forked from D-Net/dnet-hadoop
Merge branch 'doiboost' of https://code-repo.d4science.org/D-Net/dnet-hadoop into doiboost
This commit is contained in:
commit
1109d3b3fc
|
|
@ -21,11 +21,15 @@ object DoiBoostMappingUtil {
|
|||
|
||||
|
||||
def generateDataInfo(): DataInfo = {
|
||||
generateDataInfo("0.9")
|
||||
}
|
||||
|
||||
def generateDataInfo(trust:String): DataInfo = {
|
||||
val di = new DataInfo
|
||||
di.setDeletedbyinference(false)
|
||||
di.setInferred(false)
|
||||
di.setInvisible(false)
|
||||
di.setTrust("0.9")
|
||||
di.setTrust(trust)
|
||||
di.setProvenanceaction(createQualifier("sysimport:actionset", "dnet:provenanceActions"))
|
||||
di
|
||||
}
|
||||
|
|
|
|||
|
|
@ -137,9 +137,21 @@ case object Crossref2Oaf {
|
|||
if (StringUtils.isNotBlank(issuedDate)) {
|
||||
result.setDateofacceptance(asField(issuedDate))
|
||||
}
|
||||
else {
|
||||
result.setDateofacceptance(asField(createdDate.getValue))
|
||||
}
|
||||
result.setRelevantdate(List(createdDate, postedDate, acceptedDate, publishedOnlineDate, publishedPrintDate).filter(p => p != null).asJava)
|
||||
|
||||
|
||||
//Mapping Subject
|
||||
val subjectList:List[String] = (json \ "subject").extractOrElse[List[String]](List())
|
||||
|
||||
if (subjectList.nonEmpty) {
|
||||
result.setSubject(subjectList.map(s=> createSP(s, "keywords", "dnet:subject_classification_typologies")).asJava)
|
||||
}
|
||||
|
||||
|
||||
|
||||
//Mapping AUthor
|
||||
val authorList: List[mappingAuthor] = (json \ "author").extractOrElse[List[mappingAuthor]](List())
|
||||
result.setAuthor(authorList.map(a => generateAuhtor(a.given.orNull, a.family, a.ORCID.orNull)).asJava)
|
||||
|
|
@ -224,6 +236,16 @@ case object Crossref2Oaf {
|
|||
val queue = new mutable.Queue[Relation]
|
||||
|
||||
|
||||
def snfRule(award:String): String = {
|
||||
var tmp1 = StringUtils.substringAfter(award,"_")
|
||||
val tmp2 = StringUtils.substringBefore(tmp1,"/")
|
||||
logger.debug(s"From $award to $tmp2")
|
||||
tmp2
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
def extractECAward(award: String): String = {
|
||||
val awardECRegex: Regex = "[0-9]{4,9}".r
|
||||
if (awardECRegex.findAllIn(award).hasNext)
|
||||
|
|
@ -289,7 +311,7 @@ case object Crossref2Oaf {
|
|||
case "10.13039/501100006588" |
|
||||
"10.13039/501100004488" => generateSimpleRelationFromAward(funder, "irb_hr______", a=>a.replaceAll("Project No.", "").replaceAll("HRZZ-","") )
|
||||
case "10.13039/501100006769"=> generateSimpleRelationFromAward(funder, "rsf_________", a=>a)
|
||||
case "10.13039/501100001711"=> generateSimpleRelationFromAward(funder, "snsf________", extractECAward)
|
||||
case "10.13039/501100001711"=> generateSimpleRelationFromAward(funder, "snsf________", snfRule)
|
||||
case "10.13039/501100004410"=> generateSimpleRelationFromAward(funder, "tubitakf____", a =>a)
|
||||
case "10.10.13039/100004440"=> generateSimpleRelationFromAward(funder, "wt__________", a =>a)
|
||||
case "10.13039/100004440"=> queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "wt__________" )
|
||||
|
|
|
|||
|
|
@ -40,6 +40,9 @@ case class MagPaperUrl(PaperId: Long, SourceType: Option[Int], SourceUrl: Option
|
|||
|
||||
case class MagUrl(PaperId: Long, instances: List[String])
|
||||
|
||||
case class MagSubject(FieldOfStudyId:Long, DisplayName:String, MainType:Option[String], Score:Float){}
|
||||
|
||||
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]) {}
|
||||
|
||||
|
|
@ -135,6 +138,8 @@ case object ConversionUtil {
|
|||
j.setIssnPrinted(journal.Issn.get)
|
||||
pub.setJournal(j)
|
||||
}
|
||||
pub.setCollectedfrom(List(createMAGCollectedFrom()).asJava)
|
||||
pub.setDataInfo(generateDataInfo())
|
||||
pub
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,20 +1,18 @@
|
|||
package eu.dnetlib.doiboost.mag
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil.asField
