[graph cleaning] WIP: refactoring of the cleaning stages, unit tests

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

@@ -3,15 +3,18 @@ package eu.dnetlib.dhp.oa.graph.clean;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
-import java.util.List;
+import java.util.*;
-import java.util.Optional;
-import java.util.Set;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 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;
@@ -24,15 +27,19 @@ 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.oa.graph.clean.cfhb.IdCfHbMapping;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 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.ISLookUpService;
+import scala.Tuple2;
 
 public class CleanGraphSparkJob {
 
@@ -40,31 +47,43 @@ 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(
+				.toString(
-				CleanGraphSparkJob.class
+						CleanGraphSparkJob.class
-					.getResourceAsStream(
+								.getResourceAsStream(
-						"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json"));
+										"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json"));
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
 		parser.parseArgument(args);
 
 		Boolean isSparkSessionManaged = Optional
-			.ofNullable(parser.get("isSparkSessionManaged"))
+				.ofNullable(parser.get("isSparkSessionManaged"))
-			.map(Boolean::valueOf)
+				.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
+				.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);
 
@@ -80,27 +99,38 @@ public class CleanGraphSparkJob {
 		String country = parser.get("country");
 		log.info("country: {}", country);
 
-		String[] verifyCountryParam = parser.get("verifyCountryParam").split(";");
+		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,
+				conf,
-			isSparkSessionManaged,
+				isSparkSessionManaged,
-			spark -> {
+				spark -> {
-				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
+					HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
-				cleanGraphTable(
+					cleanGraphTable(
-					spark, vocs, inputPath, entityClazz, outputPath, contextId, verifyParam, datasourcePath, country,
+							spark, vocs, inputPath, entityClazz, outputPath, contextId, verifyParam, datasourcePath, country,
-					verifyCountryParam, collectedfrom);
+							verifyCountryParam, collectedfrom, dsMasterDuplicatePath, deepClean);
-			});
+				});
 	}
 
 	private static <T extends Oaf> void cleanGraphTable(
@@ -109,33 +139,74 @@ public class CleanGraphSparkJob {
 		String inputPath,
 		Class<T> clazz,
 		String outputPath, String contextId, String verifyParam, String datasourcePath, String country,
-		String[] verifyCountryParam, String collectedfrom) {
+		String[] verifyCountryParam, String collectedfrom, String dsMasterDuplicatePath,
-
+		Boolean deepClean) {
-		Set<String> hostedBy = Sets
-			.newHashSet(
-				spark
-					.read()
-					.textFile(datasourcePath)
-					.collectAsList());
 
 		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);
-			.map(
+
-				(MapFunction<T, T>) value -> GraphCleaningFunctions.cleanContext(value, contextId, verifyParam),
+		if (Boolean.FALSE.equals(deepClean)) {
-				Encoders.bean(clazz))
+			cleaned_basic
-			.map(
+				.write()
-				(MapFunction<T, T>) value -> GraphCleaningFunctions
+				.mode(SaveMode.Overwrite)
-					.cleanCountry(value, verifyCountryParam, hostedBy, collectedfrom, country),
+				.option("compression", "gzip")
-				Encoders.bean(clazz))
+				.json(outputPath);
-			.write()
+
-			.mode(SaveMode.Overwrite)
+		} else if (Boolean.TRUE.equals(ModelSupport.isSubClass(clazz, Result.class))) {
-			.option("compression", "gzip")
+
-			.json(outputPath);
+			// 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));
+
+			// 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()));
+
+			// load the hostedby mapping
+			Set<String> hostedBy = Sets
+					.newHashSet(
+							spark
+									.read()
+									.textFile(datasourcePath)
+									.collectAsList());
+
+			// perform the deep cleaning steps
+			final Dataset<T> cleaned_deep = cleaned_basic
+					.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));
+
+			// Join the results with the resolved CF|HB mapping, apply the mapping and save it
+			cleaned_deep
+				.joinWith(resolved, cleaned_deep.col("id").equalTo(resolved.col("resultId")), "left")
+				.groupByKey(
+					(MapFunction<Tuple2<T, IdCfHbMapping>, String>) t -> ((Result) t._1()).getId(), Encoders.STRING())
+				.mapGroups(getMapGroupsFunction(), Encoders.bean(clazz))
+				.write()
+				.mode(SaveMode.Overwrite)
+				.option("compression", "gzip")
+				.json(outputPath);
+		}
 	}
 
 	private static <T extends Oaf> Dataset<T> readTableFromPath(
@@ -145,9 +216,98 @@ public class CleanGraphSparkJob {
 		return spark
 			.read()
 			.textFile(inputEntityPath)
-			.map(
+			.map(as(clazz), Encoders.bean(clazz));
-				(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, 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(
+								instances -> instances
+									.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)) {
+					res.getCollectedfrom().forEach(kv -> updateKeyValue(kv, m));
+					((Result) 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());
+				}
+			}
+
+		};
 	}
 
