[scala-refactor] Module dhp-aggregation:
Moved all scala source into src/main/scala and src/test/scalapull/169/head
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package eu.dnetlib.dhp.actionmanager.scholix
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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
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import org.apache.spark.sql._
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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.mode(SaveMode.Overwrite).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"$workingDirFolder/actionSetOaf")
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log.info("saving entities")
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val entities: Dataset[(String, Result)] = spark.read.load(s"$sourcePath/entities/*").as[Result].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING, resultEncoders))
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entities
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.joinWith(idRelation, entities("_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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@ -1,86 +0,0 @@
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package eu.dnetlib.dhp.actionmanager.scholix
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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, Dataset => OafDataset,Publication, Software, OtherResearchProduct, Relation}
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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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@ -1,8 +1,8 @@
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package eu.dnetlib.dhp.datacite
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue}
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
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import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue}
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import java.io.InputStream
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import java.time.format.DateTimeFormatter
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@ -1,9 +1,8 @@
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package eu.dnetlib.dhp.sx.bio.ebi
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
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import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
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import eu.dnetlib.dhp.sx.bio.pubmed.PMJournal
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import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
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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
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