68 lines
2.5 KiB
Scala
68 lines
2.5 KiB
Scala
package eu.dnetlib.doiboost.orcid
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf.Publication
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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.rdd.RDD
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import org.apache.spark.sql.functions.{col, collect_list}
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import org.apache.spark.sql._
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import org.slf4j.{Logger, LoggerFactory}
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object SparkPreprocessORCID {
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val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)
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def fixORCIDItem(item: ORCIDItem): ORCIDItem = {
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ORCIDItem(item.doi, item.authors.groupBy(_.oid).map(_._2.head).toList)
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}
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def run(spark: SparkSession, sourcePath: String, workingPath: String): Unit = {
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import spark.implicits._
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implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
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val inputRDD: RDD[OrcidAuthor] = spark.sparkContext.textFile(s"$sourcePath/authors").map(s => ORCIDToOAF.convertORCIDAuthor(s)).filter(s => s != null).filter(s => ORCIDToOAF.authorValid(s))
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spark.createDataset(inputRDD).as[OrcidAuthor].write.mode(SaveMode.Overwrite).save(s"$workingPath/author")
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val res = spark.sparkContext.textFile(s"$sourcePath/works").flatMap(s => ORCIDToOAF.extractDOIWorks(s)).filter(s => s != null)
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spark.createDataset(res).as[OrcidWork].write.mode(SaveMode.Overwrite).save(s"$workingPath/works")
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val authors: Dataset[OrcidAuthor] = spark.read.load(s"$workingPath/author").as[OrcidAuthor]
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val works: Dataset[OrcidWork] = spark.read.load(s"$workingPath/works").as[OrcidWork]
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works.joinWith(authors, authors("oid").equalTo(works("oid")))
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.map(i => {
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val doi = i._1.doi
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val author = i._2
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(doi, author)
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}).groupBy(col("_1").alias("doi"))
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.agg(collect_list(col("_2")).alias("authors")).as[ORCIDItem]
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.map(s => fixORCIDItem(s))
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.write.mode(SaveMode.Overwrite).save(s"$workingPath/orcidworksWithAuthor")
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}
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def main(args: Array[String]): Unit = {
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/preprocess_orcid_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(getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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val sourcePath = parser.get("sourcePath")
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val workingPath = parser.get("workingPath")
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run(spark, sourcePath, workingPath)
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}
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}
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