|
||||
import eu.dnetlib.dhp.schema.oaf.{Publication, StructuredProperty}
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{asField, createSP}
|
||||
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}
|
||||
import org.apache.spark.sql.functions._
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
|
||||
object SparkPreProcessMAG {
|
||||
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
||||
val logger: Logger = LoggerFactory.getLogger(getClass)
|
||||
|
|
@ -31,15 +29,11 @@ object SparkPreProcessMAG {
|
|||
val sourcePath = parser.get("sourcePath")
|
||||
import spark.implicits._
|
||||
implicit val mapEncoderPubs: Encoder[Publication] = org.apache.spark.sql.Encoders.kryo[Publication]
|
||||
implicit val tupleForJoinEncoder = Encoders.tuple(Encoders.STRING, mapEncoderPubs)
|
||||
|
||||
|
||||
implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPubs)
|
||||
|
||||
logger.info("Phase 1) make uninque DOI in Papers:")
|
||||
|
||||
val d: Dataset[MagPapers] = spark.read.load(s"${parser.get("sourcePath")}/Papers").as[MagPapers]
|
||||
|
||||
|
||||
// Filtering Papers with DOI, and since for the same DOI we have multiple version of item with different PapersId we get the last one
|
||||
val result: RDD[MagPapers] = d.where(col("Doi").isNotNull).rdd.map { p: MagPapers => Tuple2(p.Doi, p) }.reduceByKey { case (p1: MagPapers, p2: MagPapers) =>
|
||||
var r = if (p1 == null) p2 else p1
|
||||
|
|
@ -56,6 +50,8 @@ object SparkPreProcessMAG {
|
|||
r
|
||||
}.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: ${result.count()}")
|
||||
|
|
@ -63,44 +59,36 @@ object SparkPreProcessMAG {
|
|||
logger.info("Phase 3) Group Author by PaperId")
|
||||
val authors = spark.read.load(s"$sourcePath/Authors").as[MagAuthor]
|
||||
|
||||
val affiliation =spark.read.load(s"$sourcePath/Affiliations").as[MagAffiliation]
|
||||
|
||||
val paperAuthorAffiliation =spark.read.load(s"$sourcePath/PaperAuthorAffiliations").as[MagPaperAuthorAffiliation]
|
||||
|
||||
val affiliation = spark.read.load(s"$sourcePath/Affiliations").as[MagAffiliation]
|
||||
val paperAuthorAffiliation = spark.read.load(s"$sourcePath/PaperAuthorAffiliations").as[MagPaperAuthorAffiliation]
|
||||
|
||||
paperAuthorAffiliation.joinWith(authors, paperAuthorAffiliation("AuthorId").equalTo(authors("AuthorId")))
|
||||
.map{case (a:MagPaperAuthorAffiliation,b:MagAuthor )=> (a.AffiliationId,MagPaperAuthorDenormalized(a.PaperId, b, null)) }
|
||||
.map { case (a: MagPaperAuthorAffiliation, b: MagAuthor) => (a.AffiliationId, MagPaperAuthorDenormalized(a.PaperId, b, null)) }
|
||||
.joinWith(affiliation, affiliation("AffiliationId").equalTo(col("_1")), "left")
|
||||
.map(s => {
|
||||
val mpa = s._1._2
|
||||
val af = s._2
|
||||
if (af!= null) {
|
||||
MagPaperAuthorDenormalized(mpa.PaperId, mpa.author, af.DisplayName)
|
||||
} else
|
||||
mpa
|
||||
}).groupBy("PaperId").agg(collect_list(struct($"author", $"affiliation")).as("authors"))
|
||||
val mpa = s._1._2
|
||||
val af = s._2
|
||||
if (af != null) {
|
||||
MagPaperAuthorDenormalized(mpa.PaperId, mpa.author, af.DisplayName)
|
||||
} else
|
||||
mpa
|
||||
}).groupBy("PaperId").agg(collect_list(struct($"author", $"affiliation")).as("authors"))
|
||||
.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_1_paper_authors")
|
||||
|
||||
|
||||
|
||||
logger.info("Phase 4) create First Version of publication Entity with Paper Journal and Authors")
|
||||
|
||||
|
||||
val journals = spark.read.load(s"$sourcePath/Journals").as[MagJournal]
|
||||
|
||||
val papers =spark.read.load((s"${parser.get("targetPath")}/Papers_distinct")).as[MagPapers]
|
||||
val papers = spark.read.load((s"${parser.get("targetPath")}/Papers_distinct")).as[MagPapers]
|
||||
|
||||
val paperWithAuthors = spark.read.load(s"${parser.get("targetPath")}/merge_step_1_paper_authors").as[MagPaperWithAuthorList]
