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imported from branch stable_ids generation of Actionset datacite

master
Sandro La Bruzzo 8 months ago
parent
commit
9ca438d9b1
  1. 40
      dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala
  2. 21
      dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json
  3. 23
      dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/config-default.xml
  4. 46
      dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/workflow.xml

40
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala

@ -0,0 +1,40 @@
package eu.dnetlib.dhp.actionmanager.datacite
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Oaf
import org.apache.hadoop.io.Text
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.hadoop.mapred.SequenceFileOutputFormat
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
object ExportActionSetJobNode {
val log: Logger = LoggerFactory.getLogger(ExportActionSetJobNode.getClass)
def main(args: Array[String]): Unit = {
val conf = new SparkConf
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json")).mkString)
parser.parseArgument(args)
val master = parser.get("master")
val sourcePath = parser.get("sourcePath")
val targetPath = parser.get("targetPath")
val spark: SparkSession = SparkSession.builder().config(conf)
.appName(ExportActionSetJobNode.getClass.getSimpleName)
.master(master)
.getOrCreate()
implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val tEncoder:Encoder[(String,String)] = Encoders.tuple(Encoders.STRING,Encoders.STRING)
spark.read.load(sourcePath).as[Oaf]
.map(o =>DataciteToOAFTransformation.toActionSet(o))
.filter(o => o!= null)
.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
}
}

21
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json

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[
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the source mdstore path",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "targetPath",
"paramDescription": "the target mdstore path",
"paramRequired": true
},
{
"paramName": "m",
"paramLongName": "master",
"paramDescription": "the master name",
"paramRequired": true
}
]

23
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/config-default.xml

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<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

46
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/workflow.xml

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<workflow-app name="Datacite_to_ActionSet_Workflow" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the working path of Datacite stores</description>
</property>
<property>
<name>outputPath</name>
<description>the path of Datacite ActionSet</description>
</property>
</parameters>
<start to="ExportDataset"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ExportDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExportDataset</name>
<class>eu.dnetlib.dhp.actionmanager.datacite.ExportActionSetJobNode</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${outputPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>
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