108 lines
3.9 KiB
Scala
108 lines
3.9 KiB
Scala
package eu.dnetlib.dhp.sx.graph
|
|
|
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
|
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation}
|
|
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIUnknown}
|
|
import eu.dnetlib.dhp.sx.ebi.EBIAggregator
|
|
import eu.dnetlib.dhp.sx.ebi.model.{PMArticle, PMAuthor, PMJournal}
|
|
import org.apache.commons.io.IOUtils
|
|
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
|
import org.slf4j.LoggerFactory
|
|
|
|
object SparkSplitOafTODLIEntities {
|
|
|
|
|
|
def getKeyRelation(rel:Relation):String = {
|
|
s"${rel.getSource}::${rel.getRelType}::${rel.getTarget}"
|
|
|
|
|
|
}
|
|
|
|
def main(args: Array[String]): Unit = {
|
|
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkSplitOafTODLIEntities.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json")))
|
|
val logger = LoggerFactory.getLogger(SparkSplitOafTODLIEntities.getClass)
|
|
parser.parseArgument(args)
|
|
|
|
val workingPath: String = parser.get("workingPath")
|
|
logger.info(s"Working dir path = $workingPath")
|
|
|
|
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
|
|
implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo[DLIPublication]
|
|
implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo[DLIDataset]
|
|
implicit val unkEncoder: Encoder[DLIUnknown] = Encoders.kryo[DLIUnknown]
|
|
implicit val relEncoder: Encoder[Relation] = Encoders.kryo[Relation]
|
|
|
|
|
|
|
|
val spark:SparkSession = SparkSession
|
|
.builder()
|
|
.appName(SparkSplitOafTODLIEntities.getClass.getSimpleName)
|
|
.config("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
|
|
.master(parser.get("master"))
|
|
.getOrCreate()
|
|
|
|
|
|
|
|
|
|
val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf]
|
|
|
|
val ebi_dataset:Dataset[DLIDataset] = spark.read.load(s"$workingPath/ebi/baseline_dataset_ebi").as[DLIDataset]
|
|
val ebi_publication:Dataset[DLIPublication] = spark.read.load(s"$workingPath/ebi/baseline_publication_ebi").as[DLIPublication]
|
|
val ebi_relation:Dataset[Relation] = spark.read.load(s"$workingPath/ebi/baseline_relation_ebi").as[Relation]
|
|
|
|
|
|
|
|
OAFDataset
|
|
.filter(s => s != null && s.isInstanceOf[DLIPublication])
|
|
.map(s =>s.asInstanceOf[DLIPublication])
|
|
.union(ebi_publication)
|
|
.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, pubEncoder))
|
|
.groupByKey(_._1)(Encoders.STRING)
|
|
.agg(EBIAggregator.getDLIPublicationAggregator().toColumn)
|
|
.map(p => p._2)
|
|
.repartition(1000)
|
|
.write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/publication")
|
|
|
|
OAFDataset
|
|
.filter(s => s != null && s.isInstanceOf[DLIDataset])
|
|
.map(s =>s.asInstanceOf[DLIDataset])
|
|
.union(ebi_dataset)
|
|
.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, datEncoder))
|
|
.groupByKey(_._1)(Encoders.STRING)
|
|
.agg(EBIAggregator.getDLIDatasetAggregator().toColumn)
|
|
.map(p => p._2)
|
|
.repartition(1000)
|
|
.write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/dataset")
|
|
|
|
|
|
OAFDataset
|
|
.filter(s => s != null && s.isInstanceOf[DLIUnknown])
|
|
.map(s =>s.asInstanceOf[DLIUnknown])
|
|
.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, unkEncoder))
|
|
.groupByKey(_._1)(Encoders.STRING)
|
|
.agg(EBIAggregator.getDLIUnknownAggregator().toColumn)
|
|
.map(p => p._2)
|
|
.repartition(1000)
|
|
.write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/unknown")
|
|
|
|
|
|
OAFDataset
|
|
.filter(s => s != null && s.isInstanceOf[Relation])
|
|
.map(s =>s.asInstanceOf[Relation])
|
|
.union(ebi_relation)
|
|
.map(d => (getKeyRelation(d), d))(Encoders.tuple(Encoders.STRING, relEncoder))
|
|
.groupByKey(_._1)(Encoders.STRING)
|
|
.agg(EBIAggregator.getRelationAggregator().toColumn)
|
|
.map(p => p._2)
|
|
.repartition(1000)
|
|
.write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/relation")
|
|
|
|
|
|
|
|
|
|
|
|
|
|
}
|
|
|
|
}
|