg><arg>${graphOutputPath}/organization</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
+            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
+            <arg>--deepClean</arg><arg>${shouldClean}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -271,12 +364,20 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.sql.shuffle.partitions=2000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/project</arg>
             <arg>--outputPath</arg><arg>${graphOutputPath}/project</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
+            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
+            <arg>--deepClean</arg><arg>${shouldClean}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -297,486 +398,26 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.sql.shuffle.partitions=20000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/relation</arg>
             <arg>--outputPath</arg><arg>${graphOutputPath}/relation</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
+            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
+            <arg>--deepClean</arg><arg>${shouldClean}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
     </action>
 
-    <join name="wait_clean" to="clean_context"/>
+    <join name="wait_clean" to="End"/>
-
-    <decision name="clean_context">
-        <switch>
-            <case to="fork_clean_context">${wf:conf('shouldClean') eq true}</case>
-            <default to="End"/>
-        </switch>
-    </decision>
-
-    <fork name="fork_clean_context">
-        <path start="clean_publication_context"/>
-        <path start="clean_dataset_context"/>
-        <path start="clean_otherresearchproduct_context"/>
-        <path start="clean_software_context"/>
-    </fork>
-
-    <action name="clean_publication_context">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean publications context</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/publication</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/publication</arg>
-            <arg>--contextId</arg><arg>${contextId}</arg>
-            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
-        </spark>
-        <ok to="wait_clean_context"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="clean_dataset_context">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean datasets Context</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/dataset</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/dataset</arg>
-            <arg>--contextId</arg><arg>${contextId}</arg>
-            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
-        </spark>
-        <ok to="wait_clean_context"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="clean_otherresearchproduct_context">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean otherresearchproducts context</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/otherresearchproduct</arg>
-            <arg>--contextId</arg><arg>${contextId}</arg>
-            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
-        </spark>
-        <ok to="wait_clean_context"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="clean_software_context">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean softwares context</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/software</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/software</arg>
-            <arg>--contextId</arg><arg>${contextId}</arg>
-            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
-        </spark>
-        <ok to="wait_clean_context"/>
-        <error to="Kill"/>
-    </action>
-
-    <join name="wait_clean_context" to="select_datasourceId_from_country"/>
-
-    <action name="select_datasourceId_from_country">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Select datasource ID from country</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.country.GetDatasourceFromCountry</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/hostedby</arg>
-            <arg>--country</arg><arg>${country}</arg>
-        </spark>
-        <ok to="fork_clean_country"/>
-        <error to="Kill"/>
-    </action>
-
-    <fork name="fork_clean_country">
-        <path start="clean_publication_country"/>
-        <path start="clean_dataset_country"/>
-        <path start="clean_otherresearchproduct_country"/>
-        <path start="clean_software_country"/>
-    </fork>
-
-    <action name="clean_publication_country">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean publication country</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/publication</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/publication</arg>
-            <arg>--country</arg><arg>${country}</arg>
-            <arg>--verifyParam</arg><arg>${verifyCountryParam}</arg>
-            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
-            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
-        </spark>
-        <ok to="wait_clean_country"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="clean_dataset_country">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean dataset country</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/dataset</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/dataset</arg>
-            <arg>--country</arg><arg>${country}</arg>
-            <arg>--verifyParam</arg><arg>${verifyCountryParam}</arg>
-            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
-            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
-        </spark>
-        <ok to="wait_clean_country"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="clean_otherresearchproduct_country">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean otherresearchproduct country</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/otherresearchproduct</arg>
-            <arg>--country</arg><arg>${country}</arg>
-            <arg>--verifyParam</arg><arg>${verifyCountryParam}</arg>
-            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
-            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
-        </spark>
-        <ok to="wait_clean_country"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="clean_software_country">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean software country</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/software</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/software</arg>
-            <arg>--country</arg><arg>${country}</arg>
-            <arg>--verifyParam</arg><arg>${verifyCountryParam}</arg>
-            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
-            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
-        </spark>
-        <ok to="wait_clean_country"/>
-        <error to="Kill"/>
-    </action>
-
-    <join name="wait_clean_country" to="should_patch_datasource_ids"/>
-
-    <decision name="should_patch_datasource_ids">
-        <switch>
-            <case to="get_ds_master_duplicate">${wf:conf('shouldClean') eq true}</case>
-            <default to="End"/>
-        </switch>
-    </decision>
-
-    <action name="get_ds_master_duplicate">
-        <java>
-            <main-class>eu.dnetlib.dhp.oa.graph.clean.MasterDuplicateAction</main-class>
-            <arg>--postgresUrl</arg><arg>${postgresURL}</arg>
-            <arg>--postgresUser</arg><arg>${postgresUser}</arg>
-            <arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
-            <arg>--hdfsPath</arg><arg>${workingDir}/masterduplicate</arg>
-            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
-        </java>
-        <ok to="fork_patch_cfhb"/>
-        <error to="Kill"/>
-    </action>
-
-    <fork name="fork_patch_cfhb">
-        <path start="patch_publication_cfhb"/>
-        <path start="patch_dataset_cfhb"/>
-        <path start="patch_otherresearchproduct_cfhb"/>
-        <path start="patch_software_cfhb"/>
-    </fork>
-
-    <action name="patch_publication_cfhb">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>patch publication cfhb</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/publication</arg>
-            <arg>--resolvedPath</arg><arg>${workingDir}/cfHbResolved/publication</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/cfHbPatched/publication</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
-            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
-        </spark>
-        <ok to="wait_clean_cfhb"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="patch_dataset_cfhb">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>patch dataset cfhb</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/dataset</arg>
-            <arg>--resolvedPath</arg><arg>${workingDir}/cfHbResolved/dataset</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/cfHbPatched/dataset</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
-            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
-        </spark>
-        <ok to="wait_clean_cfhb"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="patch_otherresearchproduct_cfhb">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>patch otherresearchproduct cfhb</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
-            <arg>--resolvedPath</arg><arg>${workingDir}/cfHbResolved/otherresearchproduct</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/cfHbPatched/otherresearchproduct</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
-            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
-        </spark>
-        <ok to="wait_clean_cfhb"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="patch_software_cfhb">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>patch software cfhb</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/software</arg>
-            <arg>--resolvedPath</arg><arg>${workingDir}/cfHbResolved/software</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/cfHbPatched/software</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
-            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
-        </spark>
-        <ok to="wait_clean_cfhb"/>
-        <error to="Kill"/>
-    </action>
-
-    <join name="wait_clean_cfhb" to="fork_copy_cfhb_patched_results"/>
-
-    <fork name="fork_copy_cfhb_patched_results">
-        <path start="copy_cfhb_patched_publication"/>
-        <path start="copy_cfhb_patched_dataset"/>
-        <path start="copy_cfhb_patched_otherresearchproduct"/>
-        <path start="copy_cfhb_patched_software"/>
-    </fork>
-
-    <action name="copy_cfhb_patched_publication">
-        <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <prepare>
-                <delete path="${graphOutputPath}/publication"/>
-            </prepare>
-            <arg>${workingDir}/cfHbPatched/publication</arg>
-            <arg>${graphOutputPath}/publication</arg>
-        </distcp>
-        <ok to="copy_wait"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="copy_cfhb_patched_dataset">
-        <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <prepare>
-                <delete path="${graphOutputPath}/dataset"/>
-            </prepare>
-            <arg>${workingDir}/cfHbPatched/dataset</arg>
-            <arg>${graphOutputPath}/dataset</arg>
-        </distcp>
-        <ok to="copy_wait"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="copy_cfhb_patched_otherresearchproduct">
-        <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <prepare>
-                <delete path="${graphOutputPath}/otherresearchproduct"/>
-            </prepare>
-            <arg>${workingDir}/cfHbPatched/otherresearchproduct</arg>
-            <arg>${graphOutputPath}/otherresearchproduct</arg>
-        </distcp>
-        <ok to="copy_wait"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="copy_cfhb_patched_software">
-        <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <prepare>
-                <delete path="${graphOutputPath}/software"/>
-            </prepare>
-            <arg>${workingDir}/cfHbPatched/software</arg>
-            <arg>${graphOutputPath}/software</arg>
-        </distcp>
-        <ok to="copy_wait"/>
-        <error to="Kill"/>
-    </action>
-
-    <join name="copy_wait" to="End"/>
 
