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 d16a549d3..6f8398dba 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 @@ -1,10 +1,14 @@ package eu.dnetlib.doiboost -import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Publication, Qualifier, Result, StructuredProperty} +import eu.dnetlib.dhp.schema.action.AtomicAction +import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty} import eu.dnetlib.dhp.utils.DHPUtils +import org.apache.commons.lang3.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._ import scala.io.Source @@ -12,8 +16,12 @@ import scala.io.Source case class HostedByItemType(id: String, officialName: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {} +case class DoiBoostAffiliation(PaperId:Long, AffiliationId:Long, GridId:String){} + object DoiBoostMappingUtil { + val logger: Logger = LoggerFactory.getLogger(getClass) + //STATIC STRING val MAG = "microsoft" val MAG_NAME = "Microsoft Academic Graph" @@ -30,6 +38,31 @@ object DoiBoostMappingUtil { val invalidName = List(",", "none none", "none, none", "none &na;", "(:null)", "test test test", "test test", "test", "&na; &na;") + def toActionSet(item:Oaf) :(String, String) = { + val mapper = new ObjectMapper() + + item match { + case dataset: Dataset => + val a: AtomicAction[Dataset] = new AtomicAction[Dataset] + a.setClazz(classOf[Dataset]) + a.setPayload(dataset) + (dataset.getClass.getCanonicalName, mapper.writeValueAsString(a)) + case publication: Publication => + val a: AtomicAction[Publication] = new AtomicAction[Publication] + a.setClazz(classOf[Publication]) + a.setPayload(publication) + (publication.getClass.getCanonicalName, mapper.writeValueAsString(a)) + case relation: Relation => + val a: AtomicAction[Relation] = new AtomicAction[Relation] + a.setClazz(classOf[Relation]) + a.setPayload(relation) + (relation.getClass.getCanonicalName, mapper.writeValueAsString(a)) + case _ => + null + } + + } + def retrieveHostedByMap(): Map[String, HostedByItemType] = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats @@ -52,210 +85,249 @@ object DoiBoostMappingUtil { } + def generateGridAffiliationId(gridId:String) :String = { + s"10|grid________::${DHPUtils.md5(gridId.toLowerCase().trim())}" + } + def fixResult(result: Dataset) :Dataset = { + val instanceType = result.getInstance().asScala.find(i => i.getInstancetype != null && i.getInstancetype.getClassid.nonEmpty) + if (instanceType.isDefined) { + result.getInstance().asScala.foreach(i => i.setInstancetype(instanceType.get.getInstancetype)) + } + result.getInstance().asScala.foreach(i => { + val hb = new KeyValue + hb.setValue("Unknown Repository") + hb.setKey(s"10|$OPENAIRE_PREFIX::55045bd2a65019fd8e6741a755395c8c") + i.setHostedby(hb) + }) + result + } def fixPublication(publication: Publication, hostedByMap: Map[String, HostedByItemType]): Publication = { - if (publication.getJournal == null) - return publication + val issn = if (publication.getJournal == null) null else publication.getJournal.getIssnPrinted + val eissn =if (publication.getJournal == null) null else publication.getJournal.getIssnOnline + val lissn =if (publication.getJournal == null) null else publication.getJournal.getIssnLinking - val issn = publication.getJournal.getIssnPrinted - val eissn = publication.getJournal.getIssnOnline - val lissn = publication.getJournal.getIssnLinking + val instanceType = publication.getInstance().asScala.find(i => i.getInstancetype != null && i.getInstancetype.getClassid.nonEmpty) + + if (instanceType.isDefined) { + publication.getInstance().asScala.foreach(i => i.setInstancetype(instanceType.get.getInstancetype)) + } val item = retrieveHostedByItem(issn, eissn, lissn, hostedByMap) - if (item!= null) { - val l = publication.getInstance().asScala.map(i =>{ - val hb = new KeyValue - hb.setValue (item.officialName) - hb.setKey (s"10|${item.id}" ) - i.setHostedby(hb) - if(item.openAccess) + publication.getInstance().asScala.foreach(i => { + val hb = new KeyValue + if (item != null) { + hb.setValue(item.officialName) + hb.setKey(generateDSId(item.id)) + if (item.openAccess) i.setAccessright(createQualifier("Open", "dnet:access_modes")) - i - }).asJava + publication.setBestaccessright(createQualifier("Open", "dnet:access_modes")) + } + else { + hb.setValue("Unknown Repository") + hb.setKey(s"10|$OPENAIRE_PREFIX::55045bd2a65019fd8e6741a755395c8c") + } + i.setHostedby(hb) + }) - publication.setInstance(l) + val ar = publication.getInstance().asScala.filter(i => i.getInstancetype != null && i.getAccessright!