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completed mapping of UnpayWall and ORCID

This commit is contained in:
Sandro La Bruzzo 2020-05-22 15:15:09 +02:00
parent 5818abaab4
commit 9fbb221457
34 changed files with 2354 additions and 14 deletions
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24
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala
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@ -7,6 +7,7 @@ object DoiBoostMappingUtil {
//STATIC STRING
val MAG = "microsoft"
val MAG_NAME= "Microsoft Academic Graph"
val ORCID = "ORCID"
val CROSSREF = "Crossref"
val UNPAYWALL = "UnpayWall"
@ -56,11 +57,32 @@ object DoiBoostMappingUtil {
val cf = new KeyValue
cf.setValue(CROSSREF)
cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5("crossref"))
cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(CROSSREF.toLowerCase))
cf
}
def createUnpayWallCollectedFrom(): KeyValue = {
val cf = new KeyValue
cf.setValue(UNPAYWALL)
cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(UNPAYWALL.toLowerCase))
cf
}
def createORIDCollectedFrom(): KeyValue = {
val cf = new KeyValue
cf.setValue(ORCID)
cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(ORCID.toLowerCase))
cf
}
def generateIdentifier(oaf: Result, doi: String): String = {
val id = DHPUtils.md5(doi.toLowerCase)
if (oaf.isInstanceOf[Dataset])

63
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala Normal file
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@ -0,0 +1,63 @@
package eu.dnetlib.doiboost
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Publication, Dataset => OafDataset}
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkGenerateDoiBoost {
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val crossrefPublicationPath =parser.get("crossrefPublicationPath")
val crossrefDatasetPath =parser.get("crossrefDatasetPath")
val uwPublicationPath =parser.get("uwPublicationPath")
val magPublicationPath =parser.get("magPublicationPath")
val orcidPublicationPath =parser.get("orcidPublicationPath")
val workingDirPath =parser.get("workingDirPath")
logger.info("Phase 1) repartition and move all the dataset in a same working folder")
spark.read.load(crossrefPublicationPath).as(Encoders.bean(classOf[Publication])).map(s=>s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/crossrefPublication")
spark.read.load(crossrefDatasetPath).as(Encoders.bean(classOf[OafDataset])).map(s=>s)(Encoders.kryo[OafDataset]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/crossrefDataset")
spark.read.load(uwPublicationPath).as(Encoders.bean(classOf[Publication])).map(s=>s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/uwPublication")
spark.read.load(orcidPublicationPath).as(Encoders.bean(classOf[Publication])).map(s=>s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/orcidPublication")
spark.read.load(magPublicationPath).as(Encoders.bean(classOf[Publication])).map(s=>s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/magPublication")
implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPub)
logger.info("Phase 2) Join Crossref with UnpayWall")
val crossrefPublication:Dataset[(String,Publication)] = spark.read.load(s"$workingDirPath/crossrefPublication").as[Publication].map(p =>(p.getId, p) )
val uwPublication:Dataset[(String,Publication)] = spark.read.load(s"$workingDirPath/crossrefPublication").as[Publication].map(p =>(p.getId, p) )
crossrefPublication.joinWith(uwPublication, crossrefPublication("_1").equalTo(uwPublication("_1")),"left").map(item => {
val crossrefPub = item._1._2
val unpayWallPub = item._1._2
if(unpayWallPub!= null) {
crossrefPub.mergeFrom(unpayWallPub)
}
crossrefPub
}).write.save(s"$workingDirPath/firstJoin")
}
}

9
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
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@ -165,6 +165,13 @@ case object Crossref2Oaf {
if (l.nonEmpty)
instance.setLicense(l.head)
val has_review = (json \ "relation" \"has-review" \ "id")
if(has_review != JNothing)
instance.setRefereed(asField("peerReviewed"))
instance.setAccessright(createQualifier("Restricted", "dnet:access_modes"))
result.setInstance(List(instance).asJava)
@ -186,7 +193,7 @@ case object Crossref2Oaf {
val a = new Author
a.setName(given)
a.setSurname(family)
a.setFullname(s"${given} ${family}")
a.setFullname(s"$given $family")
if (StringUtils.isNotBlank(orcid))
a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava)

