64 lines
2.7 KiB
Scala
64 lines
2.7 KiB
Scala
package eu.dnetlib.dhp.datacite
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations
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import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
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import eu.dnetlib.dhp.schema.mdstore.{MDStoreVersion, MetadataRecord}
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import eu.dnetlib.dhp.schema.oaf.Oaf
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import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile
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import eu.dnetlib.dhp.utils.ISLookupClientFactory
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import org.apache.spark.SparkConf
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import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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import scala.io.Source
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object GenerateDataciteDatasetSpark {
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val log: Logger = LoggerFactory.getLogger(GenerateDataciteDatasetSpark.getClass)
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def main(args: Array[String]): Unit = {
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val conf = new SparkConf
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/datacite/generate_dataset_params.json")).mkString)
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parser.parseArgument(args)
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val master = parser.get("master")
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val sourcePath = parser.get("sourcePath")
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val exportLinks = "true".equalsIgnoreCase(parser.get("exportLinks"))
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val isLookupUrl: String = parser.get("isLookupUrl")
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log.info("isLookupUrl: {}", isLookupUrl)
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val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
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val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
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val spark: SparkSession = SparkSession.builder().config(conf)
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.appName(GenerateDataciteDatasetSpark.getClass.getSimpleName)
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.master(master)
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.getOrCreate()
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import spark.implicits._
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implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord]
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implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
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val mdstoreOutputVersion = parser.get("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("outputBasePath: {}", outputBasePath)
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val targetPath = s"$outputBasePath/$MDSTORE_DATA_PATH"
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spark.read.load(sourcePath).as[DataciteType]
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.filter(d => d.isActive)
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.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks))
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.filter(d => d != null)
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.flatMap(i => fixRelations(i)).filter(i => i != null)
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.write.mode(SaveMode.Overwrite).save(targetPath)
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val total_items = spark.read.load(targetPath).as[Oaf].count()
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writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$total_items", outputBasePath + MDSTORE_SIZE_PATH)
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}
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}
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