extended ebiLinks to create a dataset before generation of OAF

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkEBILinksToOaf.scala

@@ -2,10 +2,12 @@ package eu.dnetlib.dhp.sx.graph.ebi
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.schema.oaf.Oaf
+import eu.dnetlib.dhp.sx.graph.bio
 import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF
 import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.EBILinkItem
 import org.apache.commons.io.IOUtils
 import org.apache.spark.SparkConf
+import org.apache.spark.rdd.RDD
 import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
 import org.slf4j.{Logger, LoggerFactory}
 object SparkEBILinksToOaf {
@@ -29,6 +31,11 @@ object SparkEBILinksToOaf {
 
     import spark.implicits._
     implicit  val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
+
+    val ebi_rdd:Dataset[EBILinkItem] = spark.createDataset(spark.sparkContext.textFile(sourcePath).map(s => BioDBToOAF.extractEBILinksFromDump(s))).as[EBILinkItem]
+
+    ebi_rdd.write.mode(SaveMode.Overwrite).save(s"${sourcePath}_dataset")
+
     val ebLinks:Dataset[EBILinkItem] = spark.read.load(sourcePath).as[EBILinkItem].filter(l => l.links!= null)
 
     ebLinks.flatMap(j =>BioDBToOAF.parse_ebi_links(j.links))