     <end name="End"/>
 

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json

@@ -28,5 +28,53 @@
     "paramLongName": "graphTableClassName",
     "paramDescription": "class name moelling the graph table",
     "paramRequired": true
+  },
+  {
+    "paramName": "ci",
+    "paramLongName": "contextId",
+    "paramDescription": "the id of the context to be removed",
+    "paramRequired": false
+  },
+  {
+    "paramName": "vf",
+    "paramLongName": "verifyParam",
+    "paramDescription": "the parameter to be verified to remove the context",
+    "paramRequired": false
+  },
+  {
+    "paramName": "c",
+    "paramLongName": "country",
+    "paramDescription": "the id of the context to be removed",
+    "paramRequired": false
+  },
+  {
+    "paramName": "vfc",
+    "paramLongName": "verifyCountryParam",
+    "paramDescription": "the parameter to be verified to remove the country",
+    "paramRequired": false
+  },
+  {
+    "paramName": "cf",
+    "paramLongName": "collectedfrom",
+    "paramDescription": "the collectedfrom value for which we should apply the cleaning",
+    "paramRequired": false
+  },
+  {
+    "paramName": "hb",
+    "paramLongName": "hostedBy",
+    "paramDescription": "the set of datasources having the specified country in the graph searched for in the hostedby of the results",
+    "paramRequired": false
+  },
+  {
+    "paramName": "md",
+    "paramLongName": "masterDuplicatePath",
+    "paramDescription": "path to the file on HDFS holding the datasource id tuples [master, duplicate]",
+    "paramRequired": false
+  },
+  {
+    "paramName": "dc",
+    "paramLongName": "deepClean",
+    "paramDescription": "flag to activate further cleaning steps",
+    "paramRequired": true
   }
 ]

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java

@@ -1,289 +0,0 @@
-
-package eu.dnetlib.dhp.oa.graph.clean;
-
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.List;
-
-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.api.java.function.MapFunction;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SparkSession;
-import org.junit.jupiter.api.AfterAll;
-import org.junit.jupiter.api.Assertions;
-import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.Test;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import eu.dnetlib.dhp.schema.oaf.Publication;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
-
-public class CleanContextTest {
-
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
-	private static SparkSession spark;
-
-	private static Path workingDir;
-
-	private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class);
-
-	@BeforeAll
-	public static void beforeAll() throws IOException {
-		workingDir = Files.createTempDirectory(CleanContextTest.class.getSimpleName());
-		log.info("using work dir {}", workingDir);
-
-		SparkConf conf = new SparkConf();
-		conf.setAppName(CleanContextTest.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(CleanContextTest.class.getSimpleName())
-			.config(conf)
-			.getOrCreate();
-	}
-
-	@AfterAll
-	public static void afterAll() throws IOException {
-		FileUtils.deleteDirectory(workingDir.toFile());
-		spark.stop();
-	}
-
-	@Test
-	public void testResultClean() throws Exception {
-		final String sourcePath = getClass()
-			.getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json")
-			.getPath();
-		final String prefix = "gcube ";
-
-		spark
-			.read()
-			.textFile(sourcePath)
-			.map(
-				(MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class),
-				Encoders.bean(Publication.class))
-			.write()
-			.json(workingDir.toString() + "/publication");
-
-		CleanContextSparkJob.main(new String[] {
-			"--isSparkSessionManaged", Boolean.FALSE.toString(),
-			"--inputPath", workingDir.toString() + "/publication",
-			"--graphTableClassName", Publication.class.getCanonicalName(),
-			"--workingDir", workingDir.toString() + "/working",
-			"--contextId", "sobigdata",
-			"--verifyParam", "gCube "
-		});
-
-		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(7, tmp.count());
-
-		// original result with sobigdata context and gcube as starting string in the main title for the publication
-		Assertions
-			.assertEquals(
-				0,
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))
-					.collect()
-					.get(0)
-					.getContext()
-					.size());
-
-		// original result with sobigdata context without gcube as starting string in the main title for the publication
-		Assertions
-			.assertEquals(
-				1,
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
-					.collect()
-					.get(0)
-					.getContext()
-					.size());
-		Assertions
-			.assertEquals(
-				"sobigdata::projects::2",
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
-					.collect()
-					.get(0)
-					.getContext()
-					.get(0)
-					.getId());
-
-		// original result with sobigdata context with gcube as starting string in the subtitle
-		Assertions
-			.assertEquals(
-				1,
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
-					.collect()
-					.get(0)
-					.getContext()
-					.size());
-		Assertions
-			.assertEquals(
-				"sobigdata::projects::2",
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
-					.collect()
-					.get(0)
-					.getContext()
-					.get(0)
-					.getId());
-		List<StructuredProperty> titles = tmp
-			.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
-			.collect()
-			.get(0)
-			.getTitle();
-		Assertions.assertEquals(1, titles.size());
-		Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
-		Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid());
-
-		// original result with sobigdata context with gcube not as starting string in the main title
-		Assertions
-			.assertEquals(
-				1,
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
-					.collect()
-					.get(0)
-					.getContext()
-					.size());
-		Assertions
-			.assertEquals(
-				"sobigdata::projects::1",
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
-					.collect()
-					.get(0)
-					.getContext()
-					.get(0)
-					.getId());
-		titles = tmp
-			.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
-			.collect()
-			.get(0)
-			.getTitle();
-		Assertions.assertEquals(1, titles.size());
-		Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix));
-		Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()));
-		Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
-
-		// original result with sobigdata in context and also other contexts with gcube as starting string for the main
-		// title
-		Assertions
-			.assertEquals(
-				1,
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
-					.collect()
-					.get(0)
-					.getContext()
-					.size());
-		Assertions
-			.assertEquals(
-				"dh-ch",
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
-					.collect()
-					.get(0)
-					.getContext()
-					.get(0)
-					.getId());
-		titles = tmp
-			.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
-			.collect()
-			.get(0)
-			.getTitle();
-		Assertions.assertEquals(1, titles.size());
-		Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
-		Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
-
-		// original result with multiple main title one of which whith gcube as starting string and with 2 contextes
-		Assertions
-			.assertEquals(
-				1,
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
-					.collect()
-					.get(0)
-					.getContext()
-					.size());
-		Assertions
-			.assertEquals(
-				"dh-ch",
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
-					.collect()
-					.get(0)
-					.getContext()
-					.get(0)
-					.getId());
-		titles = tmp
-			.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
-			.collect()
-			.get(0)
-			.getTitle();
-		Assertions.assertEquals(2, titles.size());
-		Assertions
-			.assertTrue(
-				titles
-					.stream()
-					.anyMatch(
-						t -> t.getQualifier().getClassid().equals("main title")
-							&& t.getValue().toLowerCase().startsWith(prefix)));
-
-		// original result without sobigdata in context with gcube as starting string for the main title
-		Assertions
-			.assertEquals(
-				1,
-				tmp
-					.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
-					.collect()
-					.get(0)
-					.getContext()
-					.size());
-		Assertions
-			.assertEquals(
-				"dh-ch",
-				tmp
-					.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
-					.collect()
-					.get(0)
-					.getContext()
-					.get(0)
-					.getId());
-		titles = tmp
-			.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
-			.collect()
-			.get(0)
-			.getTitle();
-		Assertions.assertEquals(2, titles.size());
-
-		Assertions
-			.assertTrue(
-				titles
-					.stream()
-					.anyMatch(
-						t -> t.getQualifier().getClassid().equals("main title")
-							&& t.getValue().toLowerCase().startsWith(prefix)));
-
-	}
-}

