formatted code

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteAPIImporter.scala

@@ -3,8 +3,7 @@ package eu.dnetlib.dhp.datacite
 import org.json4s.jackson.JsonMethods.{compact, parse, render}
 import org.json4s.{DefaultFormats, JValue}
 
-class DataciteAPIImporter(timestamp: Long = 0, blocks: Long = 10, until: Long = -1)
+class DataciteAPIImporter(timestamp: Long = 0, blocks: Long = 10, until: Long = -1) extends AbstractRestClient {
-    extends AbstractRestClient {
 
   override def extractInfo(input: String): Unit = {
     implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala

@@ -327,9 +327,7 @@ object DataciteToOAFTransformation {
       a.setFullname(c.name.orNull)
       a.setName(c.givenName.orNull)
       a.setSurname(c.familyName.orNull)
-      if (
+      if (c.nameIdentifiers != null && c.nameIdentifiers.isDefined && c.nameIdentifiers.get != null) {
-        c.nameIdentifiers != null && c.nameIdentifiers.isDefined && c.nameIdentifiers.get != null
-      ) {
         a.setPid(
           c.nameIdentifiers.get
             .map(ni => {
@@ -395,9 +393,7 @@ object DataciteToOAFTransformation {
       .find(d => d.dateType.get.equalsIgnoreCase("issued"))
       .map(d => extract_date(d.date.get))
     val a_date: Option[String] = dates
-      .filter(d =>
+      .filter(d => d.date.isDefined && d.dateType.isDefined && d.dateType.get.equalsIgnoreCase("available"))
-        d.date.isDefined && d.dateType.isDefined && d.dateType.get.equalsIgnoreCase("available")
-      )
       .map(d => extract_date(d.date.get))
       .find(d => d != null && d.isDefined)
       .map(d => d.get)

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala

@@ -2,12 +2,7 @@ package eu.dnetlib.dhp.sx.bio.pubmed
 
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
 import eu.dnetlib.dhp.schema.common.ModelConstants
-import eu.dnetlib.dhp.schema.oaf.utils.{
+import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType}
-  GraphCleaningFunctions,
-  IdentifierFactory,
-  OafMapperUtils,
-  PidType
-}
 import eu.dnetlib.dhp.schema.oaf._
 import collection.JavaConverters._
 
@@ -169,9 +164,7 @@ object PubMedToOaf {
       pubmedInstance.setInstancetype(cojbCategory)
     } else {
       val i_type = article.getPublicationTypes.asScala
-        .map(s =>
+        .map(s => getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue))
-          getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue)
-        )
         .find(q => q != null)
       if (i_type.isDefined)
         pubmedInstance.setInstancetype(i_type.get)

dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala

@@ -59,8 +59,7 @@ object SparkGenerateDoiBoost {
     val workingDirPath = parser.get("workingPath")
     val openaireOrganizationPath = parser.get("openaireOrganizationPath")
 
-    val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication]
+    val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication] with Serializable {
-      with Serializable {
       override def zero: Publication = new Publication
 
       override def reduce(b: Publication, a: (String, Publication)): Publication = {

dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala

@@ -438,11 +438,10 @@ case object Crossref2Oaf {
       funders.foreach(funder => {
         if (funder.DOI.isDefined && funder.DOI.get.nonEmpty) {
           funder.DOI.get match {
-            case "10.13039/100010663" | "10.13039/100010661" | "10.13039/501100007601" |
+            case "10.13039/100010663" | "10.13039/100010661" | "10.13039/501100007601" | "10.13039/501100000780" |
-                "10.13039/501100000780" | "10.13039/100010665" =>
+                "10.13039/100010665" =>
               generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward)
-            case "10.13039/100011199" | "10.13039/100004431" | "10.13039/501100004963" |
+            case "10.13039/100011199" | "10.13039/100004431" | "10.13039/501100004963" | "10.13039/501100000780" =>
-                "10.13039/501100000780" =>
               generateSimpleRelationFromAward(funder, "corda_______", extractECAward)
             case "10.13039/501100000781" =>
               generateSimpleRelationFromAward(funder, "corda_______", extractECAward)
@@ -512,8 +511,7 @@ case object Crossref2Oaf {
             case "European Union's" =>
               generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward)
               generateSimpleRelationFromAward(funder, "corda_______", extractECAward)
-            case "The French National Research Agency (ANR)" |
+            case "The French National Research Agency (ANR)" | "The French National Research Agency" =>
-                "The French National Research Agency" =>
               generateSimpleRelationFromAward(funder, "anr_________", a => a)
             case "CONICYT, Programa de Formación de Capital Humano Avanzado" =>
               generateSimpleRelationFromAward(funder, "conicytf____", extractECAward)

dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala

@@ -15,9 +15,7 @@ object SparkProcessMAG {
   def getDistinctResults(d: Dataset[MagPapers]): Dataset[MagPapers] = {
     d.where(col("Doi").isNotNull)
       .groupByKey(mp => DoiBoostMappingUtil.normalizeDoi(mp.Doi))(Encoders.STRING)
-      .reduceGroups((p1: MagPapers, p2: MagPapers) =>
+      .reduceGroups((p1: MagPapers, p2: MagPapers) => ConversionUtil.choiceLatestMagArtitcle(p1, p2))
-        ConversionUtil.choiceLatestMagArtitcle(p1, p2)
-      )
       .map(_._2)(Encoders.product[MagPapers])
       .map(mp => {
         MagPapers(

dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala

@@ -223,9 +223,7 @@ class CrossrefMappingTest {
 
     val collectedFromList = result.getCollectedfrom.asScala
     assert(
-      collectedFromList.exists(c =>
+      collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")),
-        c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")
-      ),
       "Wrong collected from assertion"
     )
 
@@ -301,9 +299,7 @@ class CrossrefMappingTest {
 
     val collectedFromList = result.getCollectedfrom.asScala
     assert(
-      collectedFromList.exists(c =>
+      collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")),
-        c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")
-      ),
       "Wrong collected from assertion"
     )
 
@@ -435,9 +431,7 @@ class CrossrefMappingTest {
 
     val collectedFromList = result.getCollectedfrom.asScala
     assert(
-      collectedFromList.exists(c =>
+      collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")),
-        c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")
-      ),
       "Wrong collected from assertion"
     )
 
@@ -553,9 +547,7 @@ class CrossrefMappingTest {
     println(mapper.writeValueAsString(item))
 
     assertTrue(
-      item.getInstance().asScala exists (i =>
+      item.getInstance().asScala exists (i => i.getLicense.getValue.equals("https://www.springer.com/vor"))
-        i.getLicense.getValue.equals("https://www.springer.com/vor")
-      )
     )
     assertTrue(
       item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("CLOSED"))
@@ -590,9 +582,7 @@ class CrossrefMappingTest {
     )
     assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("OPEN")))
     assertTrue(
-      item.getInstance().asScala exists (i =>
+      item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == OpenAccessRoute.hybrid)
-        i.getAccessright.getOpenAccessRoute == OpenAccessRoute.hybrid
-      )
     )
     mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
     println(mapper.writeValueAsString(item))
@@ -627,9 +617,7 @@ class CrossrefMappingTest {
     )
     assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("OPEN")))
     assertTrue(
-      item.getInstance().asScala exists (i =>
+      item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == OpenAccessRoute.hybrid)
-        i.getAccessright.getOpenAccessRoute == OpenAccessRoute.hybrid
-      )
     )
     mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
     println(mapper.writeValueAsString(item))

dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala

@@ -2,14 +2,7 @@ package eu.dnetlib.dhp.sx.graph
 
 import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetlib.dhp.schema.oaf.{
+import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset}
-  OtherResearchProduct,
-  Publication,
-  Relation,
-  Result,
-  Software,
-  Dataset => OafDataset
-}
 import org.apache.commons.io.IOUtils
 import org.apache.spark.SparkConf
 import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}

dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/PangaeaUtils.scala

@@ -90,8 +90,7 @@ object PangaeaUtils {
     )
   }
 
-  def getDatasetAggregator()
+  def getDatasetAggregator(): Aggregator[(String, PangaeaDataModel), PangaeaDataModel, PangaeaDataModel] =
-    : Aggregator[(String, PangaeaDataModel), PangaeaDataModel, PangaeaDataModel] =
     new Aggregator[(String, PangaeaDataModel), PangaeaDataModel, PangaeaDataModel] {
 
