diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala index 3980217d8..60ad790a7 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala @@ -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]) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala new file mode 100644 index 000000000..79c246d17 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -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") + + + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index b515a7330..690d937bc 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -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 $family") if (StringUtils.isNotBlank(orcid)) a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala index e83236d53..c8c725e07 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala @@ -38,7 +38,9 @@ case class MagPaperAuthorDenormalized(PaperId: Long, author: MagAuthor, affiliat case class MagPaperUrl(PaperId: Long, SourceType: Option[Int], SourceUrl: Option[String], LanguageCode: Option[String]) {} -case class MagUrl(PaperId: Long, instances: List[String]) +case class MagUrlInstance(SourceUrl:String){} + +case class MagUrl(PaperId: Long, instances: List[MagUrlInstance]) case class MagSubject(FieldOfStudyId:Long, DisplayName:String, MainType:Option[String], Score:Float){} @@ -47,6 +49,8 @@ case class MagFieldOfStudy(PaperId:Long, subjects:List[MagSubject]) {} case class MagJournal(JournalId: Long, Rank: Option[Int], NormalizedName: Option[String], DisplayName: Option[String], Issn: Option[String], Publisher: Option[String], Webpage: Option[String], PaperCount: Option[Long], CitationCount: Option[Long], CreatedDate: Option[java.sql.Timestamp]) {} +case class MagConferenceInstance(ci:Long, DisplayName:Option[String], Location:Option[String], StartDate:Option[java.sql.Timestamp], EndDate:Option[java.sql.Timestamp], PaperId:Long){} + case object ConversionUtil { def extractMagIdentifier(pids:mutable.Buffer[String]) :String ={ @@ -70,7 +74,7 @@ case object ConversionUtil { if (urls!= null) { - val l:List[String] = urls.instances.filter(k=>k.nonEmpty):::List(s"https://academic.microsoft.com/#/detail/${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/${extractMagIdentifier(pub.getOriginalId.asScala)}") i.setUrl(l.asJava) } @@ -133,7 +137,7 @@ case object ConversionUtil { j.setSp(paper.FirstPage) j.setEp(paper.LastPage) if (journal.Publisher.isDefined) - j.setEdition(journal.Publisher.get) + pub.setPublisher(asField(journal.Publisher.get)) if (journal.Issn.isDefined) j.setIssnPrinted(journal.Issn.get) pub.setJournal(j) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala index 0001c83c6..087669c27 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala @@ -1,7 +1,7 @@ package eu.dnetlib.doiboost.mag import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.{Publication, StructuredProperty} +import eu.dnetlib.dhp.schema.oaf.{Journal, Publication, StructuredProperty} import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.DoiBoostMappingUtil.{asField, createSP} import org.apache.commons.io.IOUtils @@ -10,6 +10,7 @@ import org.apache.spark.rdd.RDD import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} import org.apache.spark.sql.functions._ + import scala.collection.JavaConverters._ object SparkPreProcessMAG { @@ -51,7 +52,6 @@ object SparkPreProcessMAG { }.map(_._2) - val distinctPaper: Dataset[MagPapers] = spark.createDataset(result) distinctPaper.write.mode(SaveMode.Overwrite).save(s"${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") } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala new file mode 100644 index 000000000..e0b6390e4 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala @@ -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 $family") + if (StringUtils.isNotBlank(orcid)) + a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava) + + a + } + + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala new file mode 100644 index 000000000..3ccc9a68a --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala @@ -0,0 +1,41 @@ +package eu.dnetlib.doiboost.orcid + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.Publication +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +object SparkConvertORCIDToOAF { + + + + def main(args: Array[String]): Unit = { + + val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication]) + + val sourcePath = parser.get("sourcePath") + val targetPath = parser.get("targetPath") + val inputRDD:RDD[String] = spark.sparkContext.textFile(s"$sourcePath") + + println(s"SourcePath is $sourcePath, targetPath is $targetPath master is ${parser.get("master")} ") + + logger.info("Converting ORCID to OAF") + val d:Dataset[Publication] = spark.createDataset(inputRDD.map(ORCIDToOAF.convertTOOAF).filter(p=>p!=null)).as[Publication] + d.write.mode(SaveMode.Overwrite).save(targetPath) + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala new file mode 100644 index 000000000..eeec1af35 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala @@ -0,0 +1,42 @@ +package eu.dnetlib.doiboost.uw + +import eu.dnetlib.dhp.application.ArgumentApplicationParser + +import eu.dnetlib.dhp.schema.oaf.Publication +import eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + + +object SparkMapUnpayWallToOAF { + + def main(args: Array[String]): Unit = { + + + val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkMapDumpIntoOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication]) + + + val sourcePath = parser.get("sourcePath") + val targetPath = parser.get("targetPath") + val inputRDD:RDD[String] = spark.sparkContext.textFile(s"$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) + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala new file mode 100644 index 000000000..7f3e575eb --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala @@ -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 + + } + + + + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml index 16dbfa538..782e0fed4 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml @@ -63,8 +63,8 @@ --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} - --sourcePath${workingPath}/index_dump - --targetPath${workingPath} + --sourcePath${workingPath}/crossref/index_dump + --targetPath${workingPath}/input/crossref --masteryarn-cluster diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json new file mode 100644 index 000000000..c6115ec83 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json @@ -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} +] diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml index 6b4cad2af..2277b79b0 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml @@ -22,7 +22,7 @@ - + diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml new file mode 100644 index 000000000..cf617a84c --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml @@ -0,0 +1,38 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml new file mode 100644 index 000000000..639fb4d98 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml @@ -0,0 +1,110 @@ + + + + crossrefPublicationPath + the Crossref Publication Path + + + crossrefDatasetPath + the Crossref Dataset Path + + + uwPublicationPath + the UnpayWall Publication Path + + + magPublicationPath + the MAG Publication Path + + + orcidPublicationPath + the ORCID Publication Path + + + workingDirPath + the Working Path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + yarn-cluster + cluster + Create DOIBoost Infospace + eu.dnetlib.doiboost.SparkGenerateDoiBoost + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --crossrefPublicationPath${crossrefPublicationPath} + --crossrefDatasetPath${crossrefDatasetPath} + --uwPublicationPath${uwPublicationPath} + --magPublicationPath${magPublicationPath} + --orcidPublicationPath${orcidPublicationPath} + --workingDirPath${workingDirPath} + --masteryarn-cluster + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/config-default.xml new file mode 100644 index 000000000..cf617a84c --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/config-default.xml @@ -0,0 +1,38 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/workflow.xml new file mode 100644 index 000000000..bffde793b --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/workflow.xml @@ -0,0 +1,55 @@ + + + + sourcePath + the working dir base path + + + targetPath + the working dir base path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn-cluster + cluster + Convert ORCID to Dataset + eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --sourcePath${sourcePath} + --targetPath${targetPath} + --masteryarn-cluster + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml new file mode 100644 index 000000000..cf617a84c --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml @@ -0,0 +1,38 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml new file mode 100644 index 000000000..4dc2fd20b --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml @@ -0,0 +1,55 @@ + + + + sourcePath + the working dir base path + + + targetPath + the working dir base path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn-cluster + cluster + Convert UnpayWall to Dataset + eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --sourcePath${sourcePath}/json.gz + --targetPath${targetPath} + --masteryarn-cluster + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala similarity index 95% rename from dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/CrossrefMappingTest.scala rename to dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala index 0f9a3f8fb..5d4587a1c 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala @@ -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 = { diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala new file mode 100644 index 000000000..538f7e855 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala @@ -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)) + } + + + + + + + + +} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala new file mode 100644 index 000000000..8a6dd279b --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala @@ -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))) + + + + + + + + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/article.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article.json similarity index 100% rename from dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/article.json rename to dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article.json diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/article_funder_template.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_funder_template.json similarity index 100% rename from dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/article_funder_template.json rename to dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_funder_template.json diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/awardTest.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/awardTest.json similarity index 100% rename from dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/awardTest.json rename to dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/awardTest.json diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/book.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/book.json similarity index 100% rename from dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/book.json rename to dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/book.json diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/dataset.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/dataset.json similarity index 100% rename from dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/dataset.json rename to dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/dataset.json diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/funder_doi b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/funder_doi similarity index 100% rename from dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/funder_doi rename to dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/funder_doi diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/funder_name b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/funder_name similarity index 100% rename from dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/funder_name rename to dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/funder_name diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/preprint.