10
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala
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@ -38,7 +38,9 @@ case class MagPaperAuthorDenormalized(PaperId: Long, author: MagAuthor, affiliat
case class MagPaperUrl(PaperId: Long, SourceType: Option[Int], SourceUrl: Option[String], LanguageCode: Option[String]) {}
case class MagUrl(PaperId: Long, instances: List[String])
case class MagUrlInstance(SourceUrl:String){}
case class MagUrl(PaperId: Long, instances: List[MagUrlInstance])
case class MagSubject(FieldOfStudyId:Long, DisplayName:String, MainType:Option[String], Score:Float){}
@ -47,6 +49,8 @@ case class MagFieldOfStudy(PaperId:Long, subjects:List[MagSubject]) {}
case class MagJournal(JournalId: Long, Rank: Option[Int], NormalizedName: Option[String], DisplayName: Option[String], Issn: Option[String], Publisher: Option[String], Webpage: Option[String], PaperCount: Option[Long], CitationCount: Option[Long], CreatedDate: Option[java.sql.Timestamp]) {}
case class MagConferenceInstance(ci:Long, DisplayName:Option[String], Location:Option[String], StartDate:Option[java.sql.Timestamp], EndDate:Option[java.sql.Timestamp], PaperId:Long){}
case object ConversionUtil {
def extractMagIdentifier(pids:mutable.Buffer[String]) :String ={
@ -70,7 +74,7 @@ case object ConversionUtil {
if (urls!= null) {
val l:List[String] = urls.instances.filter(k=>k.nonEmpty):::List(s"https://academic.microsoft.com/#/detail/${extractMagIdentifier(pub.getOriginalId.asScala)}")
val l:List[String] = urls.instances.filter(k=>k.SourceUrl.nonEmpty).map(k=>k.SourceUrl):::List(s"https://academic.microsoft.com/#/detail/${extractMagIdentifier(pub.getOriginalId.asScala)}")
i.setUrl(l.asJava)
}
@ -133,7 +137,7 @@ case object ConversionUtil {
j.setSp(paper.FirstPage)
j.setEp(paper.LastPage)
if (journal.Publisher.isDefined)
j.setEdition(journal.Publisher.get)
pub.setPublisher(asField(journal.Publisher.get))
if (journal.Issn.isDefined)
j.setIssnPrinted(journal.Issn.get)
pub.setJournal(j)

36
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala
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@ -1,7 +1,7 @@
package eu.dnetlib.doiboost.mag
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Publication, StructuredProperty}
import eu.dnetlib.dhp.schema.oaf.{Journal, Publication, StructuredProperty}
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{asField, createSP}
import org.apache.commons.io.IOUtils
@ -10,6 +10,7 @@ import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import org.apache.spark.sql.functions._
import scala.collection.JavaConverters._
object SparkPreProcessMAG {
@ -51,7 +52,6 @@ object SparkPreProcessMAG {
}.map(_._2)
val distinctPaper: Dataset[MagPapers] = spark.createDataset(result)
distinctPaper.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/Papers_distinct")
logger.info(s"Total number of element: ${result.count()}")
@ -90,6 +90,36 @@ object SparkPreProcessMAG {
var magPubs: Dataset[(String, Publication)] = spark.read.load(s"${parser.get("targetPath")}/merge_step_2").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
val conference = spark.read.load(s"$sourcePath/ConferenceInstances").select($"ConferenceInstanceId".as("ci"), $"DisplayName", $"Location", $"StartDate",$"EndDate" )
val conferenceInstance = conference.joinWith(papers, papers("ConferenceInstanceId").equalTo(conference("ci"))).select($"_1.ci", $"_1.DisplayName", $"_1.Location", $"_1.StartDate",$"_1.EndDate", $"_2.PaperId").as[MagConferenceInstance]
magPubs.joinWith(conferenceInstance, col("_1").equalTo(conferenceInstance("PaperId")), "left")
.map(p => {
val publication:Publication= p._1._2
val ci:MagConferenceInstance = p._2
if (ci!= null){
val j:Journal = new Journal
if (ci.Location.isDefined)
j.setConferenceplace(ci.Location.get)
j.setName(ci.DisplayName.get)
if (ci.StartDate.isDefined && ci.EndDate.isDefined)
{
j.setConferencedate(s"${ci.StartDate.get.toString} - ${ci.EndDate.get.toString}")
}
publication.setJournal(j)
}
publication
}).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_2_conference")
magPubs= spark.read.load(s"${parser.get("targetPath")}/merge_step_2_conference").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
val paperUrlDataset = spark.read.load(s"$sourcePath/PaperUrls").as[MagPaperUrl].groupBy("PaperId").agg(collect_list(struct("sourceUrl")).as("instances")).as[MagUrl]
@ -159,6 +189,6 @@ object SparkPreProcessMAG {
publication.setSubject(p.asJava)
}
publication
}).map{s:Publication => s}(Encoders.bean(classOf[Publication])).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/mag_publication")
}).map { s: Publication => s }(Encoders.bean(classOf[Publication])).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/mag_publication")
}
}