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java

@@ -1,190 +0,0 @@
-
-package eu.dnetlib.dhp.oa.graph.clean;
-
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-
-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.api.java.function.MapFunction;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SparkSession;
-import org.junit.jupiter.api.AfterAll;
-import org.junit.jupiter.api.Assertions;
-import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.Test;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * @author miriam.baglioni
- * @Date 20/07/22
- */
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob;
-import eu.dnetlib.dhp.schema.oaf.Dataset;
-import eu.dnetlib.dhp.schema.oaf.Publication;
-
-public class CleanCountryTest {
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
-	private static SparkSession spark;
-
-	private static Path workingDir;
-
-	private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class);
-
-	@BeforeAll
-	public static void beforeAll() throws IOException {
-		workingDir = Files.createTempDirectory(CleanCountryTest.class.getSimpleName());
-		log.info("using work dir {}", workingDir);
-
-		SparkConf conf = new SparkConf();
-		conf.setAppName(CleanCountryTest.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(CleanCountryTest.class.getSimpleName())
-			.config(conf)
-			.getOrCreate();
-	}
-
-	@AfterAll
-	public static void afterAll() throws IOException {
-		FileUtils.deleteDirectory(workingDir.toFile());
-		spark.stop();
-	}
-
-	@Test
-	public void testResultClean() throws Exception {
-		final String sourcePath = getClass()
-			.getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json")
-			.getPath();
-
-		spark
-			.read()
-			.textFile(sourcePath)
-			.map(
-				(MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class),
-				Encoders.bean(Publication.class))
-			.write()
-			.json(workingDir.toString() + "/publication");
-
-		CleanCountrySparkJob.main(new String[] {
-			"--isSparkSessionManaged", Boolean.FALSE.toString(),
-			"--inputPath", workingDir.toString() + "/publication",
-			"--graphTableClassName", Publication.class.getCanonicalName(),
-			"--workingDir", workingDir.toString() + "/working",
-			"--country", "NL",
-			"--verifyParam", "10.17632",
-			"--collectedfrom", "NARCIS",
-			"--hostedBy", getClass()
-				.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")
-				.getPath()
-		});
-
-		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(8, tmp.count());
-
-		// original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS
-		Assertions
-			.assertEquals(
-				1,
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))
-					.collect()
-					.get(0)
-					.getCountry()
-					.size());
-
-		// original result with NL country and pid not starting with Mendely prefix
-		Assertions
-			.assertEquals(
-				1,
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
-					.collect()
-					.get(0)
-					.getCountry()
-					.size());
-
-		// original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not
-		// inserted with propagation
-		Assertions
-			.assertEquals(
-				1,
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
-					.collect()
-					.get(0)
-					.getCountry()
-					.size());
-
-		// original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with
-		// propagation
-		Assertions
-			.assertEquals(
-				0,
-				tmp
-					.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6ag"))
-					.collect()
-					.get(0)
-					.getCountry()
-					.size());
-	}
-
-	@Test
-	public void testDatasetClean() throws Exception {
-		final String sourcePath = getClass()
-			.getResource("/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json")
-			.getPath();
-
-		spark
-			.read()
-			.textFile(sourcePath)
-			.map(
-				(MapFunction<String, Dataset>) r -> OBJECT_MAPPER.readValue(r, Dataset.class),
-				Encoders.bean(Dataset.class))
-			.write()
-			.json(workingDir.toString() + "/dataset");
-
-		CleanCountrySparkJob.main(new String[] {
-			"--isSparkSessionManaged", Boolean.FALSE.toString(),
-			"--inputPath", workingDir.toString() + "/dataset",
-			"-graphTableClassName", Dataset.class.getCanonicalName(),
-			"-workingDir", workingDir.toString() + "/working",
-			"-country", "NL",
-			"-verifyParam", "10.17632",
-			"-collectedfrom", "NARCIS",
-			"-hostedBy", getClass()
-				.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")
-				.getPath()
-		});
-
-		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-		JavaRDD<Dataset> tmp = sc
-			.textFile(workingDir.toString() + "/dataset")
-			.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
-
-		Assertions.assertEquals(1, tmp.count());
-
-		Assertions.assertEquals(0, tmp.first().getCountry().size());
-
-	}
-
-}

