mergin with branch beta
This commit is contained in:
commit
cc0d3d8a7b
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@ -1,9 +1,10 @@
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package eu.dnetlib.dhp.actionmanager.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.entity.StringEntity
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import org.apache.http.impl.client.HttpClients
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import org.apache.http.impl.client.{HttpClientBuilder, HttpClients}
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import java.io.IOException
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@ -56,11 +57,15 @@ abstract class AbstractRestClient extends Iterator[String]{
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private def doHTTPRequest[A <: HttpUriRequest](r: A) :String ={
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val client = HttpClients.createDefault
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val timeout = 60; // seconds
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val config = RequestConfig.custom()
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.setConnectTimeout(timeout * 1000)
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.setConnectionRequestTimeout(timeout * 1000)
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.setSocketTimeout(timeout * 1000).build()
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val client =HttpClientBuilder.create().setDefaultRequestConfig(config).build()
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var tries = 4
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try {
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while (tries > 0) {
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println(s"requesting ${r.getURI}")
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val response = client.execute(r)
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println(s"get response with status${response.getStatusLine.getStatusCode}")
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@ -80,7 +85,5 @@ abstract class AbstractRestClient extends Iterator[String]{
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throw new RuntimeException("Unable to close client ", e)
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}
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}
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getBufferData()
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}
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@ -140,7 +140,7 @@ object ImportDatacite {
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private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs:Int): Long = {
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var from:Long = timestamp * 1000
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val delta:Long = 50000000L
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val delta:Long = 100000000L
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var client: DataciteAPIImporter = null
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val now :Long =System.currentTimeMillis()
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var i = 0
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@ -0,0 +1,90 @@
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package eu.dnetlib.dhp.sx.provision
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
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import org.apache.spark.{SparkConf, sql}
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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 SparkCreateActionset {
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def main(args: Array[String]): Unit = {
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val log: Logger = LoggerFactory.getLogger(getClass)
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/generate_actionset.json")).mkString)
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parser.parseArgument(args)
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val spark: SparkSession =
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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")).getOrCreate()
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val sourcePath = parser.get("sourcePath")
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log.info(s"sourcePath -> $sourcePath")
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val targetPath = parser.get("targetPath")
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log.info(s"targetPath -> $targetPath")
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val workingDirFolder = parser.get("workingDirFolder")
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log.info(s"workingDirFolder -> $workingDirFolder")
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implicit val oafEncoders:Encoder[Oaf] = Encoders.kryo[Oaf]
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implicit val resultEncoders:Encoder[Result] = Encoders.kryo[Result]
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implicit val relationEncoders:Encoder[Relation] = Encoders.kryo[Relation]
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import spark.implicits._
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val relation = spark.read.load(s"$sourcePath/relation").as[Relation]
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relation.filter(r => (r.getDataInfo== null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
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.flatMap(r => List(r.getSource,r.getTarget)).distinct().write.save(s"$workingDirFolder/id_relation")
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val idRelation = spark.read.load(s"$workingDirFolder/id_relation").as[String]
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log.info("extract source and target Identifier involved in relations")
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log.info("save relation filtered")
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relation.filter(r => (r.getDataInfo== null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
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.write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/actionSetOaf")
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log.info("saving publication")
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val publication:Dataset[(String, Result)] = spark.read.load(s"$sourcePath/publication").as[Result].map(p => (p.getId, p))
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publication
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.joinWith(idRelation, publication("_1").equalTo(idRelation("value")))
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.map(p => p._1._2)
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.write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
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log.info("saving dataset")
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val dataset:Dataset[(String, Result)] = spark.read.load(s"$sourcePath/dataset").as[Result].map(p => (p.getId, p))
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dataset
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.joinWith(idRelation, publication("_1").equalTo(idRelation("value")))
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.map(p => p._1._2)
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.write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
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log.info("saving software")
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val software:Dataset[(String, Result)] = spark.read.load(s"$sourcePath/software").as[Result].map(p => (p.getId, p))
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software
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.joinWith(idRelation, publication("_1").equalTo(idRelation("value")))
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.map(p => p._1._2)
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.write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
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log.info("saving Other Research product")
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val orp:Dataset[(String, Result)] = spark.read.load(s"$sourcePath/otherresearchproduct").as[Result].map(p => (p.getId, p))
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orp
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.joinWith(idRelation, publication("_1").equalTo(idRelation("value")))