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/preprint.json similarity index 100% rename from dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/preprint.json rename to dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/preprint.json diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/prwTest.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/prwTest.json new file mode 100644 index 000000000..756ee6dda --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/prwTest.json @@ -0,0 +1,1029 @@ +{ + "indexed": { + "date-parts": [ + [ + 2020, + 5, + 5 + ] + ], + "date-time": "2020-05-05T11:24:12Z", + "timestamp": 1588677852676 + }, + "reference-count": 59, + "publisher": "eLife Sciences Publications, Ltd", + "license": [ + { + "URL": "http:\/\/creativecommons.org\/licenses\/by\/3.0\/", + "start": { + "date-parts": [ + [ + 2014, + 3, + 18 + ] + ], + "date-time": "2014-03-18T00:00:00Z", + "timestamp": 1395100800000 + }, + "delay-in-days": 0, + "content-version": "vor" + }, + { + "URL": "http:\/\/creativecommons.org\/licenses\/by\/3.0\/", + "start": { + "date-parts": [ + [ + 2014, + 3, + 18 + ] + ], + "date-time": "2014-03-18T00:00:00Z", + "timestamp": 1395100800000 + }, + "delay-in-days": 0, + "content-version": "am" + }, + { + "URL": "http:\/\/creativecommons.org\/licenses\/by\/3.0\/", + "start": { + "date-parts": [ + [ + 2014, + 3, + 18 + ] + ], + "date-time": "2014-03-18T00:00:00Z", + "timestamp": 1395100800000 + }, + "delay-in-days": 0, + "content-version": "tdm" + }, + { + "URL": "http:\/\/creativecommons.org\/licenses\/by\/3.0\/", + "start": { + "date-parts": [ + [ + 2014, + 3, + 18 + ] + ], + "date-time": "2014-03-18T00:00:00Z", + "timestamp": 1395100800000 + }, + "delay-in-days": 0, + "content-version": "vor" + }, + { + "URL": "http:\/\/creativecommons.org\/licenses\/by\/3.0\/", + "start": { + "date-parts": [ + [ + 2014, + 3, + 18 + ] + ], + "date-time": "2014-03-18T00:00:00Z", + "timestamp": 1395100800000 + }, + "delay-in-days": 0, + "content-version": "am" + }, + { + "URL": "http:\/\/creativecommons.org\/licenses\/by\/3.0\/", + "start": { + "date-parts": [ + [ + 2014, + 3, + 18 + ] + ], + "date-time": "2014-03-18T00:00:00Z", + "timestamp": 1395100800000 + }, + "delay-in-days": 0, + "content-version": "tdm" + } + ], + "funder": [ + { + "DOI": "10.13039\/100000002", + "name": "National Institutes of Health", + "doi-asserted-by": "crossref", + "award": [ + "GM56169", + "AG39420", + "T32 GM007276" + ] + }, + { + "DOI": "10.13039\/100000968", + "name": "American Heart Association", + "doi-asserted-by": "crossref", + "award": [ + "Postdoctoral Fellowship" + ] + }, + { + "DOI": "10.13039\/501100000024", + "name": "Canadian Institutes of Health Research", + "doi-asserted-by": "crossref", + "award": [ + "Postdoctoral Fellowship" + ] + }, + { + "DOI": "10.13039\/100000002", + "name": "National Institutes of Health", + "doi-asserted-by": "publisher", + "award": [ + "GM56169", + "AG39420", + "T32 GM007276" + ] + }, + { + "DOI": "10.13039\/100000968", + "name": "American Heart Association", + "doi-asserted-by": "publisher", + "award": [ + "Postdoctoral Fellowship" + ] + }, + { + "DOI": "10.13039\/501100000024", + "name": "Canadian Institutes of Health Research", + "doi-asserted-by": "publisher", + "award": [ + "Postdoctoral Fellowship" + ] + } + ], + "content-domain": { + "domain": [ + "www.elifesciences.org" + ], + "crossmark-restriction": false + }, + "short-container-title": [], + "abstract": "Glycogen synthase kinase-3 (GSK-3) is a key regulator of many cellular signaling pathways. Unlike most kinases, GSK-3 is controlled by inhibition rather than by specific activation. In the insulin and several other signaling pathways, phosphorylation of a serine present in a conserved sequence near the amino terminus of GSK-3 generates an auto-inhibitory peptide. In contrast, Wnt\/\u03b2-catenin signal transduction requires phosphorylation of Ser\/Pro rich sequences present in the Wnt co-receptors LRP5\/6, and these motifs inhibit GSK-3 activity. We present crystal structures of GSK-3 bound to its phosphorylated N-terminus and to two of the phosphorylated LRP6 motifs. A conserved loop unique to GSK-3 undergoes a dramatic conformational change that clamps the bound pseudo-substrate peptides, and reveals the mechanism of primed substrate recognition. The structures rationalize target sequence preferences and suggest avenues for the design of inhibitors selective for a subset of pathways regulated by GSK-3.<\/jats:p>", + "DOI": "10.7554\/elife.01998", + "type": "journal-article", + "created": { + "date-parts": [ + [ + 2014, + 3, + 18 + ] + ], + "date-time": "2014-03-18T15:23:32Z", + "timestamp": 1395156212000 + }, + "source": "Crossref", + "is-referenced-by-count": 56, + "title": [ + "Structural basis of GSK-3 inhibition by N-terminal phosphorylation and by the Wnt receptor LRP6" + ], + "prefix": "10.7554", + "volume": "3", + "author": [ + { + "given": "Jennifer L", + "family": "Stamos", + "sequence": "first", + "affiliation": [ + { + "name": "Department of Structural Biology, Stanford University, Stanford, United States" + }, + { + "name": "Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States" + } + ] + }, + { + "given": "Matthew Ling-Hon", + "family": "Chu", + "sequence": "additional", + "affiliation": [ + { + "name": "Department of Structural Biology, Stanford University, Stanford, United States" + }, + { + "name": "Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States" + } + ] + }, + { + "given": "Michael D", + "family": "Enos", + "sequence": "additional", + "affiliation": [ + { + "name": "Department of Structural Biology, Stanford University, Stanford, United States" + }, + { + "name": "Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States" + } + ] + }, + { + "given": "Niket", + "family": "Shah", + "sequence": "additional", + "affiliation": [ + { + "name": "Department of Structural Biology, Stanford University, Stanford, United States" + }, + { + "name": "Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States" + } + ] + }, + { + "given": "William I", + "family": "Weis", + "sequence": "additional", + "affiliation": [ + { + "name": "Department of 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