104
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala Normal file
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@ -0,0 +1,104 @@
package eu.dnetlib.doiboost.orcid
import java.io.IOException
import eu.dnetlib.dhp.schema.oaf.{Author, Publication}
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier}
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
import org.apache.commons.lang.StringUtils
import org.codehaus.jackson.map.ObjectMapper
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
case class ORCIDItem(oid:String,name:String,surname:String,creditName:String,errorCode:String){}
object ORCIDToOAF {
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
val mapper = new ObjectMapper
def isJsonValid(inputStr: String): Boolean = {
import java.io.IOException
try {
mapper.readTree(inputStr)
true
} catch {
case e: IOException =>
false
}
}
def extractValueFromInputString(input: String): (String, String) = {
val i = input.indexOf('[')
if (i <5) {
return null
}
val orcidList = input.substring(i, input.length - 1)
val doi = input.substring(1, i - 1)
if (isJsonValid(orcidList)) {
(doi, orcidList)
} else null
}
def convertTOOAF(input:String) :Publication = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
val item:(String, String) = extractValueFromInputString(input)
if (item== null) {
return null
}
val json_str = item._2
lazy val json: json4s.JValue = parse(json_str)
val doi = item._1
val pub:Publication = new Publication
pub.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
pub.setDataInfo(generateDataInfo())
pub.setId(generateIdentifier(pub, doi.toLowerCase))
try{
val authorList:List[ORCIDItem] = json.extract[List[ORCIDItem]]
pub.setAuthor(authorList.map(a=> {
generateAuhtor(a.name, a.surname, a.creditName, a.oid)
}).asJava)
pub.setCollectedfrom(List(DoiBoostMappingUtil.createORIDCollectedFrom()).asJava)
pub
} catch {
case e: Throwable =>
logger.info(s"ERROR ON GENERATE Publication from $input")
null
}
}
def generateAuhtor(given: String, family: String, fullName:String, orcid: String): Author = {
val a = new Author
a.setName(given)
a.setSurname(family)
if (fullName!= null && fullName.nonEmpty)
a.setFullname(fullName)
else
a.setFullname(s"$given $family")
if (StringUtils.isNotBlank(orcid))
a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava)
a
}
}

41
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala Normal file
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@ -0,0 +1,41 @@
package eu.dnetlib.doiboost.orcid
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Publication
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkConvertORCIDToOAF {
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication])
val sourcePath = parser.get("sourcePath")
val targetPath = parser.get("targetPath")
val inputRDD:RDD[String] = spark.sparkContext.textFile(s"$sourcePath")
println(s"SourcePath is $sourcePath, targetPath is $targetPath master is ${parser.get("master")} ")
logger.info("Converting ORCID to OAF")
val d:Dataset[Publication] = spark.createDataset(inputRDD.map(ORCIDToOAF.convertTOOAF).filter(p=>p!=null)).as[Publication]
d.write.mode(SaveMode.Overwrite).save(targetPath)
}
}

42
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala Normal file
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@ -0,0 +1,42 @@
package eu.dnetlib.doiboost.uw
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkMapUnpayWallToOAF {
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkMapDumpIntoOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication])
val sourcePath = parser.get("sourcePath")
val targetPath = parser.get("targetPath")
val inputRDD:RDD[String] = spark.sparkContext.textFile(s"$sourcePath")
logger.info("Converting UnpayWall to OAF")
val d:Dataset[Publication] = spark.createDataset(inputRDD.repartition(1000).map(UnpayWallToOAF.convertToOAF).filter(p=>p!=null)).as[Publication]
d.write.mode(SaveMode.Overwrite).save(targetPath)
}
}

