code refactor, created and moved scala code on the correct maven folder under src/main/scala and src/test/scala

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/actionmanager/scholix/SparkSaveActionSet.scala

@@ -3,7 +3,7 @@ package eu.dnetlib.dhp.actionmanager.scholix
 import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.schema.action.AtomicAction
-import eu.dnetlib.dhp.schema.oaf.{Oaf, Dataset => OafDataset,Publication, Software, OtherResearchProduct, Relation}
+import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, Oaf, Publication, Software, OtherResearchProduct, Relation}
 import org.apache.hadoop.io.Text
 import org.apache.hadoop.io.compress.GzipCodec
 import org.apache.hadoop.mapred.SequenceFileOutputFormat

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

@@ -3,8 +3,7 @@ package eu.dnetlib.dhp.datacite
 import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations
-import eu.dnetlib.dhp.common.Constants.MDSTORE_DATA_PATH
+import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
-import eu.dnetlib.dhp.common.Constants.MDSTORE_SIZE_PATH
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
 import eu.dnetlib.dhp.schema.mdstore.{MDStoreVersion, MetadataRecord}
 import eu.dnetlib.dhp.schema.oaf.Oaf

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

@@ -7,6 +7,7 @@ import org.json4s.DefaultFormats
 import org.json4s.JsonAST.{JField, JObject, JString}
 import org.json4s.jackson.JsonMethods.{compact, parse, render}
 import collection.JavaConverters._
+
 object BioDBToOAF {
 
   case class EBILinkItem(id: Long, links: String) {}

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

@@ -1,9 +1,9 @@
 package eu.dnetlib.dhp.sx.bio
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetlib.dhp.schema.oaf.Oaf
-import BioDBToOAF.ScholixResolved
 import eu.dnetlib.dhp.collection.CollectionUtils
+import eu.dnetlib.dhp.schema.oaf.Oaf
+import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
 import org.apache.commons.io.IOUtils
 import org.apache.spark.SparkConf
 import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
@@ -36,13 +36,13 @@ object SparkTransformBioDatabaseToOAF {
     import spark.implicits._
     database.toUpperCase() match {
       case "UNIPROT" =>
-        spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
+        spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
       case "PDB" =>
-        spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
+        spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
       case "SCHOLIX" =>
-        spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
+        spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
       case "CROSSREF_LINKS" =>
-        spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
+        spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
     }
   }
 

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

@@ -3,7 +3,7 @@ package eu.dnetlib.dhp.sx.bio.ebi
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
 import eu.dnetlib.dhp.schema.oaf.Result
-import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
+import eu.dnetlib.dhp.sx.bio.pubmed._
 import eu.dnetlib.dhp.utils.ISLookupClientFactory
 import org.apache.commons.io.IOUtils
 import org.apache.hadoop.conf.Configuration

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

@@ -1,9 +1,8 @@
 package eu.dnetlib.dhp.sx.bio.ebi
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
 import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
-import eu.dnetlib.dhp.sx.bio.pubmed.PMJournal
+import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
 import org.apache.commons.io.IOUtils
 import org.apache.http.client.config.RequestConfig
 import org.apache.http.client.methods.HttpGet

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

@@ -1,11 +1,10 @@
 package eu.dnetlib.dhp.sx.bio.ebi
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
+import eu.dnetlib.dhp.collection.CollectionUtils
 import eu.dnetlib.dhp.schema.oaf.Oaf
 import eu.dnetlib.dhp.sx.bio.BioDBToOAF
 import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
-import BioDBToOAF.EBILinkItem
-import eu.dnetlib.dhp.collection.CollectionUtils
 import org.apache.commons.io.IOUtils
 import org.apache.spark.SparkConf
 import org.apache.spark.sql._
@@ -38,7 +37,7 @@ object SparkEBILinksToOaf {
     ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
       .filter(p => BioDBToOAF.EBITargetLinksFilter(p))
       .flatMap(p => BioDBToOAF.convertEBILinksToOaf(p))
-      .flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null)
+      .flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null)
       .write.mode(SaveMode.Overwrite).save(targetPath)
   }
 }

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

@@ -4,10 +4,9 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
 import eu.dnetlib.dhp.schema.common.ModelConstants
 import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType}
 import eu.dnetlib.dhp.schema.oaf._
-import scala.collection.JavaConverters._
 
 import java.util.regex.Pattern
-
+import collection.JavaConverters._
 /**
  *
  */
@@ -22,10 +21,10 @@ object PubMedToOaf {
   val collectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
 
 
-
   /**
    * Cleaning the DOI Applying regex in order to
    * remove doi starting with URL
+   *
    * @param doi input DOI
    * @return cleaned DOI
    */
@@ -49,7 +48,7 @@ object PubMedToOaf {
    * starting from OAF instanceType value
    *
    * @param cobjQualifier OAF instance type
-   * @param vocabularies All dnet vocabularies
+   * @param vocabularies  All dnet vocabularies
    * @return the correct instance
    */
   def createResult(cobjQualifier: Qualifier, vocabularies: VocabularyGroup): Result = {
@@ -65,7 +64,7 @@ object PubMedToOaf {
   }
 
   /**
-   *  Mapping the Pubmedjournal info into the OAF Journale
+   * Mapping the Pubmedjournal info into the OAF Journale
    *
    * @param j the pubmedJournal
    * @return the OAF Journal
@@ -91,9 +90,8 @@ object PubMedToOaf {
    * Find vocabulary term into synonyms and term in the vocabulary
    *
    * @param vocabularyName the input vocabulary name
-   * @param vocabularies all the vocabularies
+   * @param vocabularies   all the vocabularies
-   * @param term the term to find
+   * @param term           the term to find
-   *
    * @return the cleaned term value
    */
   def getVocabularyTerm(vocabularyName: String, vocabularies: VocabularyGroup, term: String): Qualifier = {
@@ -104,10 +102,9 @@ object PubMedToOaf {
 
 
   /**
-   *  Map the Pubmed Article into the OAF instance
+   * Map the Pubmed Article into the OAF instance
    *
-   *
+   * @param article      the pubmed articles
-   * @param article the pubmed articles
    * @param vocabularies the vocabularies
    * @return The OAF instance if the mapping did not fail
    */
@@ -185,7 +182,6 @@ object PubMedToOaf {
     //--------------------------------------------------------------------------------------
 
 
-
     // RESULT MAPPING
     //--------------------------------------------------------------------------------------
     result.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo))