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Implemented class that generates a normalized table of MAG, which is the starting point for the creation of the mag source

This commit is contained in:
Sandro La Bruzzo 2024-03-04 17:15:13 +01:00
parent ad0e9aa80c
commit f417515e43
1 changed files with 57 additions and 6 deletions
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63
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/mag/SparkCreateMagDataset.scala
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@ -1,7 +1,7 @@
package eu.dnetlib.dhp.collection.mag
import eu.dnetlib.dhp.application.AbstractScalaApplication
import org.apache.spark.sql.{Dataset, Row, SparkSession}
import org.apache.spark.sql.{Dataset, Row, SaveMode, SparkSession}
import org.apache.spark.sql.functions._
import org.apache.spark.sql.types.{StringType, StructField, StructType}
import org.slf4j.Logger
@ -19,21 +19,22 @@ class SparkCreateMagDataset (propertyPath: String, args: Array[String], log: Log
}
private def loadAndFilterPapers(spark:SparkSession, crossrefPath:String, magBasePath:String, workingPath): Unit = {
private def loadAndFilterPapers(spark:SparkSession, crossrefPath:String, magBasePath:String, workingPath:String): Unit = {
import spark.implicits._
val schema:StructType= StructType(StructField("DOI", StringType)::Nil)
log.info("Phase 1 intersect MAG Paper containing doi also present in crossref")
//Filter all the MAG Papers that intersect with a Crossref DOI
val crId= spark.read.schema(schema).json(crossrefPath).withColumn("crId", lower(col("DOI"))).distinct.select("crId")
val magPapers = MagUtility.loadMagEntity(spark, "Papers", magBasePath).withColumn("Doi", lower(col("Doi"))).where(col("Doi").isNotNull)
val magPapers = MagUtility.loadMagEntity(spark, "Papers", magBasePath)
.withColumn("Doi", lower(col("Doi")))
.where(col("Doi").isNotNull)
val intersectedPapers:Dataset[Row] =magPapers.join(crId, magPapers("Doi").equalTo(crId("crId")), "leftsemi").dropDuplicates("Doi")
intersectedPapers.cache()
intersectedPapers.count()
log.info("Create current abstract")
//log.info("Create current abstract")
//Abstract is an inverted list, we define a function that convert in string the abstract and recreate
// a table(PaperId, Abstract)
@ -67,11 +68,61 @@ class SparkCreateMagDataset (propertyPath: String, args: Array[String], log: Log
.select(j1("*"), affiliations("DisplayName").alias("AffiliationName"), affiliations("GridId"))
.groupBy("PaperId")
.agg(collect_list(struct("AffiliationId","AuthorSequenceNumber","AffiliationName","AuthorName","AuthorId","GridId")).alias("authors"))
val step1 =step0.join(paperAuthorAffiliationNormalized, step0("PaperId")=== paperAuthorAffiliationNormalized("PaperId"), "left").cache()
val step1 =step0.join(paperAuthorAffiliationNormalized, step0("PaperId")=== paperAuthorAffiliationNormalized("PaperId"), "left")
.select(step0("*"),paperAuthorAffiliationNormalized("authors"))
.cache()
step1.count()
step0.unpersist()
val conference = MagUtility.loadMagEntity(spark, "ConferenceInstances", magBasePath).select(
$"ConferenceInstanceId",
$"DisplayName".as("conferenceName"),
$"Location".as("conferenceLocation"),
$"StartDate".as("conferenceStartDate"),
$"EndDate".as("conferenceEndDate")
)
val step2 =step1.join(conference, step1("ConferenceInstanceId")=== conference("ConferenceInstanceId"),"left").select(
step1("*"), conference("conferenceName"),
conference("conferenceLocation"),
conference("conferenceStartDate"),
conference("conferenceEndDate")).cache()
step2.count()
step1.unpersist()
val fos = MagUtility.loadMagEntity(spark, "FieldsOfStudy", magBasePath)
.select($"FieldOfStudyId".alias("fos"), $"DisplayName", $"MainType")
val paperFieldsOfStudy = MagUtility.loadMagEntity(spark, "PaperFieldsOfStudy", magBasePath)
.select($"FieldOfStudyId", $"Score", $"PaperId")
val paperFoS = paperFieldsOfStudy.join(broadcast(fos),fos("fos")===paperFieldsOfStudy("FieldOfStudyId")).groupBy("PaperId")
.agg(collect_set(struct("FieldOfStudyId","DisplayName","MainType","Score")).as("FoS"))
val step3=step2.join(paperFoS, step2("PaperId")===paperFoS("PaperId"), "left")
.select(step2("*"), paperFoS("FoS")).cache()
step3.count()
step2.unpersist()
val journals= MagUtility.loadMagEntity(spark, "Journals", magBasePath)
.select(
$"JournalId",
$"DisplayName".as("journalName"),
$"Issn".as("journalIssn"),
$"Publisher".as("journalPublisher"),
$"Webpage".as("journalWebpage")
)
step3.join(journals, step3("JournalId")===journals("JournalId"), "left").
select(step3("*"),
journals("journalName"),
journals("journalIssn"),
journals("journalPublisher"),
journals("journalWebpage")
).write.mode("OverWrite")
.save(s"$workingPath/generatedMAG")
step3.unpersist()
}
}