code refactor renamed datacite package
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commit
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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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@ -1,46 +0,0 @@
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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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@ -1,12 +1,10 @@
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package eu.dnetlib.dhp.actionmanager.datacite
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package eu.dnetlib.dhp.datacite
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import org.apache.commons.io.IOUtils
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import org.apache.http.client.config.RequestConfig
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import org.apache.http.client.methods.{HttpGet, HttpPost, HttpRequestBase, HttpUriRequest}
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import org.apache.http.client.methods.{HttpGet, HttpPost, HttpUriRequest}
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import org.apache.http.entity.StringEntity
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import org.apache.http.impl.client.{HttpClientBuilder, HttpClients}
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import java.io.IOException
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import org.apache.http.impl.client.HttpClientBuilder
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abstract class AbstractRestClient extends Iterator[String] {
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@ -1,7 +1,7 @@
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package eu.dnetlib.dhp.actionmanager.datacite
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package eu.dnetlib.dhp.datacite
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import org.json4s.{DefaultFormats, JValue}
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import org.json4s.jackson.JsonMethods.{compact, parse, render}
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import org.json4s.{DefaultFormats, JValue}
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class DataciteAPIImporter(timestamp: Long = 0, blocks: Long = 10, until:Long = -1) extends AbstractRestClient {
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@ -1,4 +1,4 @@
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package eu.dnetlib.dhp.actionmanager.datacite
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package eu.dnetlib.dhp.datacite
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
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@ -1,8 +1,7 @@
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package eu.dnetlib.dhp.actionmanager.datacite
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package eu.dnetlib.dhp.datacite
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import com.fasterxml.jackson.databind.ObjectMapper
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import com.fasterxml.jackson.databind.SerializationFeature
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import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature}
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import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
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import eu.dnetlib.dhp.schema.oaf.Oaf
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import org.junit.jupiter.api.extension.ExtendWith
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