 }

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

@@ -83,12 +83,17 @@
         </property>
     </parameters>
 
-    <start to="select_datasourceId_from_country"/>
+    <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>
@@ -110,10 +115,25 @@
             <arg>--workingDir</arg><arg>${workingDir}/working/hostedby</arg>
             <arg>--country</arg><arg>${country}</arg>
         </spark>
-        <ok to="fork_clean_graph"/>
+        <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>${nameNode}</arg>
+        </java>
+        <ok to="wait_prepare"/>
+        <error to="Kill"/>
+    </action>
+
+    <join name="wait_prepare" to="fork_clean_graph"/>
+
     <fork name="fork_clean_graph">
         <path start="clean_publication"/>
         <path start="clean_dataset"/>
@@ -152,6 +172,8 @@
             <arg>--verifyCountryParam</arg><arg>${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"/>
@@ -184,6 +206,8 @@
             <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>${shouldClean}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -216,6 +240,8 @@
             <arg>--verifyCountryParam</arg><arg>${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"/>
@@ -248,6 +274,8 @@
             <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>${shouldClean}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -280,6 +308,8 @@
             <arg>--verifyCountryParam</arg><arg>${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"/>
@@ -312,6 +342,8 @@
             <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>${shouldClean}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -344,6 +376,8 @@
             <arg>--verifyCountryParam</arg><arg>${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"/>
@@ -376,206 +410,14 @@
             <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="should_patch_datasource_ids"/>
+    <join name="wait_clean" to="End"/>
-
-    <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

@@ -33,30 +33,48 @@
     "paramName": "ci",
     "paramLongName": "contextId",
     "paramDescription": "the id of the context to be removed",
-    "paramRequired": true
+    "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": true
+    "paramRequired": false
   },
   {
     "paramName": "vfc",
     "paramLongName": "verifyCountryParam",
     "paramDescription": "the parameter to be verified to remove the country",
-    "paramRequired": true
+    "paramRequired": false
   },
   {
     "paramName": "cf",
     "paramLongName": "collectedfrom",
     "paramDescription": "the collectedfrom value for which we should apply the cleaning",
-    "paramRequired": true
+    "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/CleanGraphSparkJobTest.java

@@ -0,0 +1,435 @@
+package eu.dnetlib.dhp.oa.graph.clean;
+
+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;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.filefilter.*;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.ForeachFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.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 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.Collection;
+import java.util.List;
+import java.util.Optional;
+import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.Mockito.lenient;
+
+@ExtendWith(MockitoExtension.class)
+public class CleanGraphSparkJobTest {
+
+    private static final Logger log = LoggerFactory.getLogger(CleanContextTest.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 workingDir;
+
+    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(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();
+
+
+
+        workingDir = Files.createTempDirectory(CleanGraphSparkJobTest.class.getSimpleName());
+        log.info("using work dir {}", workingDir);
+
+        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", workingDir.toString());
+        conf.set("hive.metastore.warehouse.dir", workingDir.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(workingDir.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.toString() + "/relation",
+                        "--outputPath", graphOutputPath.toString() + "/relation",
+                        "--isLookupUrl", "lookupurl",
+                        "--graphTableClassName", Relation.class.getCanonicalName(),
+                        "--deepClean", "false"
+        })).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(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(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(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 {
+
+        spark.read()
+                .textFile(graphInputPath.toString() + "/publication")
+                .map(as(Publication.class), Encoders.bean(Publication.class))
+                .collectAsList()
+                .forEach(p -> {
+                    assertNull(p.getBestaccessright());
+                    assertTrue(p instanceof Result);
+                    assertTrue(p instanceof Publication);
+                });
+        
+        new CleanGraphSparkJob(
+                args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json",
+                        new String[] {
+                                "--inputPath", graphInputPath.toString() + "/publication",
+                                "--outputPath", graphOutputPath.toString() + "/publication",
+                                "--isLookupUrl", "lookupurl",
+                                "--graphTableClassName", Publication.class.getCanonicalName(),
+                                "--deepClean", "false"
+                        })).run(false, isLookUpService);
+
+        Publication p = spark.read()
+                .textFile(graphOutputPath.toString() + "/publication")
+                .map(as(Publication.class), Encoders.bean(Publication.class))
+                .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");
+    }
+
+    private List<String> vocs() throws IOException {
+        return IOUtils
+                .readLines(
+                        GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt"));
+    }
+
+    private List<String> synonyms() throws IOException {
+        return IOUtils
+                .readLines(
+                        GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"));
+    }
+
+    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(
+                        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());
+    }
+
+    private Stream<StructuredProperty> getAuthorPids(Result pub) {
+        return pub
+                .getAuthor()
+                .stream()
+                .map(Author::getPid)
+                .flatMap(Collection::stream);
+    }
+
+}

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/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>