446 lines
13 KiB
Scala
446 lines
13 KiB
Scala
package eu.dnetlib.dhp.collection.mag
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.oaf.{Author, Journal, Publication}
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import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, PidType}
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils._
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import org.apache.spark.sql.types._
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import org.apache.spark.sql.{Dataset, Row, SparkSession}
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import org.json4s
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import org.json4s.DefaultFormats
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import org.json4s.jackson.JsonMethods.parse
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import scala.collection.JavaConverters._
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case class MAGPaper(
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paperId: Option[Long],
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doi: Option[String],
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docType: Option[String],
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paperTitle: Option[String],
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originalTitle: Option[String],
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bookTitle: Option[String],
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year: Option[Int],
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date: Option[String],
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onlineDate: Option[String],
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publisher: Option[String],
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// Journal or Conference information (one will be populated)
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journalId: Option[Long],
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journalName: Option[String],
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journalIssn: Option[String],
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journalPublisher: Option[String],
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conferenceSeriesId: Option[Long],
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conferenceInstanceId: Option[Long],
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conferenceName: Option[String],
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conferenceLocation: Option[String],
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conferenceStartDate: Option[String],
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conferenceEndDate: Option[String],
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volume: Option[String],
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issue: Option[String],
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firstPage: Option[String],
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lastPage: Option[String],
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referenceCount: Option[Long],
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citationCount: Option[Long],
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estimatedCitation: Option[Long],
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originalVenue: Option[String],
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familyId: Option[Long],
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familyRank: Option[Int],
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docSubTypes: Option[String],
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createdDate: Option[String],
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abstractText: Option[String],
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// List of authors
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authors: Option[List[MAGAuthor]],
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urls: Option[List[String]]
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)
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case class MAGAuthor(
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AffiliationId: Option[Long],
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AuthorSequenceNumber: Option[Int],
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AffiliationName: Option[String],
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AuthorName: Option[String],
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AuthorId: Option[Long],
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GridId: Option[String]
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)
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object MagUtility extends Serializable {
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val datatypedict = Map(
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"bool" -> BooleanType,
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"int" -> IntegerType,
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"uint" -> IntegerType,
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"long" -> LongType,
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"ulong" -> LongType,
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"float" -> FloatType,
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"string" -> StringType,
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"DateTime" -> DateType
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)
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val stream = Map(
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"Affiliations" -> Tuple2(
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"mag/Affiliations.txt",
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Seq(
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"AffiliationId:long",
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"Rank:uint",
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"NormalizedName:string",
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"DisplayName:string",
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"GridId:string",
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"OfficialPage:string",
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"WikiPage:string",
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"PaperCount:long",
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"PaperFamilyCount:long",
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"CitationCount:long",
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"Iso3166Code:string",
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"Latitude:float?",
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"Longitude:float?",
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"CreatedDate:DateTime"
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)
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),
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"AuthorExtendedAttributes" -> Tuple2(
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"mag/AuthorExtendedAttributes.txt",
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Seq("AuthorId:long", "AttributeType:int", "AttributeValue:string")
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),
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"Authors" -> Tuple2(
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"mag/Authors.txt",
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Seq(
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"AuthorId:long",
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"Rank:uint",
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"NormalizedName:string",
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"DisplayName:string",
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"LastKnownAffiliationId:long?",
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"PaperCount:long",
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"PaperFamilyCount:long",
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"CitationCount:long",
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"CreatedDate:DateTime"
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)
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),
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"ConferenceInstances" -> Tuple2(
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"mag/ConferenceInstances.txt",
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Seq(
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"ConferenceInstanceId:long",
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"NormalizedName:string",
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"DisplayName:string",
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"ConferenceSeriesId:long",
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"Location:string",
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"OfficialUrl:string",
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"StartDate:DateTime?",
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"EndDate:DateTime?",
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"AbstractRegistrationDate:DateTime?",