= null && i.getAccessright.getClassid!= null).map(f=> f.getAccessright.getClassid) + if (ar.nonEmpty) { + if(ar.contains("Open")){ + publication.setBestaccessright(createQualifier("Open", "dnet:access_modes")) + } + else { + publication.setBestaccessright(createQualifier(ar.head, "dnet:access_modes")) + } } publication -} + } -def generateDataInfo (): DataInfo = { - generateDataInfo ("0.9") -} + def generateDSId(input: String): String = { + + val b = StringUtils.substringBefore(input, "::") + val a = StringUtils.substringAfter(input, "::") + s"10|${b}::${DHPUtils.md5(a)}" + } - def filterPublication (publication: Publication): Boolean = { - - //Case empty publication - if (publication == null) - return false - - //Case publication with no title - if (publication.getTitle == null || publication.getTitle.size == 0) - return false + def generateDataInfo(): DataInfo = { + generateDataInfo("0.9") + } - val s = publication.getTitle.asScala.count (p => p.getValue != null - && p.getValue.nonEmpty && ! p.getValue.equalsIgnoreCase ("[NO TITLE AVAILABLE]") ) + def filterPublication(publication: Publication): Boolean = { - if (s == 0) - return false + //Case empty publication + if (publication == null) + return false - // fixes #4360 (test publisher) - val publisher = if (publication.getPublisher != null) publication.getPublisher.getValue else null - - if (publisher != null && (publisher.equalsIgnoreCase ("Test accounts") || publisher.equalsIgnoreCase ("CrossRef Test Account") ) ) { - return false; -} - - //Publication with no Author - if (publication.getAuthor == null || publication.getAuthor.size () == 0) - return false + //Case publication with no title + if (publication.getTitle == null || publication.getTitle.size == 0) + return false - //filter invalid author - val authors = publication.getAuthor.asScala.map (s => { - if (s.getFullname.nonEmpty) { - s.getFullname -} - else - s"${ - s.getName -} ${ - s.getSurname -}" -}) + val s = publication.getTitle.asScala.count(p => p.getValue != null + && p.getValue.nonEmpty && !p.getValue.equalsIgnoreCase("[NO TITLE AVAILABLE]")) - val c = authors.count (isValidAuthorName) - if (c == 0) - return false + if (s == 0) + return false - // fixes #4368 - if (authors.count (s => s.equalsIgnoreCase ("Addie Jackson") ) > 0 && "Elsevier BV".equalsIgnoreCase (publication.getPublisher.getValue) ) - return false + // fixes #4360 (test publisher) + val publisher = if (publication.getPublisher != null) publication.getPublisher.getValue else null - true -} + if (publisher != null && (publisher.equalsIgnoreCase("Test accounts") || publisher.equalsIgnoreCase("CrossRef Test Account"))) { + return false; + } + + //Publication with no Author + if (publication.getAuthor == null || publication.getAuthor.size() == 0) + return false - def isValidAuthorName (fullName: String): Boolean = { - if (fullName == null || fullName.isEmpty) - return false - if (invalidName.contains (fullName.toLowerCase.trim) ) - return false - true -} + //filter invalid author + val authors = publication.getAuthor.asScala.map(s => { + if (s.getFullname.nonEmpty) { + s.getFullname + } + else + s"${ + s.getName + } ${ + s.getSurname + }" + }) + + val c = authors.count(isValidAuthorName) + if (c == 0) + return false + + // fixes #4368 + if (authors.count(s => s.equalsIgnoreCase("Addie Jackson")) > 0 && "Elsevier BV".equalsIgnoreCase(publication.getPublisher.getValue)) + return false + + true + } - def generateDataInfo (trust: String): DataInfo = { - val di = new DataInfo - di.setDeletedbyinference (false) - di.setInferred (false) - di.setInvisible (false) - di.setTrust (trust) - di.setProvenanceaction (createQualifier ("sysimport:actionset", "dnet:provenanceActions") ) - di -} + def isValidAuthorName(fullName: String): Boolean = { + if (fullName == null || fullName.isEmpty) + return false + if (invalidName.contains(fullName.toLowerCase.trim)) + return false + true + } - def createSP (value: String, classId: String, schemeId: String): StructuredProperty = { - val sp = new StructuredProperty - sp.setQualifier (createQualifier (classId, schemeId) ) - sp.setValue (value) - sp - -} - - def createSP (value: