67 lines
2.4 KiB
Scala
67 lines
2.4 KiB
Scala
package eu.dnetlib.dhp.sx.bio.ebi
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.application.AbstractScalaApplication
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import eu.dnetlib.dhp.collection.CollectionUtils
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import eu.dnetlib.dhp.common.Constants.MDSTORE_DATA_PATH
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import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion
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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.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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class SparkTransformEBILinksToOaf(propertyPath: String, args: Array[String], log: Logger)
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extends AbstractScalaApplication(propertyPath, args, log: Logger) {
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def transformLinks(spark: SparkSession, sourcePath: String, outputBasePath: String, targetPath: String) = {
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implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
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import spark.implicits._
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val ebLinks: Dataset[EBILinkItem] = spark.read
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.load(sourcePath)
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.as[EBILinkItem]
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.filter(l => l.links != null && l.links.startsWith("{"))
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CollectionUtils.saveDataset(
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ebLinks
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.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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targetPath
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)
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reportTotalSize(targetPath, outputBasePath)
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}
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/** Here all the spark applications runs this method
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* where the whole logic of the spark node is defined
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*/
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override def run(): Unit = {
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val sourcePath = parser.get("sourcePath")
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log.info(s"sourcePath is '$sourcePath'")
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val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
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log.info(s"mdstoreOutputVersion is '$mdstoreOutputVersion'")
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val mapper = new ObjectMapper()
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val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
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val outputBasePath = cleanedMdStoreVersion.getHdfsPath
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log.info(s"outputBasePath is '$outputBasePath'")
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val targetPath = s"$outputBasePath$MDSTORE_DATA_PATH"
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log.info(s"targetPath is '$targetPath'")
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transformLinks(spark, sourcePath, outputBasePath, targetPath)
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}
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}
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object SparkTransformEBILinksToOaf {
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val log: Logger = LoggerFactory.getLogger(SparkTransformEBILinksToOaf.getClass)
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def main(args: Array[String]): Unit = {
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new SparkTransformEBILinksToOaf("/eu/dnetlib/dhp/sx/bio/ebi/transform_ebi_to_df_params.json", args, log)
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.initialize()
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.run()
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}
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}
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