forked from D-Net/dnet-hadoop
65 lines
2.6 KiB
Scala
65 lines
2.6 KiB
Scala
package eu.dnetlib.doiboost.orcid
|
|
|
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
|
import eu.dnetlib.dhp.schema.oaf.Publication
|
|
import org.apache.commons.io.IOUtils
|
|
import org.apache.spark.SparkConf
|
|
import org.apache.spark.rdd.RDD
|
|
import org.apache.spark.sql.functions._
|
|
import org.apache.spark.sql._
|
|
import org.slf4j.{Logger, LoggerFactory}
|
|
|
|
object SparkConvertORCIDToOAF {
|
|
val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)
|
|
|
|
def run(spark:SparkSession,sourcePath:String,workingPath:String, targetPath:String):Unit = {
|
|
import spark.implicits._
|
|
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
|
|
|
|
val inputRDD:RDD[OrcidAuthor] = spark.sparkContext.textFile(s"$sourcePath/authors").map(s => ORCIDToOAF.convertORCIDAuthor(s)).filter(s => s!= null).filter(s => ORCIDToOAF.authorValid(s))
|
|
|
|
spark.createDataset(inputRDD).as[OrcidAuthor].write.mode(SaveMode.Overwrite).save(s"$workingPath/author")
|
|
|
|
val res = spark.sparkContext.textFile(s"$sourcePath/works").flatMap(s => ORCIDToOAF.extractDOIWorks(s)).filter(s => s!= null)
|
|
|
|
spark.createDataset(res).as[OrcidWork].write.mode(SaveMode.Overwrite).save(s"$workingPath/works")
|
|
|
|
val authors :Dataset[OrcidAuthor] = spark.read.load(s"$workingPath/author").as[OrcidAuthor]
|
|
|
|
val works :Dataset[OrcidWork] = spark.read.load(s"$workingPath/works").as[OrcidWork]
|
|
|
|
works.joinWith(authors, authors("oid").equalTo(works("oid")))
|
|
.map(i =>{
|
|
val doi = i._1.doi
|
|
val author = i._2
|
|
(doi, author)
|
|
}).groupBy(col("_1").alias("doi"))
|
|
.agg(collect_list(col("_2")).alias("authors"))
|
|
.write.mode(SaveMode.Overwrite).save(s"$workingPath/orcidworksWithAuthor")
|
|
|
|
val dataset: Dataset[ORCIDItem] =spark.read.load(s"$workingPath/orcidworksWithAuthor").as[ORCIDItem]
|
|
|
|
logger.info("Converting ORCID to OAF")
|
|
dataset.map(o => ORCIDToOAF.convertTOOAF(o)).write.mode(SaveMode.Overwrite).save(targetPath)
|
|
}
|
|
|
|
def main(args: Array[String]): Unit = {
|
|
val conf: SparkConf = new SparkConf()
|
|
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json")))
|
|
parser.parseArgument(args)
|
|
val spark: SparkSession =
|
|
SparkSession
|
|
.builder()
|
|
.config(conf)
|
|
.appName(getClass.getSimpleName)
|
|
.master(parser.get("master")).getOrCreate()
|
|
|
|
|
|
val sourcePath = parser.get("sourcePath")
|
|
val workingPath = parser.get("workingPath")
|
|
val targetPath = parser.get("targetPath")
|
|
run(spark, sourcePath, workingPath, targetPath)
|
|
|
|
}
|
|
|
|
} |