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"SubmissionDeadlineDate:DateTime?",
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"NotificationDueDate:DateTime?",
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"FinalVersionDueDate:DateTime?",
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"PaperCount:long",
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"PaperFamilyCount:long",
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"CitationCount:long",
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"Latitude:float?",
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"Longitude:float?",
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"CreatedDate:DateTime"
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)
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),
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"ConferenceSeries" -> Tuple2(
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"mag/ConferenceSeries.txt",
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Seq(
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"ConferenceSeriesId:long",
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"Rank:uint",
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"NormalizedName:string",
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"DisplayName:string",
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"PaperCount:long",
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"PaperFamilyCount:long",
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"CitationCount:long",
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"CreatedDate:DateTime"
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)
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),
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"EntityRelatedEntities" -> Tuple2(
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"advanced/EntityRelatedEntities.txt",
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Seq(
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"EntityId:long",
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"EntityType:string",
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"RelatedEntityId:long",
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"RelatedEntityType:string",
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"RelatedType:int",
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"Score:float"
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)
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),
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"FieldOfStudyChildren" -> Tuple2(
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"advanced/FieldOfStudyChildren.txt",
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Seq("FieldOfStudyId:long", "ChildFieldOfStudyId:long")
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),
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"FieldOfStudyExtendedAttributes" -> Tuple2(
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"advanced/FieldOfStudyExtendedAttributes.txt",
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Seq("FieldOfStudyId:long", "AttributeType:int", "AttributeValue:string")
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),
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"FieldsOfStudy" -> Tuple2(
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"advanced/FieldsOfStudy.txt",
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Seq(
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"FieldOfStudyId:long",
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"Rank:uint",
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"NormalizedName:string",
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"DisplayName:string",
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"MainType:string",
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"Level:int",
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"PaperCount:long",
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"PaperFamilyCount:long",
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"CitationCount:long",
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"CreatedDate:DateTime"
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)
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),
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"Journals" -> Tuple2(
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"mag/Journals.txt",
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Seq(
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"JournalId:long",
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"Rank:uint",
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"NormalizedName:string",
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"DisplayName:string",
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"Issn:string",
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"Publisher:string",
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"Webpage:string",
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"PaperCount:long",
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"PaperFamilyCount:long",
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"CitationCount:long",
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"CreatedDate:DateTime"
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)
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),
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"PaperAbstractsInvertedIndex" -> Tuple2(
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"nlp/PaperAbstractsInvertedIndex.txt.*",
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Seq("PaperId:long", "IndexedAbstract:string")
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),
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"PaperAuthorAffiliations" -> Tuple2(
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"mag/PaperAuthorAffiliations.txt",
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Seq(
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"PaperId:long",
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"AuthorId:long",
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"AffiliationId:long?",
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"AuthorSequenceNumber:uint",
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"OriginalAuthor:string",
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"OriginalAffiliation:string"
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)
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),
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"PaperCitationContexts" -> Tuple2(
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"nlp/PaperCitationContexts.txt",
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Seq("PaperId:long", "PaperReferenceId:long", "CitationContext:string")
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),
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"PaperExtendedAttributes" -> Tuple2(
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"mag/PaperExtendedAttributes.txt",
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Seq("PaperId:long", "AttributeType:int", "AttributeValue:string")
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),
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"PaperFieldsOfStudy" -> Tuple2(
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"advanced/PaperFieldsOfStudy.txt",
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Seq("PaperId:long", "FieldOfStudyId:long", "Score:float")
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),
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"PaperMeSH" -> Tuple2(
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"advanced/PaperMeSH.txt",
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Seq(
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"PaperId:long",
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"DescriptorUI:string",
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"DescriptorName:string",
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"QualifierUI:string",
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"QualifierName:string",
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"IsMajorTopic:bool"
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)
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),
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"PaperRecommendations" -> Tuple2(
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"advanced/PaperRecommendations.txt",
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Seq("PaperId:long", "RecommendedPaperId:long", "Score:float")
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),
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"PaperReferences" -> Tuple2(
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"mag/PaperReferences.txt",
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Seq("PaperId:long", "PaperReferenceId:long")
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),
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"PaperResources" -> Tuple2(
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"mag/PaperResources.txt",
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Seq(