|
||||
|
||||
|
||||
|
||||
val firstJoin =papers.joinWith(journals, papers("JournalId").equalTo(journals("JournalId")),"left")
|
||||
val firstJoin = papers.joinWith(journals, papers("JournalId").equalTo(journals("JournalId")), "left")
|
||||
firstJoin.joinWith(paperWithAuthors, firstJoin("_1.PaperId").equalTo(paperWithAuthors("PaperId")), "left")
|
||||
.map { a: ((MagPapers, MagJournal), MagPaperWithAuthorList) => ConversionUtil.createOAFFromJournalAuthorPaper(a) }.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_2")
|
||||
|
||||
|
||||
|
||||
var magPubs:Dataset[(String,Publication)] = spark.read.load(s"${parser.get("targetPath")}/merge_step_2").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String,Publication)]
|
||||
var magPubs: Dataset[(String, Publication)] = spark.read.load(s"${parser.get("targetPath")}/merge_step_2").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
|
||||
|
||||
val paperUrlDataset = spark.read.load(s"$sourcePath/PaperUrls").as[MagPaperUrl].groupBy("PaperId").agg(collect_list(struct("sourceUrl")).as("instances")).as[MagUrl]
|
||||
|
||||
|
|
@ -108,33 +96,69 @@ object SparkPreProcessMAG {
|
|||
logger.info("Phase 5) enrich publication with URL and Instances")
|
||||
|
||||
magPubs.joinWith(paperUrlDataset, col("_1").equalTo(paperUrlDataset("PaperId")), "left")
|
||||
.map{a:((String,Publication), MagUrl) => ConversionUtil.addInstances((a._1._2, a._2))}
|
||||
.map { a: ((String, Publication), MagUrl) => ConversionUtil.addInstances((a._1._2, a._2)) }
|
||||
.write.mode(SaveMode.Overwrite)
|
||||
.save(s"${parser.get("targetPath")}/merge_step_3")
|
||||
|
||||
|
||||
|
||||
logger.info("Phase 6) Enrich Publication with description")
|
||||
val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract]
|
||||
pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract")
|
||||
|
||||
val paperAbstract =spark.read.load((s"${parser.get("targetPath")}/PaperAbstract")).as[MagPaperAbstract]
|
||||
val paperAbstract = spark.read.load((s"${parser.get("targetPath")}/PaperAbstract")).as[MagPaperAbstract]
|
||||
|
||||
|
||||
magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_3").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String,Publication)]
|
||||
magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_3").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
|
||||
|
||||
magPubs.joinWith(paperAbstract,col("_1").equalTo(paperAbstract("PaperId")), "left").map(p=>
|
||||
{
|
||||
val pub = p._1._2
|
||||
val abst = p._2
|
||||
if (abst!= null) {
|
||||
pub.setDescription(List(asField(abst.IndexedAbstract)).asJava)
|
||||
magPubs.joinWith(paperAbstract, col("_1").equalTo(paperAbstract("PaperId")), "left").map(p => {
|
||||
val pub = p._1._2
|
||||
val abst = p._2
|
||||
if (abst != null) {
|
||||
pub.setDescription(List(asField(abst.IndexedAbstract)).asJava)
|
||||
}
|
||||
pub
|
||||
}
|
||||
).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_4")
|
||||
|
||||
|
||||
logger.info("Phase 7) Enrich Publication with FieldOfStudy")
|
||||
|
||||
magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_4").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
|
||||
|
||||
val fos = spark.read.load(s"$sourcePath/FieldsOfStudy").select($"FieldOfStudyId".alias("fos"), $"DisplayName", $"MainType")
|
||||
|
||||
val pfos = spark.read.load(s"$sourcePath/PaperFieldsOfStudy")
|
||||
|
||||
val paperField = pfos.joinWith(fos, fos("fos").equalTo(pfos("FieldOfStudyId")))
|
||||
.select($"_1.FieldOfStudyId", $"_2.DisplayName", $"_2.MainType", $"_1.PaperId", $"_1.Score")
|
||||
.groupBy($"PaperId").agg(collect_list(struct($"FieldOfStudyId", $"DisplayName", $"MainType", $"Score")).as("subjects"))
|
||||
.as[MagFieldOfStudy]
|
||||
|
||||
magPubs.joinWith(paperField, col("_1").equalTo(paperField("PaperId")), "left").