String, classId: String, schemeId: String, dataInfo: DataInfo): StructuredProperty = { - val sp = new StructuredProperty - sp.setQualifier (createQualifier (classId, schemeId) ) - sp.setValue (value) - sp.setDataInfo (dataInfo) - sp - -} - - def createCrossrefCollectedFrom (): KeyValue = { - - val cf = new KeyValue - cf.setValue (CROSSREF) - cf.setKey ("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5 (CROSSREF.toLowerCase) ) - cf - -} + def generateDataInfo(trust: String): DataInfo = { + val di = new DataInfo + di.setDeletedbyinference(false) + di.setInferred(false) + di.setInvisible(false) + di.setTrust(trust) + di.setProvenanceaction(createQualifier("sysimport:actionset", "dnet:provenanceActions")) + di + } - def createUnpayWallCollectedFrom (): KeyValue = { + def createSP(value: String, classId: String, schemeId: String): StructuredProperty = { + val sp = new StructuredProperty + sp.setQualifier(createQualifier(classId, schemeId)) + sp.setValue(value) + sp - val cf = new KeyValue - cf.setValue (UNPAYWALL) - cf.setKey ("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5 (UNPAYWALL.toLowerCase) ) - cf + } -} + def createSP(value: String, classId: String, schemeId: String, dataInfo: DataInfo): StructuredProperty = { + val sp = new StructuredProperty + sp.setQualifier(createQualifier(classId, schemeId)) + sp.setValue(value) + sp.setDataInfo(dataInfo) + sp - def createORIDCollectedFrom (): KeyValue = { + } - val cf = new KeyValue - cf.setValue (ORCID) - cf.setKey ("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5 (ORCID.toLowerCase) ) - cf + def createCrossrefCollectedFrom(): KeyValue = { -} + val cf = new KeyValue + cf.setValue(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] ) - return s"60|${ - doiBoostNSPREFIX -}${ - SEPARATOR -}${ - id -}" - s"50|${ - doiBoostNSPREFIX -}${ - SEPARATOR -}${ - id -}" -} + val id = DHPUtils.md5 (doi.toLowerCase) + if (oaf.isInstanceOf[Dataset] ) + return s"60|${ + doiBoostNSPREFIX + }${ + SEPARATOR + }${ + id + }" + s"50|${ + doiBoostNSPREFIX + }${ + SEPARATOR + }${ + id + }" + } - def createMAGCollectedFrom (): KeyValue = { + def createMAGCollectedFrom(): KeyValue = { - val cf = new KeyValue - cf.setValue (MAG) - cf.setKey ("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5 (MAG) ) - cf + val cf = new KeyValue + cf.setValue(MAG_NAME) + cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(MAG)) + cf -} + } - def createQualifier (clsName: String, clsValue: String, schName: String, schValue: String): Qualifier = { - val q = new Qualifier - q.setClassid (clsName) - q.setClassname (clsValue) - q.setSchemeid (schName) - q.setSchemename (schValue) - q -} + def createQualifier(clsName: String, clsValue: String, schName: String, schValue: String): Qualifier = { + val q = new Qualifier + q.setClassid(clsName) + q.setClassname(clsValue) + q.setSchemeid(schName) + q.setSchemename(schValue) + q + } - def createQualifier (cls: String, sch: String): Qualifier = { - createQualifier (cls, cls, sch, sch) -} + def createQualifier(cls: String, sch: String): Qualifier = { + createQualifier(cls, cls, sch, sch) + } - def asField[T] (value: T): Field[T] = { - val tmp = new Field[T] - tmp.setValue (value) - tmp - - -} + def asField[T](value: T): Field[T] = { + val tmp = new Field[T] + tmp.setValue(value) + tmp + + + } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala new file mode 100644 index 000000000..6c7627d82 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala @@ -0,0 +1,80 @@ +package eu.dnetlib.doiboost + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.action.AtomicAction +import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset} +import org.apache.hadoop.io.Text +import org.apache.commons.io.IOUtils +import org.apache.hadoop.io.compress.GzipCodec +import org.apache.hadoop.mapred.{SequenceFileOutputFormat, TextOutputFormat} +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +object SparkGenerateDOIBoostActionSet { + val logger: Logger = LoggerFactory.getLogger(getClass) + def main(args: Array[String]): Unit = { + + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + +// implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] +// implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset] +// implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation] +// +// implicit val mapEncoderAtomiAction: Encoder[AtomicAction[OafDataset]] = Encoders.kryo[AtomicAction[OafDataset]] +// +// +// +// val dbPublicationPath = parser.get("dbPublicationPath") +// val dbDatasetPath = parser.get("dbDatasetPath") +// val crossRefRelation = parser.get("crossRefRelation") +// val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath") + val workingDirPath = parser.get("targetPath") +// +// spark.read.load(dbDatasetPath).as[OafDataset] +// .map(d =>DoiBoostMappingUtil.fixResult(d)) +// .