115 lines
3.1 KiB
Scala
115 lines
3.1 KiB
Scala
package eu.dnetlib.doiboost.crossref
|
|
|
|
import eu.dnetlib.dhp.application.{AbstractScalaApplication, ArgumentApplicationParser, SparkScalaApplication}
|
|
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
|
import org.apache.spark.rdd.RDD
|
|
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
|
import org.apache.spark.{SparkConf, SparkContext}
|
|
import org.json4s
|
|
import org.json4s.DefaultFormats
|
|
import org.json4s.jackson.JsonMethods.parse
|
|
import org.slf4j.{Logger, LoggerFactory}
|
|
|
|
import scala.io.Source
|
|
|
|
|
|
class SparkGenerateCrossrefDataset (propertyPath: String, args: Array[String], log: Logger)
|
|
extends AbstractScalaApplication(propertyPath, args, log: Logger) {
|
|
|
|
|
|
/**
|
|
* This method convert the Json crossoref to CrossrefDT class
|
|
*
|
|
* @param metadata the json metadata
|
|
* @return the CrossrefDT
|
|
*/
|
|
def crossrefElement(metadata: String): CrossrefDT = {
|
|
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
|
lazy val json: json4s.JValue = parse(metadata)
|
|
val doi: String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String])
|
|
val timestamp: Long = (json \ "indexed" \ "timestamp").extract[Long]
|
|
CrossrefDT(doi, metadata, timestamp)
|
|
|
|
}
|
|
|
|
|
|
|
|
def convertDataset(spark:SparkSession, sourcePath:String, targetPath:String):Unit = {
|
|
import spark.implicits._
|
|
spark.read.text(sourcePath).as[String].map(entry => crossrefElement(entry))
|
|
.write
|
|
.mode(SaveMode.Overwrite)
|
|
.save(targetPath)
|
|
|
|
}
|
|
|
|
|
|
|
|
/** Here all the spark applications runs this method
|
|
* where the whole logic of the spark node is defined
|
|
*/
|
|
override def run(): Unit = {
|
|
|
|
|
|
val sourcePath = parser.get("sourcePath")
|
|
log.info(s"sourcePath is $sourcePath")
|
|
|
|
val targetPath = parser.get("targetPath")
|
|
log.info(s"targetPath is $targetPath")
|
|
|
|
|
|
convertDataset(spark, sourcePath, targetPath)
|
|
|
|
|
|
|
|
}
|
|
}
|
|
|
|
|
|
|
|
//object GenerateCrossrefDataset {
|
|
//
|
|
// val log: Logger = LoggerFactory.getLogger(GenerateCrossrefDataset.getClass)
|
|
//
|
|
// implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT]
|
|
//
|
|
//
|
|
//
|
|
// def main(args: Array[String]): Unit = {
|
|
// val conf = new SparkConf
|
|
// val parser = new ArgumentApplicationParser(
|
|
// Source
|
|
// .fromInputStream(
|
|
// getClass.getResourceAsStream(
|
|
// "/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json"
|
|
// )
|
|
// )
|
|
// .mkString
|
|
// )
|
|
// parser.parseArgument(args)
|
|
// val master = parser.get("master")
|
|
// val sourcePath = parser.get("sourcePath")
|
|
// val targetPath = parser.get("targetPath")
|
|
//
|
|
// val spark: SparkSession = SparkSession
|
|
// .builder()
|
|
// .config(conf)
|
|
// .appName(UnpackCrtossrefEntries.getClass.getSimpleName)
|
|
// .master(master)
|
|
// .getOrCreate()
|
|
// val sc: SparkContext = spark.sparkContext
|
|
//
|
|
// import spark.implicits._
|
|
//
|
|
// val tmp: RDD[String] = sc.textFile(sourcePath, 6000)
|
|
//
|
|
// spark
|
|
// .createDataset(tmp)
|
|
// .map(entry => crossrefElement(entry))
|
|
// .write
|
|
// .mode(SaveMode.Overwrite)
|
|
// .save(targetPath)
|
|
// }
|
|
//
|
|
//}
|