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java

@@ -0,0 +1,924 @@
+
+package eu.dnetlib.dhp.oa.graph.clean;
+
+import static org.junit.jupiter.api.Assertions.*;
+import static org.mockito.Mockito.lenient;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.*;
+import java.util.stream.Collectors;
+
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.filefilter.FalseFileFilter;
+import org.apache.commons.io.filefilter.TrueFileFilter;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
+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.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+
+@ExtendWith(MockitoExtension.class)
+public class CleanGraphSparkJobTest {
+
+	private static final Logger log = LoggerFactory.getLogger(CleanGraphSparkJobTest.class);
+
+	public static final ObjectMapper MAPPER = new ObjectMapper()
+		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+
+	@Mock
+	private ISLookUpService isLookUpService;
+
+	private VocabularyGroup vocabularies;
+
+	private CleaningRuleMap mapping;
+
+	private static SparkSession spark;
+
+	private static Path testBaseTmpPath;
+
+	private static String graphInputPath;
+
+	private static String graphOutputPath;
+
+	private static String dsMasterDuplicatePath;
+
+	@BeforeAll
+	public static void beforeAll() throws IOException, URISyntaxException {
+		testBaseTmpPath = Files.createTempDirectory(CleanGraphSparkJobTest.class.getSimpleName());
+		log.info("using test base path {}", testBaseTmpPath);
+
+		File basePath = Paths
+			.get(
+				Objects
+					.requireNonNull(
+						CleanGraphSparkJobTest.class.getResource("/eu/dnetlib/dhp/oa/graph/clean/graph"))
+					.toURI())
+			.toFile();
+
+		List<File> paths = FileUtils
+			.listFilesAndDirs(basePath, FalseFileFilter.FALSE, TrueFileFilter.TRUE)
+			.stream()
+			.filter(f -> !f.getAbsolutePath().endsWith("/graph"))
+			.collect(Collectors.toList());
+
+		for (File path : paths) {
+			String type = StringUtils.substringAfterLast(path.getAbsolutePath(), "/");
+			FileUtils
+				.copyDirectory(
+					path,
+					testBaseTmpPath.resolve("input").resolve("graph").resolve(type).toFile());
+		}
+
+		FileUtils
+			.copyFileToDirectory(
+				Paths
+					.get(
+						CleanGraphSparkJobTest.class
+							.getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/masterduplicate.json")
+							.toURI())
+					.toFile(),
+				testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toFile());
+
+		graphInputPath = testBaseTmpPath.resolve("input").resolve("graph").toString();
+		graphOutputPath = testBaseTmpPath.resolve("output").resolve("graph").toString();
+		dsMasterDuplicatePath = testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toString();
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(CleanGraphSparkJobTest.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", testBaseTmpPath.toString());
+		conf.set("hive.metastore.warehouse.dir", testBaseTmpPath.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@BeforeEach
+	public void setUp() throws ISLookUpException, IOException {
+		lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs());
+		lenient()
+			.when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY))
+			.thenReturn(synonyms());
+
+		vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService);
+		mapping = CleaningRuleMap.create(vocabularies);
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(testBaseTmpPath.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void testCleanRelations() throws Exception {
+
+		spark
+			.read()
+			.textFile(graphInputPath.toString() + "/relation")
+			.map(as(Relation.class), Encoders.bean(Relation.class))
+			.collectAsList()
+			.forEach(
+				r -> assertFalse(
+					vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r.getRelClass())));
+
+		new CleanGraphSparkJob(
+			args(
+				"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json",
+				new String[] {
+					"--inputPath", graphInputPath + "/relation",
+					"--outputPath", graphOutputPath + "/relation",
+					"--isLookupUrl", "lookupurl",
+					"--graphTableClassName", Relation.class.getCanonicalName(),
+					"--deepClean", "false",
+					"--masterDuplicatePath", dsMasterDuplicatePath,
+				})).run(false, isLookUpService);
+
+		spark
+			.read()
+			.textFile(graphOutputPath.toString() + "/relation")
+			.map(as(Relation.class), Encoders.bean(Relation.class))
+			.collectAsList()
+			.forEach(r -> {
+
+				assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r.getRelClass()));
+				assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_SUBRELTYPE).contains(r.getSubRelType()));
+
+				assertEquals("iis", r.getDataInfo().getProvenanceaction().getClassid());
+				assertEquals("Inferred by OpenAIRE", r.getDataInfo().getProvenanceaction().getClassname());
+			});
+	}
+
+	@Test
+	void testFilter_invisible_true() throws Exception {
+
+		assertNotNull(vocabularies);
+		assertNotNull(mapping);
+
+		String json = IOUtils
+			.toString(
+				Objects
+					.requireNonNull(
+						getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json")));
+		Publication p_in = MAPPER.readValue(json, Publication.class);
+
+		assertTrue(p_in instanceof Result);
+		assertTrue(p_in instanceof Publication);
+
+		assertEquals(true, GraphCleaningFunctions.filter(p_in));
+	}
+
+	@Test
+	void testFilter_true_nothing_to_filter() throws Exception {
+
+		assertNotNull(vocabularies);
+		assertNotNull(mapping);
+
+		String json = IOUtils
+			.toString(
+				Objects
+					.requireNonNull(
+						getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json")));
+		Publication p_in = MAPPER.readValue(json, Publication.class);
+
+		assertTrue(p_in instanceof Result);
+		assertTrue(p_in instanceof Publication);
+
+		assertEquals(true, GraphCleaningFunctions.filter(p_in));
+	}
+
+	@Test
+	void testFilter_missing_invisible() throws Exception {
+
+		assertNotNull(vocabularies);
+		assertNotNull(mapping);
+
+		String json = IOUtils
+			.toString(
+				Objects
+					.requireNonNull(
+						getClass()
+							.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json")));
+		Publication p_in = MAPPER.readValue(json, Publication.class);
+
+		assertTrue(p_in instanceof Result);
+		assertTrue(p_in instanceof Publication);
+
+		assertEquals(true, GraphCleaningFunctions.filter(p_in));
+	}
+
+	@Test
+	void testCleaning_publication() throws Exception {
+
+		final String id = "50|CSC_________::2250a70c903c6ac6e4c01438259e9375";
+
+		Publication p_in = read(spark, graphInputPath + "/publication", Publication.class)
+			.filter(String.format("id = '%s'", id))
+			.first();
+
+		assertNull(p_in.getBestaccessright());
+		assertTrue(p_in instanceof Result);
+		assertTrue(p_in instanceof Publication);
+
+		new CleanGraphSparkJob(
+			args(
+				"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json",
+				new String[] {
+					"--inputPath", graphInputPath + "/publication",
+					"--outputPath", graphOutputPath + "/publication",
