Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala

@@ -27,7 +27,8 @@ object SparkCreateBaselineDataFrame {
   def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = {
     val data = requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/")
 
-    val result = data.linesWithSeparators.map(l => l.stripLineEnd)
+    val result = data.linesWithSeparators
+      .map(l => l.stripLineEnd)
       .filter(l => l.startsWith("<a href="))
       .map { l =>
         val end = l.lastIndexOf("\">")

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt

@@ -130,7 +130,7 @@
 				</xsl:if>
 				
 				<oaf:hostedBy name="{$varOfficialName}" id="{$varDataSourceId}" />
-				<oaf:collectedFrom name="{$varOfficialName}" id="{$varDataSourceId}ß" />
+				<oaf:collectedFrom name="{$varOfficialName}" id="{$varDataSourceId}" />
 
 				<xsl:variable name="varKnownFileEndings" select="('.bmp', '.doc', '.docx', '.epub', '.flv', '.jpeg', '.jpg', '.m4v', '.mp4', '.mpg', '.odp', '.pdf', '.png', '.ppt', '.tiv', '.txt', '.xls', '.xlsx', '.zip')" />
 				<xsl:variable name="varIdDoi" select="distinct-values((//dc:identifier[starts-with(., '10.')][matches(., '(10[.][0-9]{4,}[^\s/&gt;]*/[^\s&gt;]+)')], //dc:identifier[starts-with(., 'http') and (contains(., '://dx.doi.org/10.') or contains(., '://doi.org/10.'))]/substring-after(., 'doi.org/'), //dc:identifier[starts-with(lower-case(.), 'doi:10.')]/substring-after(lower-case(.), 'doi:')))" />

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala

@@ -63,7 +63,9 @@ class BioScholixTest extends AbstractVocabularyTest {
     val records: String = Source
       .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump"))
       .mkString
-    val r: List[Oaf] = records.linesWithSeparators.map(l => l.stripLineEnd).toList
+    val r: List[Oaf] = records.linesWithSeparators
+      .map(l => l.stripLineEnd)
+      .toList
       .map(s => mapper.readValue(s, classOf[PMArticle]))
       .map(a => PubMedToOaf.convert(a, vocabularies))
     assertEquals(10, r.size)
@@ -175,7 +177,8 @@ class BioScholixTest extends AbstractVocabularyTest {
       .mkString
     records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
 
-    val result: List[Oaf] = records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.pdbTOOaf(o))
+    val result: List[Oaf] =
+      records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.pdbTOOaf(o))
 
     assertTrue(result.nonEmpty)
     result.foreach(r => assertNotNull(r))
@@ -196,7 +199,8 @@ class BioScholixTest extends AbstractVocabularyTest {
       .mkString
     records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
 
-    val result: List[Oaf] = records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.uniprotToOAF(o))
+    val result: List[Oaf] =
+      records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.uniprotToOAF(o))
 
     assertTrue(result.nonEmpty)
     result.foreach(r => assertNotNull(r))
@@ -241,7 +245,8 @@ class BioScholixTest extends AbstractVocabularyTest {
       .mkString
     records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
 
-    val result: List[Oaf] = records.linesWithSeparators.map(l => l.stripLineEnd).map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList
+    val result: List[Oaf] =
+      records.linesWithSeparators.map(l => l.stripLineEnd).map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList
 
     assertNotNull(result)
     assertTrue(result.nonEmpty)
@@ -280,10 +285,13 @@ class BioScholixTest extends AbstractVocabularyTest {
 
     implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
 
-    val l: List[ScholixResolved] = records.linesWithSeparators.map(l => l.stripLineEnd).map { input =>
+    val l: List[ScholixResolved] = records.linesWithSeparators
+      .map(l => l.stripLineEnd)
+      .map { input =>
         lazy val json = parse(input)
         json.extract[ScholixResolved]
-    }.toList
+      }
+      .toList
 
     val result: List[Oaf] = l.map(s => BioDBToOAF.scholixResolvedToOAF(s))
 