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) +// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") +// +// spark.read.load(dbPublicationPath).as[Publication] +// .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) +// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") +// +// spark.read.load(crossRefRelation).as[Relation] +// .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) +// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") +// +// spark.read.load(dbaffiliationRelationPath).as[Relation] +// .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) +// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") + + + implicit val mapEncoderPub: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING) + + val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)] + + SequenceFileOutputFormat + + d.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingDirPath/rawset_a8c2f90b-a3ae-4d6e-8187-47a437156e18_1590223414", classOf[Text], classOf[Text], classOf[TextOutputFormat[Text,Text]], classOf[GzipCodec]) + + + + + + + + + + + + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 2efa3aa5e..092715a35 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -1,11 +1,14 @@ package eu.dnetlib.doiboost import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.{Publication, Dataset => OafDataset} +import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset} +import eu.dnetlib.doiboost.mag.ConversionUtil import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf +import org.apache.spark.sql.functions.col import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} +import scala.collection.JavaConverters._ object SparkGenerateDoiBoost { @@ -22,7 +25,7 @@ object SparkGenerateDoiBoost { .appName(getClass.getSimpleName) .master(parser.get("master")).getOrCreate() - + import spark.implicits._ val crossrefPublicationPath = parser.get("crossrefPublicationPath") val crossrefDatasetPath = parser.get("crossrefDatasetPath") val uwPublicationPath = parser.get("uwPublicationPath") @@ -32,15 +35,16 @@ object SparkGenerateDoiBoost { logger.info("Phase 1) repartition and move all the dataset in a same working folder") -// spark.read.load(crossrefPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$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") + 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"$workingDirPath/magPublication") implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset] implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPub) + implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation] logger.info("Phase 2) Join Crossref with UnpayWall") @@ -73,11 +77,49 @@ object SparkGenerateDoiBoost { val doiBoostPublication: Dataset[Publication] = spark.read.load(s"$workingDirPath/doiBoostPublication").as[Publication] - doiBoostPublication.filter(p=>DoiBoostMappingUtil.filterPublication(p)).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationFiltered") + val map = DoiBoostMappingUtil.retrieveHostedByMap() + + doiBoostPublication.filter(p=>DoiBoostMappingUtil.filterPublication(p)).map(p => DoiBoostMappingUtil.fixPublication(p, map)).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationFiltered") + + + val affiliationPath = parser.get("affiliationPath") + val paperAffiliationPath = parser.get("paperAffiliationPath") + + val affiliation = spark.read.load(affiliationPath).where(col("GridId").isNotNull).select(col("AffiliationId"), col("GridId")) + + val paperAffiliation = spark.read.load(paperAffiliationPath).select(col("AffiliationId").alias("affId"), col("PaperId")) + + + val a:Dataset[DoiBoostAffiliation] = paperAffiliation + .joinWith(affiliation, paperAffiliation("affId").equalTo(affiliation("AffiliationId"))).select(col("_1.PaperId"), col("_2.AffiliationId"), col("_2.GridId")).as[DoiBoostAffiliation] + val magPubs:Dataset[(String,Publication)]= spark.read.load(s"$workingDirPath/doiBoostPublicationFiltered").as[Publication] + .