+					"--isLookupUrl", "lookupurl",
+					"--graphTableClassName", Publication.class.getCanonicalName(),
+					"--deepClean", "false",
+					"--masterDuplicatePath", dsMasterDuplicatePath,
+				})).run(false, isLookUpService);
+
+		Publication p = read(spark, graphOutputPath + "/publication", Publication.class)
+			.filter(String.format("id = '%s'", id))
+			.first();
+
+		assertNull(p.getPublisher());
+
+		assertEquals("und", p.getLanguage().getClassid());
+		assertEquals("Undetermined", p.getLanguage().getClassname());
+
+		assertEquals("DE", p.getCountry().get(0).getClassid());
+		assertEquals("Germany", p.getCountry().get(0).getClassname());
+
+		assertEquals("0018", p.getInstance().get(0).getInstancetype().getClassid());
+		assertEquals("Annotation", p.getInstance().get(0).getInstancetype().getClassname());
+
+		assertEquals("0027", p.getInstance().get(1).getInstancetype().getClassid());
+		assertEquals("Model", p.getInstance().get(1).getInstancetype().getClassname());
+
+		assertEquals("0038", p.getInstance().get(2).getInstancetype().getClassid());
+		assertEquals("Other literature type", p.getInstance().get(2).getInstancetype().getClassname());
+
+		assertEquals("CLOSED", p.getInstance().get(0).getAccessright().getClassid());
+		assertEquals("Closed Access", p.getInstance().get(0).getAccessright().getClassname());
+
+		Set<String> pidTerms = vocabularies.getTerms(ModelConstants.DNET_PID_TYPES);
+		assertTrue(
+			p
+				.getPid()
+				.stream()
+				.map(StructuredProperty::getQualifier)
+				.allMatch(q -> pidTerms.contains(q.getClassid())));
+
+		List<Instance> poi = p.getInstance();
+		assertNotNull(poi);
+		assertEquals(3, poi.size());
+
+		final Instance poii = poi.get(0);
+		assertNotNull(poii);
+		assertNotNull(poii.getPid());
+
+		assertEquals(2, poii.getPid().size());
+
+		assertTrue(
+			poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x")));
+		assertTrue(poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd")));
+
+		assertNotNull(poii.getAlternateIdentifier());
+		assertEquals(1, poii.getAlternateIdentifier().size());
+
+		assertTrue(
+			poii
+				.getAlternateIdentifier()
+				.stream()
+				.anyMatch(s -> s.getValue().equals("10.1009/qwerty")));
+
+		assertEquals(3, p.getTitle().size());
+
+		List<String> titles = p
+			.getTitle()
+			.stream()
+			.map(StructuredProperty::getValue)
+			.collect(Collectors.toList());
+		assertTrue(titles.contains("omic"));
+		assertTrue(
+			titles.contains("Optical response of strained- and unstrained-silicon cold-electron bolometers test"));
+		assertTrue(titles.contains("｢マキャベリ的知性と心の理論の進化論｣ リチャード・バーン， アンドリュー・ホワイトゥン 編／藤田和生， 山下博志， 友永雅巳 監訳"));
+
+		assertEquals("CLOSED", p.getBestaccessright().getClassid());
+		assertNull(p.getPublisher());
+
+		assertEquals("1970-10-07", p.getDateofacceptance().getValue());
+
+		assertEquals("0038", p.getInstance().get(2).getInstancetype().getClassid());
+		assertEquals("Other literature type", p.getInstance().get(2).getInstancetype().getClassname());
+
+		final List<Instance> pci = p.getInstance();
+		assertNotNull(pci);
+		assertEquals(3, pci.size());
+
+		final Instance pcii = pci.get(0);
+		assertNotNull(pcii);
+		assertNotNull(pcii.getPid());
+
+		assertEquals(2, pcii.getPid().size());
+
+		assertTrue(
+			pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x")));
+		assertTrue(pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd")));
+
+		assertNotNull(pcii.getAlternateIdentifier());
+		assertEquals(1, pcii.getAlternateIdentifier().size());
+		assertTrue(
+			pcii
+				.getAlternateIdentifier()
+				.stream()
+				.anyMatch(s -> s.getValue().equals("10.1009/qwerty")));
+
+		assertNotNull(p.getSubject());
+
+		List<Subject> fos_subjects = p
+			.getSubject()
+			.stream()
+			.filter(s -> ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))
+			.collect(Collectors.toList());
+
+		assertNotNull(fos_subjects);
+		assertEquals(2, fos_subjects.size());
+
+		assertTrue(
+			fos_subjects
+				.stream()
+				.anyMatch(
+					s -> "0101 mathematics".equals(s.getValue()) &
+						ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) &
+						"sysimport:crosswalk:datasetarchive"
+							.equals(s.getDataInfo().getProvenanceaction().getClassid())));
+
+		assertTrue(
+			fos_subjects
+				.stream()
+				.anyMatch(
+					s -> "0102 computer and information sciences".equals(s.getValue()) &
+						ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid())));
+
+		verify_keyword(p, "In Situ Hybridization");
+		verify_keyword(p, "Avicennia");
+	}
+
+	@Test
+	void testCleanDoiBoost() throws IOException, ParseException, ISLookUpException, ClassNotFoundException {
+		verifyFiltering(1, "50|doi_________::b0baa0eb88a5788f0b8815560d2a32f2");
+	}
+
+	@Test
+	void testCleanDoiBoost2() throws IOException, ParseException, ISLookUpException, ClassNotFoundException {
+		verifyFiltering(1, "50|doi_________::4972b0ca81b96b225aed8038bb965656");
+	}
+
+	private void verifyFiltering(int expectedCount, String id)
+		throws ISLookUpException, ClassNotFoundException, IOException, ParseException {
+		new CleanGraphSparkJob(
+			args(
+				"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json",
+				new String[] {
+					"--inputPath", graphInputPath + "/publication",
+					"--outputPath", graphOutputPath + "/publication",
+					"--isLookupUrl", "lookupurl",
+					"--graphTableClassName", Publication.class.getCanonicalName(),
+					"--deepClean", "false",
+					"--masterDuplicatePath", dsMasterDuplicatePath,
+				})).run(false, isLookUpService);
+
+		Dataset<Publication> p = read(spark, graphOutputPath + "/publication", Publication.class)
+			.filter(String.format("id = '%s'", id));
+
+		assertEquals(expectedCount, p.count());
+	}
+
+	@Test
+	void testCleanContext() throws Exception {
+		final String prefix = "gcube ";
+
+		new CleanGraphSparkJob(
+			args(
+				"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json",
+				new String[] {
+					"--inputPath", graphInputPath + "/publication",
+					"--outputPath", graphOutputPath + "/publication",
+					"--isLookupUrl", "lookupurl",
+					"--graphTableClassName", Publication.class.getCanonicalName(),
+					"--deepClean", "true",
+					"--contextId", "sobigdata",
+					"--verifyParam", "gCube ",
+					"--masterDuplicatePath", dsMasterDuplicatePath,
+					"--country", "NL",
+					"--verifyCountryParam", "10.17632",
+					"--collectedfrom", "NARCIS",
+					"--hostedBy", Objects
+						.requireNonNull(
+							getClass()
+								.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy"))
+						.getPath()
+				})).run(false, isLookUpService);
+
+		Dataset<Publication> pubs = read(spark, graphOutputPath + "/publication", Publication.class)
+			.filter((FilterFunction<Publication>) p1 -> StringUtils.endsWith(p1.getId(), "_ctx"));
+
+		assertEquals(7, pubs.count());
+
+		// original result with sobigdata context and gcube as starting string in the main title for the publication
+		assertEquals(
+			0,
+			pubs