63
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala Normal file
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@ -0,0 +1,63 @@
package eu.dnetlib.doiboost.uw
import eu.dnetlib.dhp.schema.oaf.{Instance, Publication}
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
case class OALocation(evidence:Option[String], host_type:Option[String], is_best:Option[Boolean], license: Option[String], pmh_id:Option[String], updated:Option[String],
url:Option[String], url_for_landing_page:Option[String], url_for_pdf:Option[String], version:Option[String]) {}
object UnpayWallToOAF {
val logger: Logger = LoggerFactory.getLogger(getClass)
def convertToOAF(input:String):Publication = {
val pub = new Publication
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
val doi = (json \"doi").extract[String]
val is_oa = (json\ "is_oa").extract[Boolean]
val oaLocation:OALocation = (json \ "best_oa_location").extractOrElse[OALocation](null)
pub.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
pub.setId(generateIdentifier(pub, doi.toLowerCase))
pub.setCollectedfrom(List(createUnpayWallCollectedFrom()).asJava)
pub.setDataInfo(generateDataInfo())
if (!is_oa)
return null
if(oaLocation== null || oaLocation.url.isEmpty)
return null
val i :Instance= new Instance()
i.setCollectedfrom(createUnpayWallCollectedFrom())
i.setAccessright(createQualifier("Open", "dnet:access_modes"))
i.setUrl(List(oaLocation.url.get).asJava)
if (oaLocation.license.isDefined)
i.setLicense(asField(oaLocation.license.get))
pub.setInstance(List(i).asJava)
pub
}
}

4
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml
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@ -63,8 +63,8 @@
--driver-memory=${sparkDriverMemory}
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingPath}/index_dump</arg>
<arg>--targetPath</arg><arg>${workingPath}</arg>
<arg>--sourcePath</arg><arg>${workingPath}/crossref/index_dump</arg>
<arg>--targetPath</arg><arg>${workingPath}/input/crossref</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>

9
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json Normal file
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@ -0,0 +1,9 @@
[
{"paramName": "m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true},
{"paramName": "cp", "paramLongName":"crossrefPublicationPath", "paramDescription": "the Crossref Publication Path", "paramRequired": true},
{"paramName": "cd", "paramLongName":"crossrefDatasetPath", "paramDescription": "the Crossref Dataset Path", "paramRequired": true},
{"paramName": "up", "paramLongName":"uwPublicationPath", "paramDescription": "the UnpayWall Publication Path", "paramRequired": true},
{"paramName": "mp", "paramLongName":"magPublicationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true},
{"paramName": "op", "paramLongName":"orcidPublicationPath", "paramDescription": "the ORCID Publication Path", "paramRequired": true},
{"paramName": "w", "paramLongName":"workingDirPath", "paramDescription": "the Working Path", "paramRequired": true}
]

2
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml
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@ -22,7 +22,7 @@
</property>
</parameters>
<start to="PreprocessMag"/>
<start to="ResetWorkingPath"/>
<kill name="Kill">

38
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml Normal file
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@ -0,0 +1,38 @@
<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>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
</property>
</configuration>