       override def zero: PangaeaDataModel = null

dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPrepare.scala

@@ -1,11 +1,7 @@
 package eu.dnetlib.dhp.oa.graph.hostedbymap
 
 import com.fasterxml.jackson.databind.ObjectMapper
-import eu.dnetlib.dhp.oa.graph.hostedbymap.SparkPrepareHostedByInfoToApply.{
+import eu.dnetlib.dhp.oa.graph.hostedbymap.SparkPrepareHostedByInfoToApply.{joinResHBM, prepareResultInfo, toEntityInfo}
-  joinResHBM,
-  prepareResultInfo,
-  toEntityInfo
-}
 import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
 import org.apache.spark.SparkConf
 import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}

dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPreprocess.scala

@@ -51,8 +51,7 @@ class TestPreprocess extends java.io.Serializable {
       ds.filter(hbi => hbi.issn.equals("0212-8365") && hbi.eissn.equals("2253-900X")).count == 1
     )
     assertTrue(
-      ds.filter(hbi => hbi.issn.equals("0212-8365") && hbi.officialname.equals("Thémata"))
+      ds.filter(hbi => hbi.issn.equals("0212-8365") && hbi.officialname.equals("Thémata")).count == 1
-        .count == 1
     )
     assertTrue(
       ds.filter(hbi =>

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

@@ -189,11 +189,7 @@ class ResolveEntitiesTest extends Serializable {
 
     var ct = pubDS.count()
     var et = pubDS
-      .filter(p =>
+      .filter(p => p.getTitle != null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty))
-        p.getTitle != null && p.getTitle.asScala.forall(t =>
-          t.getValue != null && t.getValue.nonEmpty
-        )
-      )
       .count()
 
     assertEquals(ct, et)
@@ -208,11 +204,7 @@ class ResolveEntitiesTest extends Serializable {
       .count()
     ct = datDS.count()
     et = datDS
-      .filter(p =>
+      .filter(p => p.getTitle != null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty))
-        p.getTitle != null && p.getTitle.asScala.forall(t =>
-          t.getValue != null && t.getValue.nonEmpty
-        )
-      )
       .count()
     assertEquals(ct, et)
 
@@ -226,11 +218,7 @@ class ResolveEntitiesTest extends Serializable {
       .count()
     ct = softDS.count()
     et = softDS
-      .filter(p =>
+      .filter(p => p.getTitle != null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty))
-        p.getTitle != null && p.getTitle.asScala.forall(t =>
-          t.getValue != null && t.getValue.nonEmpty
-        )
-      )
       .count()
     assertEquals(ct, et)
 
@@ -245,11 +233,7 @@ class ResolveEntitiesTest extends Serializable {
 
     ct = orpDS.count()
     et = orpDS
-      .filter(p =>
+      .filter(p => p.getTitle != null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty))
-        p.getTitle != null && p.getTitle.asScala.forall(t =>
-          t.getValue != null && t.getValue.nonEmpty
-        )
-      )
       .count()
     assertEquals(ct, et)
 

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

@@ -56,9 +56,7 @@ class ScholixGraphTest extends AbstractVocabularyTest {
     assertNotNull(result)
 
     assertEquals(result.size, items.size)
-    val d = result.find(s =>
+    val d = result.find(s => s.getLocalIdentifier.asScala.exists(i => i.getUrl == null || i.getUrl.isEmpty))
-      s.getLocalIdentifier.asScala.exists(i => i.getUrl == null || i.getUrl.isEmpty)
-    )
     assertFalse(d.isDefined)
     println(mapper.writeValueAsString(result.head))
 
@@ -74,9 +72,7 @@ class ScholixGraphTest extends AbstractVocabularyTest {
     val result: List[(Relation, ScholixSummary)] = inputRelations.lines
       .sliding(2)
       .map(s => (s.head, s(1)))
-      .map(p =>
+      .map(p => (mapper.readValue(p._1, classOf[Relation]), mapper.readValue(p._2, classOf[ScholixSummary])))
-        (mapper.readValue(p._1, classOf[Relation]), mapper.readValue(p._2, classOf[ScholixSummary]))
-      )
       .toList
     assertNotNull(result)
     assertTrue(result.nonEmpty)