forked from D-Net/dnet-hadoop
imported from branch stable_ids generation of Actionset datacite
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package eu.dnetlib.dhp.actionmanager.datacite
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf.Oaf
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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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import scala.io.Source
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object ExportActionSetJobNode {
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val log: Logger = LoggerFactory.getLogger(ExportActionSetJobNode.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/actionmanager/datacite/exportDataset_parameters.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 targetPath = parser.get("targetPath")
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val spark: SparkSession = SparkSession.builder().config(conf)
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.appName(ExportActionSetJobNode.getClass.getSimpleName)
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.master(master)
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.getOrCreate()
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implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
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implicit val tEncoder:Encoder[(String,String)] = Encoders.tuple(Encoders.STRING,Encoders.STRING)
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spark.read.load(sourcePath).as[Oaf]
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.map(o =>DataciteToOAFTransformation.toActionSet(o))
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.filter(o => o!= null)
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.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
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}
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}
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[
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{
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"paramName": "s",
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"paramLongName": "sourcePath",
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"paramDescription": "the source mdstore path",
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"paramRequired": true
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},
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{
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"paramName": "t",
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"paramLongName": "targetPath",
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"paramDescription": "the target mdstore path",
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"paramRequired": true
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},
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{
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"paramName": "m",
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"paramLongName": "master",
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"paramDescription": "the master name",
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"paramRequired": true
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}
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]
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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</configuration>
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<workflow-app name="Datacite_to_ActionSet_Workflow" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sourcePath</name>
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<description>the working path of Datacite stores</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>the path of Datacite ActionSet</description>
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</property>
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</parameters>
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<start to="ExportDataset"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ExportDataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>ExportDataset</name>
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<class>eu.dnetlib.dhp.actionmanager.datacite.ExportActionSetJobNode</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--targetPath</arg><arg>${outputPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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