110
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml Normal file
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@ -0,0 +1,110 @@
<workflow-app name="import MAG into HDFS" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>crossrefPublicationPath</name>
<description>the Crossref Publication Path</description>
</property>
<property>
<name>crossrefDatasetPath</name>
<description>the Crossref Dataset Path</description>
</property>
<property>
<name>uwPublicationPath</name>
<description>the UnpayWall Publication Path</description>
</property>
<property>
<name>magPublicationPath</name>
<description>the MAG Publication Path</description>
</property>
<property>
<name>orcidPublicationPath</name>
<description>the ORCID Publication Path</description>
</property>
<property>
<name>workingDirPath</name>
<description>the Working Path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${workingDirPath}'/>
<mkdir path='${workingDirPath}'/>
</fs>
<ok to="CreateDOIBoost"/>
<error to="Kill"/>
</action>
<action name="CreateDOIBoost">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create DOIBoost Infospace</name>
<class>eu.dnetlib.doiboost.SparkGenerateDoiBoost</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--crossrefPublicationPath</arg><arg>${crossrefPublicationPath}</arg>
<arg>--crossrefDatasetPath</arg><arg>${crossrefDatasetPath}</arg>
<arg>--uwPublicationPath</arg><arg>${uwPublicationPath}</arg>
<arg>--magPublicationPath</arg><arg>${magPublicationPath}</arg>
<arg>--orcidPublicationPath</arg><arg>${orcidPublicationPath}</arg>
<arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<!-- <action name="PreprocessMag">-->
<!-- <spark xmlns="uri:oozie:spark-action:0.2">-->
<!-- <master>yarn-cluster</master>-->
<!-- <mode>cluster</mode>-->
<!-- <name>Convert Mag to Dataset</name>-->
<!-- <class>eu.dnetlib.doiboost.mag.SparkPreProcessMAG</class>-->
<!-- <jar>dhp-doiboost-${projectVersion}.jar</jar>-->
<!-- <spark-opts>-->
<!-- &#45;&#45;executor-memory=${sparkExecutorMemory}-->
<!-- &#45;&#45;executor-cores=${sparkExecutorCores}-->
<!-- &#45;&#45;driver-memory=${sparkDriverMemory}-->
<!-- &#45;&#45;conf spark.sql.shuffle.partitions=3840-->
<!-- ${sparkExtraOPT}-->
<!-- </spark-opts>-->
<!-- <arg>&#45;&#45;sourcePath</arg><arg>${sourcePath}</arg>-->
<!-- <arg>&#45;&#45;targetPath</arg><arg>${targetPath}</arg>-->
<!-- <arg>&#45;&#45;master</arg><arg>yarn-cluster</arg>-->
<!-- </spark>-->
<!-- <ok to="End"/>-->
<!-- <error to="Kill"/>-->
<!-- </action>-->
<end name="End"/>
</workflow-app>

38
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/config-default.xml Normal file
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@ -0,0 +1,38 @@
<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>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
</property>
</configuration>

55
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/workflow.xml Normal file
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@ -0,0 +1,55 @@
<workflow-app name="import ORCID into HDFS" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the working dir base path</description>
</property>
<property>
<name>targetPath</name>
<description>the working dir base path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
</parameters>
<start to="PreprocessORCID"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="PreprocessORCID">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert ORCID to Dataset</name>
<class>eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

38
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml Normal file
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@ -0,0 +1,38 @@
<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>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
</property>
</configuration>

55
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml Normal file
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@ -0,0 +1,55 @@
<workflow-app name="import UnpayWall into HDFS" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the working dir base path</description>
</property>
<property>
<name>targetPath</name>
<description>the working dir base path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
</parameters>
<start to="PreprocessUW"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="PreprocessUW">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert UnpayWall to Dataset</name>
<class>eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/json.gz</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

28
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/CrossrefMappingTest.scala → dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala
View File

@ -1,9 +1,8 @@
package eu.dnetlib.doiboost
package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.schema.oaf._
import eu.dnetlib.dhp.utils.DHPUtils
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
import org.codehaus.jackson.map.ObjectMapper
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test
import org.slf4j.{Logger, LoggerFactory}
@ -56,6 +55,29 @@ class CrossrefMappingTest {
})
}
@Test
def testPeerReviewed(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("prwTest.json")).mkString
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val items = resultList.filter(p => p.isInstanceOf[Result])
items.foreach(p => logger.info(mapper.writeValueAsString(p)))
}
def extractECAward(award: String): String = {

52
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala Normal file
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@ -0,0 +1,52 @@
package eu.dnetlib.doiboost.orcid
import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Test
import org.slf4j.{Logger, LoggerFactory}
import org.junit.jupiter.api.Assertions._
import scala.io.Source
class MappingORCIDToOAFTest {
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
val mapper = new ObjectMapper()
@Test
def testExtractData():Unit ={
val json = Source.fromInputStream(getClass.getResourceAsStream("dataOutput")).mkString
assertNotNull(json)
assertFalse(json.isEmpty)
json.lines.foreach(s => {
assertNotNull(ORCIDToOAF.extractValueFromInputString(s))
})
}
@Test
def testConvertOrcidToOAF():Unit ={
val json = Source.fromInputStream(getClass.getResourceAsStream("dataOutput")).mkString
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
assertNotNull(json)
assertFalse(json.isEmpty)
// json.lines.foreach(s => {
//
// })
val p :Publication = ORCIDToOAF.convertTOOAF(json.lines.next())
logger.info(mapper.writeValueAsString(p))
}
}