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java

@@ -2,7 +2,10 @@
 package eu.dnetlib.dhp.broker.oa.util;
 
 import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Objects;
 import java.util.function.Function;
 import java.util.stream.Collectors;
@@ -80,7 +83,7 @@ public class ConversionUtils {
 		res.setOpenaireId(cleanOpenaireId(d.getId()));
 		res.setOriginalId(first(d.getOriginalId()));
 		res.setTitle(structPropValue(d.getTitle()));
-		res.setPids(mappedList(d.getPid(), ConversionUtils::oafPidToBrokerPid));
+		res.setPids(allResultPids(d));
 		res.setInstances(flatMappedList(d.getInstance(), ConversionUtils::oafInstanceToBrokerInstances));
 		res.setCollectedFrom(mappedFirst(d.getCollectedfrom(), KeyValue::getValue));
 		return res;
@@ -95,7 +98,7 @@ public class ConversionUtils {
 		res.setOpenaireId(cleanOpenaireId(p.getId()));
 		res.setOriginalId(first(p.getOriginalId()));
 		res.setTitle(structPropValue(p.getTitle()));
-		res.setPids(mappedList(p.getPid(), ConversionUtils::oafPidToBrokerPid));
+		res.setPids(allResultPids(p));
 		res.setInstances(flatMappedList(p.getInstance(), ConversionUtils::oafInstanceToBrokerInstances));
 		res.setCollectedFrom(mappedFirst(p.getCollectedfrom(), KeyValue::getValue));
 
@@ -124,7 +127,7 @@ public class ConversionUtils {
 		res
 			.setJournal(
 				result instanceof Publication ? oafJournalToBrokerJournal(((Publication) result).getJournal()) : null);
-		res.setPids(mappedList(result.getPid(), ConversionUtils::oafPidToBrokerPid));
+		res.setPids(allResultPids(result));
 		res.setInstances(flatMappedList(result.getInstance(), ConversionUtils::oafInstanceToBrokerInstances));
 		res
 			.setExternalReferences(mappedList(result.getExternalReference(), ConversionUtils::oafExtRefToBrokerExtRef));
@@ -132,6 +135,26 @@ public class ConversionUtils {
 		return res;
 	}
 
+	protected static List<OaBrokerTypedValue> allResultPids(final Result result) {
+		final Map<String, StructuredProperty> map = new HashMap<>();
+
+		if (result.getPid() != null) {
+			result.getPid().forEach(sp -> map.put(sp.getValue(), sp));
+		}
+
+		if (result.getInstance() != null) {
+			result.getInstance().forEach(i -> {
+				if (i.getPid() != null) {
+					i.getPid().forEach(sp -> map.put(sp.getValue(), sp));
+				}
+				if (i.getAlternateIdentifier() != null) {
+					i.getAlternateIdentifier().forEach(sp -> map.put(sp.getValue(), sp));
+				}
+			});
+		}
+		return mappedList(map.values(), ConversionUtils::oafPidToBrokerPid);
+	}
+
 	public static String cleanOpenaireId(final String id) {
 		return id.contains("|") ? StringUtils.substringAfter(id, "|") : id;
 	}
@@ -304,7 +327,7 @@ public class ConversionUtils {
 			.collect(Collectors.toList());
 	}
 
-	private static <F, T> List<T> mappedList(final List<F> list, final Function<F, T> func) {
+	private static <F, T> List<T> mappedList(final Collection<F> list, final Function<F, T> func) {
 		if (list == null) {
 			return new ArrayList<>();
 		}

dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtilsTest.java

@@ -0,0 +1,94 @@
+
+package eu.dnetlib.dhp.broker.oa.util;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import eu.dnetlib.broker.objects.OaBrokerTypedValue;
+import eu.dnetlib.dhp.schema.oaf.Instance;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+
+class ConversionUtilsTest {
+
+	@BeforeEach
+	void setUp() throws Exception {
+	}
+
+	@Test
+	void testAllResultPids() {
+		final Qualifier qf = new Qualifier();
+		qf.setClassid("test");
+		qf.setClassname("test");
+		qf.setSchemeid("test");
+		qf.setSchemename("test");
+
+		final StructuredProperty sp1 = new StructuredProperty();
+		sp1.setValue("1");
+		sp1.setQualifier(qf);
+
+		final StructuredProperty sp2 = new StructuredProperty();
+		sp2.setValue("2");
+		sp2.setQualifier(qf);
+
+		final StructuredProperty sp3 = new StructuredProperty();
+		sp3.setValue("3");
+		sp3.setQualifier(qf);
+
+		final StructuredProperty sp4a = new StructuredProperty();
+		sp4a.setValue("4");
+		sp4a.setQualifier(qf);
+
+		final StructuredProperty sp4b = new StructuredProperty();
+		sp4b.setValue("4");
+		sp4b.setQualifier(qf);
+
+		final StructuredProperty sp5 = new StructuredProperty();
+		sp5.setValue("5");
+		sp5.setQualifier(qf);
+
+		final StructuredProperty sp6a = new StructuredProperty();
+		sp6a.setValue("6");
+		sp6a.setQualifier(qf);
+
+		final StructuredProperty sp6b = new StructuredProperty();
+		sp6b.setValue("6");
+		sp6b.setQualifier(qf);
+
+		final Result oaf = new Result();
+		oaf.setPid(new ArrayList<>());
+		oaf.getPid().add(sp1);
+		oaf.getPid().add(sp2);
+		oaf.getPid().add(sp4a);
+
+		final Instance instance1 = new Instance();
+		instance1.setPid(new ArrayList<>());
+		instance1.setAlternateIdentifier(new ArrayList<>());
+		instance1.getPid().add(sp3);
+		instance1.getPid().add(sp4b);
+		instance1.getAlternateIdentifier().add(sp5);
+		instance1.getAlternateIdentifier().add(sp6a);
+
+		final Instance instance2 = new Instance();
+		instance2.setPid(new ArrayList<>());
+		instance2.setAlternateIdentifier(new ArrayList<>());
+		instance2.getPid().add(sp6b);
+
+		oaf.setInstance(new ArrayList<>());
+		oaf.getInstance().add(instance1);
+		oaf.getInstance().add(instance2);
+
+		final List<OaBrokerTypedValue> list = ConversionUtils.allResultPids(oaf);
+
+		// list.forEach(x -> System.out.println(x.getValue()));
+
+		assertEquals(6, list.size());
+	}
+
+}

dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala

@@ -25,7 +25,9 @@ class MappingORCIDToOAFTest {
       .mkString
     assertNotNull(json)
     assertFalse(json.isEmpty)
-    json.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => {
+    json.linesWithSeparators
+      .map(l => l.stripLineEnd)
+      .foreach(s => {
         assertNotNull(ORCIDToOAF.extractValueFromInputString(s))
       })
   }

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

@@ -14,6 +14,7 @@ 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.Row;
 import org.apache.spark.sql.SaveMode;
 import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
@@ -84,11 +85,12 @@ public class SparkCountryPropagationJob {
 		Dataset<R> res = readPath(spark, sourcePath, resultClazz);
 
 		log.info("Reading prepared info: {}", preparedInfoPath);
-		Dataset<ResultCountrySet> prepared = spark
+		final Dataset<Row> preparedInfoRaw = spark
 			.read()
-			.json(preparedInfoPath)
-			.as(Encoders.bean(ResultCountrySet.class));
+			.json(preparedInfoPath);
 
+		if (!preparedInfoRaw.isEmpty()) {
+			final Dataset<ResultCountrySet> prepared = preparedInfoRaw.as(Encoders.bean(ResultCountrySet.class));
 			res
 				.joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer")
 				.map(getCountryMergeFn(), Encoders.bean(resultClazz))
@@ -96,7 +98,13 @@ public class SparkCountryPropagationJob {
 				.option("compression", "gzip")
 				.mode(SaveMode.Overwrite)
 				.json(outputPath);
-
+		} else {
+			res
+				.write()
+				.option("compression", "gzip")
+				.mode(SaveMode.Overwrite)
+				.json(outputPath);
+		}
 	}
 
 	private static <R extends Result> MapFunction<Tuple2<R, ResultCountrySet>, R> getCountryMergeFn() {

