implemented branch workflow to import datacite and crossref in scholexplorer
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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.common.vocabulary.VocabularyGroup
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import eu.dnetlib.dhp.schema.mdstore.MetadataRecord
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
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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.{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 FilterCrossrefEntitiesSpark {
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val log: Logger = LoggerFactory.getLogger(getClass.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/filter_crossref_param.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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log.info("sourcePath: {}", sourcePath)
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val targetPath = parser.get("targetPath")
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log.info("targetPath: {}", targetPath)
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val spark: SparkSession = SparkSession.builder().config(conf)
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.appName(getClass.getSimpleName)
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.master(master)
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.getOrCreate()
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implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
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implicit val resEncoder: Encoder[Result] = Encoders.kryo[Result]
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val d:Dataset[Oaf]= spark.read.load(sourcePath).as[Oaf]
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d.filter(r => r.isInstanceOf[Result]).map(r => r.asInstanceOf[Result]).write.mode(SaveMode.Overwrite).save(targetPath)
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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="Generate_Datacite_and_Crossref_dump_for_Scholexplorer" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>datacitePath</name>
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<description>the path of Datacite spark dataset</description>
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</property>
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<property>
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<name>isLookupUrl</name>
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<description>The IS lookUp service endopoint</description>
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</property>
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<property>
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<name>crossrefPath</name>
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<description>the path of Crossref spark dataset</description>
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</property>
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<property>
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<name>targetPath</name>
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<description>the path of Crossref spark dataset</description>
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</property>
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</parameters>
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<start to="ImportDatacite"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ImportDatacite">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>ImportDatacite</name>
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<class>eu.dnetlib.dhp.actionmanager.datacite.GenerateDataciteDatasetSpark</class>
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<jar>dhp-aggregation-${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>${datacitePath}</arg>
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<arg>--targetPath</arg><arg>${targetPath}/datacite_oaf</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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<arg>--exportLinks</arg><arg>true</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="FilterCrossrefEntities"/>
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<error to="Kill"/>
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</action>
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<action name="FilterCrossrefEntities">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>FilterCrossrefEntities</name>
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<class>eu.dnetlib.dhp.actionmanager.datacite.FilterCrossrefEntitiesSpark</class>
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<jar>dhp-aggregation-${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>${crossrefPath}</arg>
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<arg>--targetPath</arg><arg>${targetPath}/crossref_oaf</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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</property>
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</parameters>
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<start to="CreateScholix"/>
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<start to="ExtractEntities"/>
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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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