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p))(tupleForJoinEncoder).filter(s =>s._1!= null ) + + magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).flatMap(item => { + val pub:Publication = item._1._2 + val affiliation = item._2 + val r:Relation = new Relation + r.setSource(pub.getId) + r.setTarget(DoiBoostMappingUtil.generateGridAffiliationId(affiliation.GridId)) + r.setRelType("resultOrganization") + r.setRelClass("hasAuthorInstitution") + r.setSubRelType("affiliation") + r.setDataInfo(pub.getDataInfo) + r.setCollectedfrom(pub.getCollectedfrom) + val r1:Relation = new Relation + r1.setTarget(pub.getId) + r1.setSource(DoiBoostMappingUtil.generateGridAffiliationId(affiliation.GridId)) + r1.setRelType("resultOrganization") + r1.setRelClass("isAuthorInstitutionOf") + r1.setSubRelType("affiliation") + r1.setDataInfo(pub.getDataInfo) + r1.setCollectedfrom(pub.getCollectedfrom) + List(r, r1) + })(mapEncoderRel).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation") } } diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json new file mode 100644 index 000000000..76059665f --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json @@ -0,0 +1,8 @@ +[ + {"paramName": "m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true}, + {"paramName": "dp", "paramLongName":"dbPublicationPath", "paramDescription": "the Crossref Publication Path", "paramRequired": true}, + {"paramName": "dd", "paramLongName":"dbDatasetPath", "paramDescription": "the Crossref Dataset Path", "paramRequired": true}, + {"paramName": "cr", "paramLongName":"crossRefRelation", "paramDescription": "the UnpayWall Publication Path", "paramRequired": true}, + {"paramName": "da", "paramLongName":"dbaffiliationRelationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true}, + {"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true} +] 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 index c6115ec83..d5ef3726b 100644 --- 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 @@ -1,9 +1,11 @@ [ - {"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} + {"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": "ap", "paramLongName":"affiliationPath", "paramDescription": "the Affliation Path", "paramRequired": true}, + {"paramName": "pa", "paramLongName":"paperAffiliationPath", "paramDescription": "the paperAffiliation 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/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml index f07ed944e..62fb2a5d9 100644 --- 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 @@ -20,6 +20,18 @@ orcidPublicationPath the ORCID Publication Path + + + affiliationPath + the Affliation Path + + + + paperAffiliationPath + the paperAffiliation Path + + + workingDirPath the Working Path @@ -40,7 +52,7 @@ - + @@ -75,36 +87,40 @@ --uwPublicationPath${uwPublicationPath} --magPublicationPath${magPublicationPath} --orcidPublicationPath${orcidPublicationPath} + --affiliationPath${affiliationPath} + --paperAffiliationPath${paperAffiliationPath} --workingDirPath${workingDirPath} --masteryarn-cluster + + + + + + + + yarn-cluster + cluster + Generate DOIBoost ActionSet + eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --dbPublicationPath${workingDirPath}/doiBoostPublicationFiltered + --dbDatasetPath${workingDirPath}/crossrefDataset + --crossRefRelation/data/doiboost/input/crossref/relations + --dbaffiliationRelationPath${workingDirPath}/doiBoostPublicationAffiliation + --targetPath${workingDirPath}/actionDataSet + --masteryarn-cluster + - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostHostedByMapTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostHostedByMapTest.scala index 2b223bbe9..2c530206c 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostHostedByMapTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostHostedByMapTest.scala @@ -1,7 +1,11 @@ package eu.dnetlib.dhp.doiboost - +import eu.dnetlib.dhp.schema.oaf.