|
||||
map(item => {
|
||||
val publication = item._1._2
|
||||
val fieldOfStudy = item._2
|
||||
if (fieldOfStudy != null && fieldOfStudy.subjects != null && fieldOfStudy.subjects.nonEmpty) {
|
||||
val p: List[StructuredProperty] = fieldOfStudy.subjects.flatMap(s => {
|
||||
val s1 = createSP(s.DisplayName, "keywords", "dnet:subject_classification_typologies")
|
||||
val di = DoiBoostMappingUtil.generateDataInfo(s.Score.toString)
|
||||
var resList: List[StructuredProperty] = List(s1)
|
||||
if (s.MainType.isDefined) {
|
||||
val maintp = s.MainType.get
|
||||
val s2 = createSP(s.MainType.get, "keywords", "dnet:subject_classification_typologies")
|
||||
s2.setDataInfo(di)
|
||||
resList = resList ::: List(s2)
|
||||
if (maintp.contains(".")) {
|
||||
val s3 = createSP(maintp.split("\\.").head, "keywords", "dnet:subject_classification_typologies")
|
||||
s3.setDataInfo(di)
|
||||
resList = resList ::: List(s3)
|
||||
}
|
||||
}
|
||||
resList
|
||||
})
|
||||
publication.setSubject(p.asJava)
|
||||
}
|
||||
pub
|
||||
}
|
||||
).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_4")
|
||||
|
||||
publication
|
||||
}).map{s:Publication => s}(Encoders.bean(classOf[Publication])).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/mag_publication")
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -22,7 +22,7 @@
|
|||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="ResetWorkingPath"/>
|
||||
<start to="PreprocessMag"/>
|
||||
|
||||
|
||||
<kill name="Kill">
|
||||
|
|
|
|||
|
|
@ -90,9 +90,9 @@ class CrossrefMappingTest {
|
|||
val rels:List[Relation] = resultList.filter(p => p.isInstanceOf[Relation]).map(r=> r.asInstanceOf[Relation])
|
||||
|
||||
|
||||
assertEquals(rels.size, 4)
|
||||
rels.foreach(s => logger.info(s.getTarget))
|
||||
|
||||
rels.foreach(s => logger.info(s.getTarget))
|
||||
assertEquals(rels.size, 3 )
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -24,47 +24,21 @@ class MAGMappingTest {
|
|||
val mapper = new ObjectMapper()
|
||||
|
||||
|
||||
|
||||
|
||||
@Test
|
||||
def testMAGCSV(): Unit = {
|
||||
// SparkPreProcessMAG.main("-m local[*] -s /data/doiboost/mag/datasets -t /data/doiboost/mag/datasets/preprocess".split(" "))
|
||||
|
||||
val sparkConf: SparkConf = new SparkConf
|
||||
|
||||
val spark: SparkSession = SparkSession.builder()
|
||||
.config(sparkConf)
|
||||
.appName(getClass.getSimpleName)
|
||||
.master("local[*]")
|
||||
.getOrCreate()
|
||||
|
||||
import spark.implicits._
|
||||
def testSplitter():Unit = {
|
||||
val s = "sports.team"
|
||||
|
||||
|
||||
implicit val mapEncoderPubs: Encoder[Publication] = org.apache.spark.sql.Encoders.kryo[Publication]
|
||||
implicit val longBarEncoder = Encoders.tuple(Encoders.STRING, mapEncoderPubs)
|
||||
|
||||
val sourcePath = "/data/doiboost/mag/input"
|
||||
|
||||
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
|
||||
|
||||
|
||||
val magOAF = spark.read.load("$sourcePath/merge_step_4").as[Publication]
|
||||
|
||||
println(magOAF.first().getOriginalId)
|
||||
|
||||
|
||||
magOAF.map(k => (ConversionUtil.extractMagIdentifier(k.getOriginalId.asScala),k)).as[(String,Publication)].show()
|
||||
|
||||
|
||||
println((ConversionUtil.extractMagIdentifier(magOAF.first().getOriginalId.asScala)))
|
||||
|
||||
val magIDRegex: Regex = "^[0-9]+$".r
|
||||
|
||||
|
||||
println(magIDRegex.findFirstMatchIn("suca").isDefined)
|
||||
if (s.contains(".")) {
|
||||
println(s.split("\\.")head)
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Test
|
||||
def buildInvertedIndexTest(): Unit = {
|
||||
val json_input = Source.fromInputStream(getClass.getResourceAsStream("invertedIndex.json")).mkString
|
||||
|
|
|
|||
|
|
@ -179,12 +179,13 @@
|
|||
],
|
||||
"funder": [
|
||||
{
|
||||
"DOI": "10.13039/501100001711",
|
||||
"name": "Swiss National Science Foundation (Schweizerische Nationalfonds)",
|
||||
"doi-asserted-by": "publisher",
|
||||
"DOI": "10.13039/501100000781",
|
||||
"name": "European Research Council",
|
||||
"award": [
|
||||
"284236-REPCOLLAB",
|
||||
"FP7/2007-2013"
|
||||
"CR32I3_156724",
|
||||
"31003A_173281/1",
|
||||
"200021_165850"
|
||||
]
|
||||
}
|
||||
],
|
||||
|
|
|
|||
Loading…
Reference in New Issue