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.map(p => p._1._2)
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.write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
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}
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}
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@ -0,0 +1,86 @@
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package eu.dnetlib.dhp.sx.provision
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.action.AtomicAction
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import eu.dnetlib.dhp.schema.oaf.{Oaf, OtherResearchProduct, Publication, Relation, Software, Dataset => OafDataset}
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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.{Encoder, Encoders, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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import scala.io.Source
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object SparkSaveActionSet {
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def toActionSet(item: Oaf): (String, String) = {
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val mapper = new ObjectMapper()
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item match {
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case dataset: OafDataset =>
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val a: AtomicAction[OafDataset] = new AtomicAction[OafDataset]
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a.setClazz(classOf[OafDataset])
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a.setPayload(dataset)
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(dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case publication: Publication =>
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val a: AtomicAction[Publication] = new AtomicAction[Publication]
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a.setClazz(classOf[Publication])
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a.setPayload(publication)
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(publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case software: Software =>
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val a: AtomicAction[Software] = new AtomicAction[Software]
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a.setClazz(classOf[Software])
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a.setPayload(software)
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(software.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case orp: OtherResearchProduct =>
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val a: AtomicAction[OtherResearchProduct] = new AtomicAction[OtherResearchProduct]
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a.setClazz(classOf[OtherResearchProduct])
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a.setPayload(orp)
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(orp.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case relation: Relation =>
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val a: AtomicAction[Relation] = new AtomicAction[Relation]
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a.setClazz(classOf[Relation])
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a.setPayload(relation)
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(relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case _ =>
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null
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}
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}
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def main(args: Array[String]): Unit = {
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val log: Logger = LoggerFactory.getLogger(getClass)
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/save_actionset.json")).mkString)
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parser.parseArgument(args)
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val spark: SparkSession =
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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")).getOrCreate()
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val sourcePath = parser.get("sourcePath")
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log.info(s"sourcePath -> $sourcePath")
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val targetPath = parser.get("targetPath")
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log.info(s"targetPath -> $targetPath")
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implicit val oafEncoders:Encoder[Oaf] = Encoders.kryo[Oaf]
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implicit val tEncoder:Encoder[(String,String)] = Encoders.tuple(Encoders.STRING,Encoders.STRING)
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spark.read.load(sourcePath).as[Oaf]
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.map(o =>toActionSet(o))
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.filter(o => o!= null)
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.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
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}
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}
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@ -0,0 +1,6 @@
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[
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{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
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{"paramName":"s", "paramLongName":"sourcePath","paramDescription": "source path", "paramRequired": true},
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{"paramName":"w", "paramLongName":"workingDirFolder","paramDescription": "the working Dir Folder", "paramRequired": true},
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{"paramName":"t", "paramLongName":"targetPath","paramDescription": "the target path ", "paramRequired": true}
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]
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@ -0,0 +1,23 @@
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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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@ -0,0 +1,76 @@
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<workflow-app name="Scholexplorer_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 path of the consistent graph</description>
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</property>
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<property>
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<name>workingDirFolder</name>
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<description>the path of working dir ActionSet</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 Scholexplorer 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[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="createActionSet">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Create Action Set</name>
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<class>eu.dnetlib.dhp.sx.provision.SparkCreateActionset</class>
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<jar>dhp-aggregation-${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>--workingDirFolder</arg><arg>${workingDirFolder}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<action name="SaveActionSet">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Save Action Set</name>
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<class>eu.dnetlib.dhp.sx.provision.SparkSaveActionSet</class>
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<jar>dhp-aggregation-${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>${workingDirFolder}/actionSetOaf</arg>
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<arg>--targetPath</arg><arg>${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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@ -0,0 +1,5 @@
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[
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{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
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{"paramName":"s", "paramLongName":"sourcePath","paramDescription": "source path", "paramRequired": true},
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{"paramName":"t", "paramLongName":"targetPath","paramDescription": "the target path ", "paramRequired": true}
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]
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