49
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala Normal file
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@ -0,0 +1,49 @@
package eu.dnetlib.doiboost.uw
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Test
import scala.io.Source
import org.junit.jupiter.api.Assertions._
import org.slf4j.{Logger, LoggerFactory}
class UnpayWallMappingTest {
val logger: Logger = LoggerFactory.getLogger(getClass)
val mapper = new ObjectMapper()
@Test
def testMappingToOAF():Unit ={
val Ilist = Source.fromInputStream(getClass.getResourceAsStream("input.json")).mkString
for (line <-Ilist.lines) {
val p = UnpayWallToOAF.convertToOAF(line)
if(p!= null) {
assertTrue(p.getPid.size()==1)
logger.info(p.getId)
}
assertNotNull(line)
assertTrue(line.nonEmpty)
}
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
val l = Ilist.lines.next()
logger.info(mapper.writeValueAsString(UnpayWallToOAF.convertToOAF(l)))
}
}

0
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/article.json → dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article.json
View File

0
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/article_funder_template.json → dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_funder_template.json
View File

0
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/awardTest.json → dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/awardTest.json
View File

0
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/book.json → dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/book.json
View File

0
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/dataset.json → dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/dataset.json
View File

0
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/funder_doi → dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/funder_doi
View File

0
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/funder_name → dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/funder_name
View File

0
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/preprint.json → dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/preprint.json
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1029
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/prwTest.json Normal file
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File diff suppressed because it is too large Load Diff

0
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/response.json → dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/response.json
View File