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::0224aae28af558f21768dbc6439a_ctx"))
+				.first()
+				.getContext()
+				.size());
+
+		// original result with sobigdata context without gcube as starting string in the main title for the publication
+		assertEquals(
+			1,
+			pubs
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx"))
+				.first()
+				.getContext()
+				.size());
+		assertEquals(
+			"sobigdata::projects::2",
+			pubs
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx"))
+				.first()
+				.getContext()
+				.get(0)
+				.getId());
+
+		// original result with sobigdata context with gcube as starting string in the subtitle
+		assertEquals(
+			1,
+			pubs
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx"))
+				.first()
+				.getContext()
+				.size());
+		assertEquals(
+			"sobigdata::projects::2",
+			pubs
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx"))
+				.first()
+				.getContext()
+				.get(0)
+				.getId());
+
+		List<StructuredProperty> titles = pubs
+			.filter(
+				(FilterFunction<Publication>) p -> p
+					.getId()
+					.equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx"))
+			.first()
+			.getTitle();
+
+		assertEquals(1, titles.size());
+		assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
+		assertEquals("subtitle", titles.get(0).getQualifier().getClassid());
+
+		// original result with sobigdata context with gcube not as starting string in the main title
+		assertEquals(
+			1,
+			pubs
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx"))
+				.first()
+				.getContext()
+				.size());
+		assertEquals(
+			"sobigdata::projects::1",
+			pubs
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx"))
+				.first()
+				.getContext()
+				.get(0)
+				.getId());
+		titles = pubs
+			.filter(
+				(FilterFunction<Publication>) p -> p
+					.getId()
+					.equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx"))
+			.first()
+			.getTitle();
+
+		assertEquals(1, titles.size());
+		assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix));
+		assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()));
+		assertEquals("main title", titles.get(0).getQualifier().getClassid());
+
+		// original result with sobigdata in context and also other contexts with gcube as starting string for the main
+		// title
+		assertEquals(
+			1,
+			pubs
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx"))
+				.first()
+				.getContext()
+				.size());
+		assertEquals(
+			"dh-ch",
+			pubs
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx"))
+				.first()
+				.getContext()
+				.get(0)
+				.getId());
+		titles = pubs
+			.filter(
+				(FilterFunction<Publication>) p -> p
+					.getId()
+					.equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx"))
+			.first()
+			.getTitle();
+
+		assertEquals(1, titles.size());
+		assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
+		assertEquals("main title", titles.get(0).getQualifier().getClassid());
+
+		// original result with multiple main title one of which whith gcube as starting string and with 2 contextes
+		assertEquals(
+			1,
+			pubs
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx"))
+				.first()
+				.getContext()
+				.size());
+		assertEquals(
+			"dh-ch",
+			pubs
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx"))
+				.first()
+				.getContext()
+				.get(0)
+				.getId());
+		titles = pubs
+			.filter(
+				(FilterFunction<Publication>) p -> p
+					.getId()
+					.equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx"))
+			.first()
+			.getTitle();
+
+		assertEquals(2, titles.size());
+		assertTrue(
+			titles
+				.stream()
+				.anyMatch(
+					t -> t.getQualifier().getClassid().equals("main title")
+						&& t.getValue().toLowerCase().startsWith(prefix)));
+
+		// original result without sobigdata in context with gcube as starting string for the main title
+		assertEquals(
+			1,
+			pubs
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx"))
+				.first()
+				.getContext()
+				.size());
+		assertEquals(
+			"dh-ch",
+			pubs
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx"))
+				.first()
+				.getContext()
+				.get(0)
+				.getId());
+		titles = pubs
+			.filter(
+				(FilterFunction<Publication>) p -> p
+					.getId()
+					.equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx"))
+			.first()
+			.getTitle();
+
+		assertEquals(2, titles.size());
+
+		assertTrue(
+			titles
+				.stream()
+				.anyMatch(
+					t -> t.getQualifier().getClassid().equals("main title")
+						&& t.getValue().toLowerCase().startsWith(prefix)));
+
+	}
+
+	@Test
+	void testCleanCfHbSparkJob() throws Exception {
+
+		final Dataset<Publication> pubs_in = read(spark, graphInputPath + "/publication", Publication.class);
+		final Publication p1_in = pubs_in
+			.filter("id = '50|doi_________::09821844208a5cd6300b2bfb13b_cfhb'")
+			.first();
+		assertEquals("10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", p1_in.getCollectedfrom().get(0).getKey());
+		assertEquals("Bacterial Protein Interaction Database - DUP", p1_in.getCollectedfrom().get(0).getValue());
+		assertEquals(
+			"10|re3data_____::4c4416659cb74c2e0e891a883a047cbc",
+			p1_in.getInstance().get(0).getCollectedfrom().getKey());
+		assertEquals(
+			"Bacterial Protein Interaction Database - DUP", p1_in.getInstance().get(0).getCollectedfrom().getValue());
+
+		final Publication p2_in = pubs_in
+			.filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3a_cfhb'")
+			.first();
+		assertEquals("10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", p2_in.getCollectedfrom().get(0).getKey());
+		assertEquals("FILUR DATA - DUP", p2_in.getCollectedfrom().get(0).getValue());
+		assertEquals(
+			"10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35",
+			p2_in.getInstance().get(0).getCollectedfrom().getKey());
+		assertEquals("FILUR DATA - DUP", p2_in.getInstance().get(0).getCollectedfrom().getValue());
+		assertEquals(
+			"10|re3data_____::6ffd7bc058f762912dc494cd9c175341", p2_in.getInstance().get(0).getHostedby().getKey());
+		assertEquals("depositar - DUP", p2_in.getInstance().get(0).getHostedby().getValue());
+
+		final Publication p3_in = pubs_in
+			.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7d_cfhb'")
+			.first();
+		assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getCollectedfrom().get(0).getKey());
+		assertEquals("DANS (Data Archiving and Networked Services)", p3_in.getCollectedfrom().get(0).getValue());
+		assertEquals(
+			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f",
+			p3_in.getInstance().get(0).getCollectedfrom().getKey());
+		assertEquals(
+			"DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getCollectedfrom().getValue());
+		assertEquals(
+			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getInstance().get(0).getHostedby().getKey());
+		assertEquals(
+			"DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getHostedby().getValue());
