44 lines
1.7 KiB
Scala
44 lines
1.7 KiB
Scala
package eu.dnetlib.dhp.sx.bio.ebi
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.collection.CollectionUtils
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import eu.dnetlib.dhp.schema.oaf.Oaf
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import eu.dnetlib.dhp.sx.bio.BioDBToOAF
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import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
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import org.apache.commons.io.IOUtils
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import org.apache.spark.SparkConf
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import org.apache.spark.sql._
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import org.slf4j.{Logger, LoggerFactory}
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object SparkEBILinksToOaf {
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def main(args: Array[String]): Unit = {
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val log: Logger = LoggerFactory.getLogger(getClass)
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json")))
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parser.parseArgument(args)
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val spark: SparkSession =
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SparkSession
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.builder()
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.config(conf)
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.appName(SparkEBILinksToOaf.getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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import spark.implicits._
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val sourcePath = parser.get("sourcePath")
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log.info(s"sourcePath -> $sourcePath")
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val targetPath = parser.get("targetPath")
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log.info(s"targetPath -> $targetPath")
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implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
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val ebLinks: Dataset[EBILinkItem] = spark.read.load(sourcePath).as[EBILinkItem].filter(l => l.links != null && l.links.startsWith("{"))
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ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
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.filter(p => BioDBToOAF.EBITargetLinksFilter(p))
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.flatMap(p => BioDBToOAF.convertEBILinksToOaf(p))
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.flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null)
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.write.mode(SaveMode.Overwrite).save(targetPath)
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}
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}
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