0
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/s.json → dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/s.json
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309
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/dataOutput Normal file
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@ -0,0 +1,309 @@
(10.1109/JPHOT.2018.2880319,[{"oid":"0000-0002-1473-2224","name":"zhong","surname":"chen","creditName":null,"errorCode":null},{"oid":"0000-0002-5739-2127","name":"Yue","surname":"Lin","creditName":null,"errorCode":null}])
(10.1073/pnas.1816459115,[{"oid":"0000-0001-6260-4326","name":"Igor","surname":"Sokolov","creditName":null,"errorCode":null},{"oid":"0000-0001-6260-4326","name":"Igor","surname":"Sokolov","creditName":null,"errorCode":null}])
(10.1016/j.mjafi.2016.05.007,[{"oid":"0000-0002-4342-6656","name":"Anoop","surname":"Sharma","creditName":null,"errorCode":null}])
(10.1152/japplphysiol.00476.2016,[{"oid":"0000-0001-9039-0302","name":"Graeme","surname":"Zosky","creditName":"Graeme R. Zosky","errorCode":null},{"oid":"0000-0001-8355-7362","name":"Stephen","surname":"Dubsky","creditName":"Stephen Eric Dubsky","errorCode":null}])
(10.1111/j.1365-2621.1995.tb09798.x,[{"oid":"0000-0001-6457-4044","name":"jose martin","surname":"yañez limon","creditName":null,"errorCode":null},{"oid":"0000-0002-7108-8447","name":"Orlando","surname":"Zelaya-Angel","creditName":null,"errorCode":null},{"oid":"0000-0002-9267-4621","name":"Jean","surname":"Martinez","creditName":null,"errorCode":null},{"oid":"0000-0003-3060-2638","name":"Juan Jose","surname":"Alvarado-Gil","creditName":null,"errorCode":null}])
(10.1007/s10461-019-02391-1,[{"oid":"0000-0003-4375-7452","name":"Cathy","surname":"Reback","creditName":null,"errorCode":null}])
(10.1039/C4TA03030C,[{"oid":"0000-0003-1615-5034","name":"Jihong","surname":"Yu","creditName":null,"errorCode":null}])
(10.1016/0306-4522(89)90381-3,[{"oid":"0000-0002-7272-8370","name":"PAOLA","surname":"D'ASCANIO","creditName":null,"errorCode":null}])
(10.1016/S0921-4526(01)00945-0,[{"oid":"0000-0002-5360-1008","name":"Tomasz","surname":"Nowak","creditName":null,"errorCode":null},{"oid":"0000-0001-5554-8178","name":"Pawel","surname":"Olko","creditName":null,"errorCode":null},{"oid":"0000-0002-1993-9320","name":"Michael","surname":"Waligorski","creditName":null,"errorCode":null},{"oid":"0000-0002-1993-9320","name":"Michael","surname":"Waligorski","creditName":null,"errorCode":null}])
(10.1074/jbc.m312875200,[{"oid":"0000-0003-3631-2252","name":"Isabelle","surname":"Dugail","creditName":null,"errorCode":null},{"oid":"0000-0001-6577-9009","name":"Bruno","surname":"Feve","creditName":null,"errorCode":null},{"oid":"0000-0002-4502-3543","name":"Martine","surname":"GLORIAN","creditName":"GLORIAN","errorCode":null},{"oid":"0000-0002-1275-9861","name":"KHADIJA","surname":"EL HADRI","creditName":null,"errorCode":null}])
(10.1038/nrc3802,[{"oid":"0000-0001-7427-4651","name":"William","surname":"Foulkes","creditName":null,"errorCode":null},{"oid":"0000-0001-7427-4651","name":"William","surname":"Foulkes","creditName":null,"errorCode":null}])
(10.1186/s12974-018-1125-5,[{"oid":"0000-0001-5270-9888","name":"I-Chen","surname":"Yu","creditName":null,"errorCode":null}])
(10.4997/JRCPE.2016.310,[{"oid":"0000-0001-7658-1209","name":"David","surname":"Burn","creditName":null,"errorCode":null}])
(10.13140/RG.2.2.20772.48006,[{"oid":"0000-0003-2825-5884","name":"Abdelkader","surname":"Mezghani","creditName":null,"errorCode":null}])
(10.1039/c8ay00816g,[{"oid":"0000-0002-5444-7276","name":"Torbjörn","surname":"Pettersson","creditName":null,"errorCode":null}])
(10.2147/dhps.s6226,[{"oid":"0000-0001-8558-3396","name":"Mario Francisco","surname":"Juruena","creditName":"JURUENA OR JURUENA M OR JURUENA M F OR OR JURUENA MARIO OR JURUENA MARIO F OR JURUENA MARIO FRANCISCO OR JURUENA MF","errorCode":null}])
(10.1007/s00415-004-0351-1,[{"oid":"0000-0002-2737-3662","name":"Gian Domenico","surname":"Borasio","creditName":null,"errorCode":null}])
(10.1088/0967-3334/23/1/318,[{"oid":"0000-0002-3549-4309","name":"Gavin","surname":"Screaton","creditName":null,"errorCode":null},{"oid":"0000-0002-0124-5072","name":"Carlos-Augusto","surname":"Gonzalez-Correa","creditName":null,"errorCode":null}])
(10.1111/aogs.13316,[{"oid":"0000-0002-1241-9875","name":"Lena","surname":"Liljestrom","creditName":null,"errorCode":null}])
(10.1038/sj.thj.6200111,[{"oid":"0000-0001-6115-8790","name":"Felipe","surname":"Prosper","creditName":null,"errorCode":null},{"oid":"0000-0001-6115-8790","name":"Felipe","surname":"Prosper","creditName":null,"errorCode":null},{"oid":"0000-0002-9467-932X","name":"Maria J","surname":"Terol","creditName":null,"errorCode":null},{"oid":"0000-0001-9622-1649","name":"María del Mar","surname":"Tormo Díaz","creditName":"Mar Tormo","errorCode":null},{"oid":"0000-0002-7938-3950","name":"Jose A","surname":"Martinez-Climent","creditName":null,"errorCode":null}])
(10.1021/jo052299f,[{"oid":"0000-0002-2419-0705","name":"Per-Ola","surname":"Norrby","creditName":null,"errorCode":null},{"oid":"0000-0002-2548-7025","name":"Mogens","surname":"Johannsen","creditName":null,"errorCode":null},{"oid":"0000-0002-2548-7025","name":"Mogens","surname":"Johannsen","creditName":null,"errorCode":null}])
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