+
+		new CleanGraphSparkJob(
+			args(
+				"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json",
+				new String[] {
+					"--inputPath", graphInputPath + "/publication",
+					"--outputPath", graphOutputPath + "/publication",
+					"--isLookupUrl", "lookupurl",
+					"--graphTableClassName", Publication.class.getCanonicalName(),
+					"--deepClean", "true",
+					"--contextId", "sobigdata",
+					"--verifyParam", "gCube ",
+					"--masterDuplicatePath", dsMasterDuplicatePath,
+					"--country", "NL",
+					"--verifyCountryParam", "10.17632",
+					"--collectedfrom", "NARCIS",
+					"--hostedBy", Objects
+						.requireNonNull(
+							getClass()
+								.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy"))
+						.getPath()
+				})).run(false, isLookUpService);
+
+		assertTrue(Files.exists(Paths.get(graphOutputPath, "publication")));
+
+		final Dataset<Publication> pubs_out = read(spark, graphOutputPath + "/publication", Publication.class)
+			.filter((FilterFunction<Publication>) p -> StringUtils.endsWith(p.getId(), "_cfhb"));
+
+		assertEquals(3, pubs_out.count());
+
+		final Publication p1_out = pubs_out
+			.filter("id = '50|doi_________::09821844208a5cd6300b2bfb13b_cfhb'")
+			.first();
+		assertEquals("10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", p1_out.getCollectedfrom().get(0).getKey());
+		assertEquals("Bacterial Protein Interaction Database", p1_out.getCollectedfrom().get(0).getValue());
+		assertEquals(
+			"10|fairsharing_::a29d1598024f9e87beab4b98411d48ce",
+			p1_out.getInstance().get(0).getCollectedfrom().getKey());
+		assertEquals(
+			"Bacterial Protein Interaction Database", p1_out.getInstance().get(0).getCollectedfrom().getValue());
+
+		final Publication p2_out = pubs_out
+			.filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3a_cfhb'")
+			.first();
+		assertEquals("10|re3data_____::fc1db64b3964826913b1e9eafe830490", p2_out.getCollectedfrom().get(0).getKey());
+		assertEquals("FULIR Data", p2_out.getCollectedfrom().get(0).getValue());
+		assertEquals(
+			"10|re3data_____::fc1db64b3964826913b1e9eafe830490",
+			p2_out.getInstance().get(0).getCollectedfrom().getKey());
+		assertEquals("FULIR Data", p2_out.getInstance().get(0).getCollectedfrom().getValue());
+		assertEquals(
+			"10|fairsharing_::3f647cadf56541fb9513cb63ec370187", p2_out.getInstance().get(0).getHostedby().getKey());
+		assertEquals("depositar", p2_out.getInstance().get(0).getHostedby().getValue());
+
+		final Publication p3_out = pubs_out
+			.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7d_cfhb'")
+			.first();
+		assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getCollectedfrom().get(0).getKey());
+		assertEquals("DANS (Data Archiving and Networked Services)", p3_out.getCollectedfrom().get(0).getValue());
+		assertEquals(
+			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f",
+			p3_out.getInstance().get(0).getCollectedfrom().getKey());
+		assertEquals(
+			"DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getCollectedfrom().getValue());
+		assertEquals(
+			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getInstance().get(0).getHostedby().getKey());
+		assertEquals(
+			"DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getHostedby().getValue());
+	}
+
+	@Test
+	void testCleanCountry() throws Exception {
+
+		new CleanGraphSparkJob(
+			args(
+				"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json",
+				new String[] {
+					"--inputPath", graphInputPath + "/publication",
+					"--outputPath", graphOutputPath + "/publication",
+					"--isLookupUrl", "lookupurl",
+					"--graphTableClassName", Publication.class.getCanonicalName(),
+					"--deepClean", "true",
+					"--contextId", "sobigdata",
+					"--verifyParam", "gCube ",
+					"--masterDuplicatePath", dsMasterDuplicatePath,
+					"--country", "NL",
+					"--verifyCountryParam", "10.17632",
+					"--collectedfrom", "NARCIS",
+					"--hostedBy", Objects
+						.requireNonNull(
+							getClass()
+								.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy"))
+						.getPath()
+				})).run(false, isLookUpService);
+
+		final Dataset<Publication> pubs_out = read(spark, graphOutputPath + "/publication", Publication.class)
+			.filter((FilterFunction<Publication>) p -> StringUtils.endsWith(p.getId(), "_country"));
+
+		assertEquals(8, pubs_out.count());
+
+		// original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS
+		assertEquals(
+			1,
+			pubs_out
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::0224aae28af558f21768dbc6_country"))
+				.first()
+				.getCountry()
+				.size());
+
+		// original result with NL country and pid not starting with Mendely prefix
+		assertEquals(
+			1,
+			pubs_out
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1_country"))
+				.first()
+				.getCountry()
+				.size());
+
+		// original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not
+		// inserted with propagation
+		assertEquals(
+			1,
+			pubs_out
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::3c81248c335f0aa07e06817e_country"))
+				.first()
+				.getCountry()
+				.size());
+
+		// original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with
+		// propagation
+		assertEquals(
+			0,
+			pubs_out
+				.filter(
+					(FilterFunction<Publication>) p -> p
+						.getId()
+						.equals("50|DansKnawCris::3c81248c335f0aa07e06817d_country"))
+				.first()
+				.getCountry()
+				.size());
+	}
+
+	private List<String> vocs() throws IOException {
+		return IOUtils
+			.readLines(
+				Objects
+					.requireNonNull(
+						getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")));
+	}
+
+	private List<String> synonyms() throws IOException {
+		return IOUtils
+			.readLines(
+				Objects
+					.requireNonNull(
+						getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")));
+	}
+
+	private <R> org.apache.spark.sql.Dataset<R> read(SparkSession spark, String path, Class<R> clazz) {
+		return spark
+			.read()
+			.textFile(path)
+			.map(as(clazz), Encoders.bean(clazz));
+	}
+
+	private static <R> MapFunction<String, R> as(Class<R> clazz) {
+		return s -> MAPPER.readValue(s, clazz);
+	}
+
+	private static String classPathResourceAsString(String path) throws IOException {
+		return IOUtils
+			.toString(
+				Objects
+					.requireNonNull(
+						CleanGraphSparkJobTest.class.getResourceAsStream(path)));
+	}
+
+	private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException {
+		ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs));
+		parser.parseArgument(args);
+		return parser;
+	}
+
+	private static void verify_keyword(Publication p_cleaned, String subject) {
+		Optional<Subject> s1 = p_cleaned
+			.getSubject()
+			.stream()
+			.filter(s -> s.getValue().equals(subject))
+			.findFirst();
+
+		assertTrue(s1.isPresent());
+		assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassid());
+		assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassname());
+	}
+
+}

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java

@@ -13,7 +13,6 @@ import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.hdfs.server.datanode.fsdataset.impl.MappableBlock;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -59,7 +58,7 @@ public class GraphCleaningFunctionsTest {
 	void testCleanRelations() throws Exception {
 
 		List<String> lines = IOUtils
-			.readLines(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/relation.json"));
+			.readLines(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/graph/relation/relation.json"));
 		for (String json : lines) {
 			Relation r_in = MAPPER.readValue(json, Relation.class);
 			assertNotNull(r_in);

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java

@@ -1,213 +0,0 @@
-
-package eu.dnetlib.dhp.oa.graph.clean.cfhb;
-
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.JavaSparkContext;
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SparkSession;
-import org.junit.jupiter.api.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import eu.dnetlib.dhp.schema.oaf.Dataset;
-import eu.dnetlib.dhp.schema.oaf.Publication;
-
-public class CleanCfHbSparkJobTest {
-
-	private static final Logger log = LoggerFactory.getLogger(CleanCfHbSparkJobTest.class);
-
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
-	private static SparkSession spark;
-
-	private static Path testBaseTmpPath;
-
-	private static String resolvedPath;
-
-	private static String graphInputPath;
-
-	private static String graphOutputPath;
-
-	private static String dsMasterDuplicatePath;
-
-	@BeforeAll
-	public static void beforeAll() throws IOException, URISyntaxException {
-
-		testBaseTmpPath = Files.createTempDirectory(CleanCfHbSparkJobTest.class.getSimpleName());
-		log.info("using test base path {}", testBaseTmpPath);
-
-		final File entitiesSources = Paths
-			.get(CleanCfHbSparkJobTest.class.getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities").toURI())
-			.toFile();
-
-		FileUtils
-			.copyDirectory(
-				entitiesSources,
-				testBaseTmpPath.resolve("input").resolve("entities").toFile());
-
-		FileUtils
-			.copyFileToDirectory(
-				Paths
-					.get(
-						CleanCfHbSparkJobTest.class
-							.getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/masterduplicate.json")
-							.toURI())
-					.toFile(),
-				testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toFile());
-
-		graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString();
-		resolvedPath = testBaseTmpPath.resolve("workingDir").resolve("cfHbResolved").toString();
-		graphOutputPath = testBaseTmpPath.resolve("workingDir").resolve("cfHbPatched").toString();
-		dsMasterDuplicatePath = testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toString();
-
-		SparkConf conf = new SparkConf();
-		conf.setAppName(CleanCfHbSparkJobTest.class.getSimpleName());
-
-		conf.setMaster("local[*]");
-		conf.set("spark.driver.host", "localhost");
-		conf.set("spark.ui.enabled", "false");
-
-		spark = SparkSession
-			.builder()
-			.appName(CleanCfHbSparkJobTest.class.getSimpleName())
-			.config(conf)
-			.getOrCreate();
-	}
-
-	@AfterAll
-	public static void afterAll() throws IOException {
-		FileUtils.deleteDirectory(testBaseTmpPath.toFile());
-		spark.stop();
-	}
-
-	@Test
-	void testCleanCfHbSparkJob() throws Exception {
-		final String outputPath = graphOutputPath + "/dataset";
-		final String inputPath = graphInputPath + "/dataset";
-
-		org.apache.spark.sql.Dataset<Dataset> records = read(spark, inputPath, Dataset.class);
-		Dataset d = records
-			.filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'")
-			.first();
-		assertEquals("10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", d.getCollectedfrom().get(0).getKey());
-		assertEquals("Bacterial Protein Interaction Database - DUP", d.getCollectedfrom().get(0).getValue());
-		assertEquals(
-			"10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", d.getInstance().get(0).getCollectedfrom().getKey());
-		assertEquals(
-			"Bacterial Protein Interaction Database - DUP", d.getInstance().get(0).getCollectedfrom().getValue());
-
-		d = records
-			.filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3adc37a'")
-			.first();
-		assertEquals("10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", d.getCollectedfrom().get(0).getKey());
-		assertEquals("FILUR DATA - DUP", d.getCollectedfrom().get(0).getValue());
-		assertEquals(
-			"10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", d.getInstance().get(0).getCollectedfrom().getKey());
-		assertEquals("FILUR DATA - DUP", d.getInstance().get(0).getCollectedfrom().getValue());
-		assertEquals(
-			"10|re3data_____::6ffd7bc058f762912dc494cd9c175341", d.getInstance().get(0).getHostedby().getKey());
-		assertEquals("depositar - DUP", d.getInstance().get(0).getHostedby().getValue());
-
-		d = records
-			.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'")
-			.first();
-		assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey());
-		assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue());
-		assertEquals(
-			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey());
-		assertEquals(
-			"DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue());
-		assertEquals(
-			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey());
-		assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue());
-
-		CleanCfHbSparkJob
-			.main(
-				new String[] {
-					"--isSparkSessionManaged", Boolean.FALSE.toString(),
-					"--inputPath", inputPath,
-					"--outputPath", outputPath,
-					"--resolvedPath", resolvedPath + "/dataset",
-					"--graphTableClassName", Dataset.class.getCanonicalName(),
-					"--masterDuplicatePath", dsMasterDuplicatePath
-				});
-
-		assertTrue(Files.exists(Paths.get(graphOutputPath, "dataset")));
-
-		records = read(spark, outputPath, Dataset.class);
-
-		assertEquals(3, records.count());
-
-		d = records
-			.filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'")
-			.first();
-		assertEquals("10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", d.getCollectedfrom().get(0).getKey());
-		assertEquals("Bacterial Protein Interaction Database", d.getCollectedfrom().get(0).getValue());
-		assertEquals(
-			"10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", d.getInstance().get(0).getCollectedfrom().getKey());
-		assertEquals("Bacterial Protein Interaction Database", d.getInstance().get(0).getCollectedfrom().getValue());
-
-		d = records
-			.filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3adc37a'")
-			.first();
-		assertEquals("10|re3data_____::fc1db64b3964826913b1e9eafe830490", d.getCollectedfrom().get(0).getKey());
-		assertEquals("FULIR Data", d.getCollectedfrom().get(0).getValue());
-		assertEquals(
-			"10|re3data_____::fc1db64b3964826913b1e9eafe830490", d.getInstance().get(0).getCollectedfrom().getKey());
-		assertEquals("FULIR Data", d.getInstance().get(0).getCollectedfrom().getValue());
-		assertEquals(
-			"10|fairsharing_::3f647cadf56541fb9513cb63ec370187", d.getInstance().get(0).getHostedby().getKey());
-		assertEquals("depositar", d.getInstance().get(0).getHostedby().getValue());
-
-		d = records
-			.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'")
-			.first();
-		assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey());
-		assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue());
-		assertEquals(
-			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey());
-		assertEquals(
-			"DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue());
-		assertEquals(
-			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey());
-		assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue());
-
-		d = records
-			.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'")
-			.first();
-		assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey());
-		assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue());
-		assertEquals(
-			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey());
-		assertEquals(
-			"DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue());
-		assertEquals(
-			"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey());
-		assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue());
-	}
-
-	private <R> org.apache.spark.sql.Dataset<R> read(SparkSession spark, String path, Class<R> clazz) {
-		return spark
-			.read()
-			.textFile(path)
-			.map(as(clazz), Encoders.bean(clazz));
-	}
-
-	private static <R> MapFunction<String, R> as(Class<R> clazz) {
-		return s -> OBJECT_MAPPER.readValue(s, clazz);
-	}
-}

dhp-workflows/dhp-graph-mapper/src/test/resources/logback.xml

@@ -0,0 +1,11 @@
+<configuration>
+    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
+        <encoder>
+            <pattern>%d{HH:mm:ss.SSS} %-5level %logger{36} - %msg%n</pattern>
+        </encoder>
+    </appender>
+
+    <root level="info">
+        <appender-ref ref="STDOUT" />
+    </root>
+</configuration>