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@ -32,14 +32,9 @@ object SparkEBILinksToOaf {
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import spark.implicits._
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implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
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val ebi_rdd:Dataset[EBILinkItem] = spark.createDataset(spark.sparkContext.textFile(sourcePath).map(s => BioDBToOAF.extractEBILinksFromDump(s))).as[EBILinkItem]
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ebi_rdd.write.mode(SaveMode.Overwrite).save(s"${sourcePath}_dataset")
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val ebLinks:Dataset[EBILinkItem] = spark.read.load(s"${sourcePath}_dataset").as[EBILinkItem].filter(l => l.links!= null)
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ebLinks.flatMap(j =>BioDBToOAF.parse_ebi_links(j.links))
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.repartition(4000)
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.filter(p => BioDBToOAF.EBITargetLinksFilter(p))
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.flatMap(p => BioDBToOAF.convertEBILinksToOaf(p))
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.write.mode(SaveMode.Overwrite).save(targetPath)
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