102 lines
3.3 KiB
Scala
102 lines
3.3 KiB
Scala
package eu.dnetlib.dhp.oa.graph.raw
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import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper}
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.common.HdfsSupport
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import eu.dnetlib.dhp.schema.common.ModelSupport
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import eu.dnetlib.dhp.schema.oaf.Oaf
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import eu.dnetlib.dhp.utils.DHPUtils
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import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
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import org.apache.spark.{SparkConf, SparkContext}
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import org.json4s.DefaultFormats
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import org.json4s.jackson.JsonMethods.parse
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import org.slf4j.LoggerFactory
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import scala.collection.JavaConverters._
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import scala.io.Source
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object CopyHdfsOafSparkApplication {
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def main(args: Array[String]): Unit = {
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val log = LoggerFactory.getLogger(getClass)
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val conf = new SparkConf()
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val parser = new ArgumentApplicationParser(
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Source
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.fromInputStream(
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getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json")
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)
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.mkString
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)
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parser.parseArgument(args)
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val spark =
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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"))
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.getOrCreate()
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val sc: SparkContext = spark.sparkContext
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val mdstoreManagerUrl = parser.get("mdstoreManagerUrl")
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log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl)
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val mdFormat = parser.get("mdFormat")
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log.info("mdFormat: {}", mdFormat)
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val mdLayout = parser.get("mdLayout")
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log.info("mdLayout: {}", mdLayout)
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val mdInterpretation = parser.get("mdInterpretation")
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log.info("mdInterpretation: {}", mdInterpretation)
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val hdfsPath = parser.get("hdfsPath")
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log.info("hdfsPath: {}", hdfsPath)
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implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
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val paths =
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DHPUtils.mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation, true).asScala
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val validPaths: List[String] =
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paths.filter(p => HdfsSupport.exists(p, sc.hadoopConfiguration)).toList
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val types = ModelSupport.oafTypes.entrySet.asScala
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.map(e => Tuple2(e.getKey, e.getValue))
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if (validPaths.nonEmpty) {
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val oaf = spark.read.textFile(validPaths: _*)
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val mapper =
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new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false)
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types.foreach(t =>
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oaf
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.filter(o => isOafType(o, t._1))
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.map(j => mapper.readValue(j, t._2).asInstanceOf[Oaf])
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.map(s => mapper.writeValueAsString(s))(Encoders.STRING)
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.write
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.option("compression", "gzip")
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.mode(SaveMode.Append)
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.text(s"$hdfsPath/${t._1}")
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)
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}
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}
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def isOafType(input: String, oafType: String): Boolean = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: org.json4s.JValue = parse(input)
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if (oafType == "relation") {
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val hasSource = (json \ "source").extractOrElse[String](null)
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val hasTarget = (json \ "target").extractOrElse[String](null)
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hasSource != null && hasTarget != null
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} else {
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val hasId = (json \ "id").extractOrElse[String](null)
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val resultType = (json \ "resulttype" \ "classid").extractOrElse[String](null)
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hasId != null && oafType.equalsIgnoreCase(resultType)
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}
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}
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}
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