forked from D-Net/dnet-hadoop
86 lines
3.8 KiB
Scala
86 lines
3.8 KiB
Scala
package eu.dnetlib.doiboost
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.action.AtomicAction
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import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset}
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import org.apache.commons.io.IOUtils
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import org.apache.hadoop.io.Text
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import org.apache.hadoop.io.compress.GzipCodec
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import org.apache.hadoop.mapred.SequenceFileOutputFormat
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import org.apache.spark.SparkConf
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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object SparkGenerateDOIBoostActionSet {
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val logger: Logger = LoggerFactory.getLogger(getClass)
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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(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/generate_doiboost_as_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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implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
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implicit val mapEncoderOrg: Encoder[Organization] = Encoders.kryo[Organization]
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implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
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implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation]
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implicit val mapEncoderAS: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING)
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implicit val mapEncoderAtomiAction: Encoder[AtomicAction[OafDataset]] = Encoders.kryo[AtomicAction[OafDataset]]
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val dbPublicationPath = parser.get("dbPublicationPath")
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val dbDatasetPath = parser.get("dbDatasetPath")
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val crossRefRelation = parser.get("crossRefRelation")
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val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath")
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val dbOrganizationPath = parser.get("dbOrganizationPath")
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val workingDirPath = parser.get("targetPath")
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val sequenceFilePath = parser.get("sFilePath")
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val asDataset = spark.read.load(dbDatasetPath).as[OafDataset]
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.map(d =>DoiBoostMappingUtil.fixResult(d))
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.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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// .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet")
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val asPublication =spark.read.load(dbPublicationPath).as[Publication]
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.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
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val asOrganization = spark.read.load(dbOrganizationPath).as[Organization]
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.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
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val asCRelation = spark.read.load(crossRefRelation).as[Relation]
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.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
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val asRelAffiliation = spark.read.load(dbaffiliationRelationPath).as[Relation]
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.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
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val d: Dataset[(String, String)] = asDataset.union(asPublication).union(asOrganization).union(asCRelation).union(asRelAffiliation)
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// spark.read.load(s"$workingDirPath/actionSet").as[(String,String)]
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d.rdd.repartition(6000).map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$sequenceFilePath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
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}
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}
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