{Publication, Dataset => OafDataset} import eu.dnetlib.doiboost.DoiBoostMappingUtil +import eu.dnetlib.doiboost.SparkGenerateDoiBoost.getClass +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Encoder, Encoders, SparkSession} +import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} import org.junit.jupiter.api.Test class DoiBoostHostedByMapTest { @@ -13,4 +17,46 @@ class DoiBoostHostedByMapTest { } + + @Test + def testFilter():Unit = { + val conf: SparkConf = new SparkConf() + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master("local[*]").getOrCreate() + + + 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) + + + + val pub =spark.read.load("/data/doiboost/doiboostPublicationFiltered").as[Publication] + + val mapper = new ObjectMapper() + + val map = DoiBoostMappingUtil.retrieveHostedByMap() + + println(pub.map(p => DoiBoostMappingUtil.fixPublication(p, map)).count()) + + + } + + + @Test + def idDSGeneration():Unit = { + val s ="doajarticles::0066-782X" + + + + println(DoiBoostMappingUtil.generateDSId(s)) + + + } + + } diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/publicationInput.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/publicationInput.json new file mode 100644 index 000000000..4e6db2a12 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/publicationInput.json @@ -0,0 +1,20 @@ +[{"journal":{"issnOnline":null,"vol":"37","issnLinking":null,"edition":null,"issnPrinted":"2415-8038","dataInfo":null,"conferencedate":null,"iss":null,"ep":"34","sp":"30","conferenceplace":null,"name":"Scientific Herald of Uzhhorod University.Series Physics"},"format":[],"source":[{"dataInfo":null,"value":"Crossref"},{"dataInfo":null,"value":null}],"description":[],"subject":[{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Instability"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Softening"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Composite material"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Self-organization"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Materials science"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Crystalline materials"}],"author":[{"surname":"Мар’ян","affiliation":null,"fullname":"М. 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Here, the analysis of the characteristics of bitcoins is compared with the guidelines and concepts of IFRS, in order to elaborate the recommendation for accounting treatment, and it suggests that the most adequate procedure would be that of foreign currency, which would go against the tax treatment adopted up until now by the Brazilian Internal Revenue Service (Receita Federal) or the Internal Revenue Service (IRS) of the United States of America (USA), which suggest treating virtual currencies as goods and not as currencies. 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The initial dynamical conditions (wind and temperature) essentially control the horizontal location and area of the cloud. However, the choice of the microphysics scheme influences the ice water content and the cloud vertical position. Last, the fair agreement with the observations allows to estimate the cloud impact in the TTL in the simulations. The cirrus clouds have a small but not negligible impact on the radiative budget of the local TTL. However, for this particular case, the cloud radiative heating does not significantly influence the simulated dynamics. This result is due to (1) the lifetime of air parcels in the cloud system, which is too short to significantly influence the dynamics, and (2) the fact that induced vertical motions would be comparable to or smaller than the typical mesoscale motions present. Finally, the simulation also provides an estimate of the vertical redistribution of water by the cloud and the results emphasize the importance in our case of both rehydration and dehydration in the vicinity of the cirrus.\n "}],"subject":[{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Atmospheric Science"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Cirrus"},{"qualifier":{"blank":false,"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null,"value":"Weather Research and Forecasting 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The greatest obstacle to reduction was a constriction of the capsule. At a mean follow-up of 13.2 months (9 to 24), all eight hips remained stable. Three developed avascular necrosis. The mean acetabular index decreased from 35.5° (30° to 40°) pre-operatively to 23.3° (17° to 28°).\n\nThis study demonstrates that arthroscopic reduction is feasible using two standardised portals. 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