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml

@@ -105,13 +105,13 @@
     <join name="copy_wait" to="fork_exec_bulktag"/>
 
     <fork name="fork_exec_bulktag">
-        <path start="join_bulktag_publication"/>
-        <path start="join_bulktag_dataset"/>
-        <path start="join_bulktag_otherresearchproduct"/>
-        <path start="join_bulktag_software"/>
+        <path start="bulktag_publication"/>
+        <path start="bulktag_dataset"/>
+        <path start="bulktag_otherresearchproduct"/>
+        <path start="bulktag_software"/>
     </fork>
 
-    <action name="join_bulktag_publication">
+    <action name="bulktag_publication">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn-cluster</master>
             <mode>cluster</mode>
@@ -138,7 +138,7 @@
         <error to="Kill"/>
     </action>
 
-    <action name="join_bulktag_dataset">
+    <action name="bulktag_dataset">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn-cluster</master>
             <mode>cluster</mode>
@@ -165,7 +165,7 @@
         <error to="Kill"/>
     </action>
 
-    <action name="join_bulktag_otherresearchproduct">
+    <action name="bulktag_otherresearchproduct">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn-cluster</master>
             <mode>cluster</mode>
@@ -192,7 +192,7 @@
         <error to="Kill"/>
     </action>
 
-    <action name="join_bulktag_software">
+    <action name="bulktag_software">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn-cluster</master>
             <mode>cluster</mode>
@@ -269,7 +269,7 @@
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn-cluster</master>
             <mode>cluster</mode>
-            <name>EOSC_tagging</name>
+            <name>EOSC tagging publication</name>
             <class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag</class>
             <jar>dhp-enrichment-${projectVersion}.jar</jar>
             <spark-opts>
@@ -296,7 +296,7 @@
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn-cluster</master>
             <mode>cluster</mode>
-            <name>EOSC_tagging</name>
+            <name>EOSC tagging dataset</name>
             <class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag</class>
             <jar>dhp-enrichment-${projectVersion}.jar</jar>
             <spark-opts>
@@ -322,7 +322,7 @@
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn-cluster</master>
             <mode>cluster</mode>
-            <name>EOSC_tagging</name>
+            <name>EOSC tagging software</name>
             <class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag</class>
             <jar>dhp-enrichment-${projectVersion}.jar</jar>
             <spark-opts>
@@ -348,7 +348,7 @@
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn-cluster</master>
             <mode>cluster</mode>
-            <name>EOSC_tagging</name>
+            <name>EOSC tagging ORP</name>
             <class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag</class>
             <jar>dhp-enrichment-${projectVersion}.jar</jar>
             <spark-opts>

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

@@ -582,201 +582,7 @@
         <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"/>
+    <join name="wait_clean_country" to="End"/>
 
     <end name="End"/>
 

dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala

@@ -53,7 +53,8 @@ class ResolveEntitiesTest extends Serializable {
   def generateUpdates(spark: SparkSession): Unit = {
     val template = Source.fromInputStream(this.getClass.getResourceAsStream("updates")).mkString
 
-    val pids: List[String] = template.linesWithSeparators.map(l => l.stripLineEnd)
+    val pids: List[String] = template.linesWithSeparators
+      .map(l => l.stripLineEnd)
       .map { id =>
         val r = new Result
         r.setId(id.toLowerCase.trim)
@@ -264,7 +265,8 @@ class ResolveEntitiesTest extends Serializable {
       Source
         .fromInputStream(this.getClass.getResourceAsStream(s"publication"))
         .mkString
-        .linesWithSeparators.map(l => l.stripLineEnd)
+        .linesWithSeparators
+        .map(l => l.stripLineEnd)
         .next(),
       classOf[Publication]
     )

dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala

@@ -69,7 +69,8 @@ class ScholixGraphTest extends AbstractVocabularyTest {
         getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/merge_result_scholix")
       )
       .mkString
-    val result: List[(Relation, ScholixSummary)] = inputRelations.linesWithSeparators.map(l => l.stripLineEnd)
+    val result: List[(Relation, ScholixSummary)] = inputRelations.linesWithSeparators
+      .map(l => l.stripLineEnd)
       .sliding(2)
       .map(s => (s.head, s(1)))
       .map(p => (mapper.readValue(p._1, classOf[Relation]), mapper.readValue(p._2, classOf[ScholixSummary])))