223 lines
8.1 KiB
Scala
223 lines
8.1 KiB
Scala
|
package eu.dnetlib.dhp.collection.mag
|
||
|
|
||
|
import eu.dnetlib.dhp.application.AbstractScalaApplication
|
||
|
import org.apache.spark.sql.functions._
|
||
|
import org.apache.spark.sql.types.{StringType, StructField, StructType}
|
||
|
import org.apache.spark.sql.{Dataset, Row, SparkSession}
|
||
|
import org.slf4j.{Logger, LoggerFactory}
|
||
|
|
||
|
class SparkCreateMagDenormalizedTable(propertyPath: String, args: Array[String], log: Logger)
|
||
|
extends AbstractScalaApplication(propertyPath, args, log: Logger) {
|
||
|
|
||
|
/** Here all the spark applications runs this method
|
||
|
* where the whole logic of the spark node is defined
|
||
|
*/
|
||
|
override def run(): Unit = {
|
||
|
val crossrefPath: String = parser.get("crossrefPath")
|
||
|
log.info("found parameters crossrefPath: {}", crossrefPath)
|
||
|
val magBasePath: String = parser.get("magBasePath")
|
||
|
log.info("found parameters magBasePath: {}", magBasePath)
|
||
|
val workingPath: String = parser.get("workingPath")
|
||
|
log.info("found parameters workingPath: {}", workingPath)
|
||
|
generatedDenormalizedMAGTable(spark, crossrefPath, magBasePath, workingPath)
|
||
|
}
|
||
|
|
||
|
private def generatedDenormalizedMAGTable(
|
||
|
spark: SparkSession,
|
||
|
crossrefPath: String,
|
||
|
magBasePath: String,
|
||
|
workingPath: String
|
||
|
): Unit = {
|
||
|
|
||
|
import spark.implicits._
|
||
|
val schema: StructType = StructType(StructField("DOI", StringType) :: Nil)
|
||
|
|
||
|
//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 intersectedPapers: Dataset[Row] =
|
||
|
magPapers.join(crId, magPapers("Doi").equalTo(crId("crId")), "leftsemi").dropDuplicates("Doi")
|
||
|
intersectedPapers.cache()
|
||
|
intersectedPapers.count()
|
||
|
//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)
|
||
|
val paperAbstract = MagUtility
|
||
|
.loadMagEntity(spark, "PaperAbstractsInvertedIndex", magBasePath)
|
||
|
.map(s => (s.getLong(0), MagUtility.convertInvertedIndexString(s.getString(1))))
|
||
|
.withColumnRenamed("_1", "PaperId")
|
||
|
.withColumnRenamed("_2", "Abstract")
|
||
|
|
||
|
//We define Step0 as the result of the Join between PaperIntersection and the PaperAbstract
|
||
|
|
||
|
val step0 = intersectedPapers
|
||
|
.join(paperAbstract, intersectedPapers("PaperId") === paperAbstract("PaperId"), "left")
|
||
|
.select(intersectedPapers("*"), paperAbstract("Abstract"))
|
||
|
.cache()
|
||
|
|
||
|
step0.count()
|
||
|
|
||
|
intersectedPapers.unpersist()
|
||
|
|
||
|
// We have three table Author, Affiliation, and PaperAuthorAffiliation, in the
|
||
|
//next step we create a table containing
|
||
|
val authors = MagUtility.loadMagEntity(spark, "Authors", magBasePath)
|
||
|
val affiliations = MagUtility.loadMagEntity(spark, "Affiliations", magBasePath)
|
||
|
val paaf = MagUtility.loadMagEntity(spark, "PaperAuthorAffiliations", magBasePath)
|
||
|
|
||
|
val paperAuthorAffiliations = paaf.join(step0, paaf("PaperId") === step0("PaperId"), "leftsemi")
|
||
|
|
||
|
val j1 = paperAuthorAffiliations
|
||
|
.join(authors, paperAuthorAffiliations("AuthorId") === authors("AuthorId"), "inner")
|
||
|
.select(
|
||
|
col("PaperId"),
|
||
|
col("AffiliationId"),
|
||
|
col("AuthorSequenceNumber"),
|
||
|
authors("DisplayName").alias("AuthorName"),
|
||
|
authors("AuthorId")
|
||
|
)
|
||
|
|
||
|
val paperAuthorAffiliationNormalized = j1
|
||
|
.join(affiliations, j1("AffiliationId") === affiliations("AffiliationId"), "left")
|
||
|
.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")
|
||
|
.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")
|
||
|
)
|
||
|
.select(
|
||
|
$"PaperId".as("paperId"),
|
||
|
$"Rank".as("rank"),
|
||
|
$"Doi".as("doi"),
|
||
|
$"DocType".as("docType"),
|
||
|
$"PaperTitle".as("paperTitle"),
|
||
|
$"OriginalTitle".as("originalTitle"),
|
||
|
$"BookTitle".as("bookTitle"),
|
||
|
$"Year".as("year"),
|
||
|
$"Date".as("date"),
|
||
|
$"OnlineDate".as("onlineDate"),
|
||
|
$"Publisher".as("publisher"),
|
||
|
$"JournalId".as("journalId"),
|
||
|
$"ConferenceSeriesId".as("conferenceSeriesId"),
|
||
|
$"ConferenceInstanceId".as("conferenceInstanceId"),
|
||
|
$"Volume".as("volume"),
|
||
|
$"Issue".as("issue"),
|
||
|
$"FirstPage".as("firstPage"),
|
||
|
$"LastPage".as("lastPage"),
|
||
|
$"ReferenceCount".as("referenceCount"),
|
||
|
$"CitationCount".as("citationCount"),
|
||
|
$"EstimatedCitation".as("estimatedCitation"),
|
||
|
$"OriginalVenue".as("originalVenue"),
|
||
|
$"FamilyId".as("familyId"),
|
||
|
$"FamilyRank".as("familyRank"),
|
||
|
$"DocSubTypes".as("docSubTypes"),
|
||
|
$"CreatedDate".as("createdDate"),
|
||
|
$"Abstract".as("abstractText"),
|
||
|
$"authors".as("authors"),
|
||
|
$"conferenceName".as("conferenceName"),
|
||
|
$"conferenceLocation".as("conferenceLocation"),
|
||
|
$"conferenceStartDate".as("conferenceStartDate"),
|
||
|
$"conferenceEndDate".as("conferenceEndDate"),
|
||
|
$"FoS".as("fos"),
|
||
|
$"journalName".as("journalName"),
|
||
|
$"journalIssn".as("journalIssn"),
|
||
|
$"journalPublisher".as("journalPublisher"),
|
||
|
$"journalWebpage".as("journalWebpage")
|
||
|
)
|
||
|
.write
|
||
|
.mode("OverWrite")
|
||
|
.save(s"$workingPath/mag")
|
||
|
step3.unpersist()
|
||
|
}
|
||
|
}
|
||
|
|
||
|
object SparkCreateMagDenormalizedTable {
|
||
|
|
||
|
val log: Logger = LoggerFactory.getLogger(SparkCreateMagDenormalizedTable.getClass)
|
||
|
|
||
|
def main(args: Array[String]): Unit = {
|
||
|
new SparkCreateMagDenormalizedTable(
|
||
|
"/eu/dnetlib/dhp/collection/mag/create_MAG_denormalized_table_properites.json",
|
||
|
args,
|
||
|
log
|
||
|
)
|
||
|
}
|
||
|
}
|