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"PaperId:long",
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"ResourceType:int",
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"ResourceUrl:string",
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"SourceUrl:string",
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"RelationshipType:int"
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)
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),
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"PaperUrls" -> Tuple2(
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"mag/PaperUrls.txt",
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Seq("PaperId:long", "SourceType:int?", "SourceUrl:string", "LanguageCode:string")
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),
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"Papers" -> Tuple2(
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"mag/Papers.txt",
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Seq(
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"PaperId:long",
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"Rank:uint",
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"Doi:string",
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"DocType:string",
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"PaperTitle:string",
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"OriginalTitle:string",
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"BookTitle:string",
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"Year:int?",
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"Date:DateTime?",
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"OnlineDate:DateTime?",
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"Publisher:string",
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"JournalId:long?",
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"ConferenceSeriesId:long?",
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"ConferenceInstanceId:long?",
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"Volume:string",
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"Issue:string",
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"FirstPage:string",
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"LastPage:string",
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"ReferenceCount:long",
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"CitationCount:long",
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"EstimatedCitation:long",
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"OriginalVenue:string",
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"FamilyId:long?",
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"FamilyRank:uint?",
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"DocSubTypes:string",
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"CreatedDate:DateTime"
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)
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),
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"RelatedFieldOfStudy" -> Tuple2(
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"advanced/RelatedFieldOfStudy.txt",
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Seq(
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"FieldOfStudyId1:long",
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"Type1:string",
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"FieldOfStudyId2:long",
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"Type2:string",
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"Rank:float"
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)
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)
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)
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def getSchema(streamName: String): StructType = {
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var schema = new StructType()
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val d: Seq[String] = stream(streamName)._2
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d.foreach { case t =>
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val currentType = t.split(":")
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val fieldName: String = currentType.head
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var fieldType: String = currentType.last
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val nullable: Boolean = fieldType.endsWith("?")
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if (nullable)
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fieldType = fieldType.replace("?", "")
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schema = schema.add(StructField(fieldName, datatypedict(fieldType), nullable))
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}
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schema
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}
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def loadMagEntity(spark: SparkSession, entity: String, basePath: String): Dataset[Row] = {
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if (stream.contains(entity)) {
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val s = getSchema(entity)
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val pt = stream(entity)._1
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spark.read
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.option("header", "false")
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.option("charset", "UTF8")
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.option("delimiter", "\t")
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.schema(s)
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.csv(s"$basePath/$pt")
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} else
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null
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}
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def convertMAGtoOAF(paper: MAGPaper): Publication = {
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if (paper.doi.isDefined) {
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val pub = new Publication
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pub.setPid(
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List(
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structuredProperty(
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paper.doi.get,
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qualifier(
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PidType.doi.toString,
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PidType.doi.toString,
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ModelConstants.DNET_PID_TYPES,
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ModelConstants.DNET_PID_TYPES
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),
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null
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)
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).asJava
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)
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pub.setOriginalId(List(paper.paperId.get.toString, paper.doi.get).asJava)
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//IMPORTANT
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//The old method result.setId(generateIdentifier(result, doi))
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//will be replaced using IdentifierFactory
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pub.setId(IdentifierFactory.createDOIBoostIdentifier(pub))
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val mainTitles = structuredProperty(paper.originalTitle.get, ModelConstants.MAIN_TITLE_QUALIFIER, null)
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val originalTitles = structuredProperty(paper.paperTitle.get, ModelConstants.ALTERNATIVE_TITLE_QUALIFIER, null)
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pub.setTitle(List(mainTitles, originalTitles).asJava)
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if (paper.bookTitle.isDefined)
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pub.setSource(List(field[String](paper.bookTitle.get, null)).asJava)
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if (paper.abstractText.isDefined)
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pub.setDescription(List(field(paper.abstractText.get, null)).asJava)
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if (paper.authors.isDefined && paper.authors.get.nonEmpty) {
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pub.setAuthor(
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paper.authors.get
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.filter(a => a.AuthorName.isDefined)
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.map(a => {
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val author = new Author
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author.setFullname(a.AuthorName.get)
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if (a.AffiliationName.isDefined)
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author.setAffiliation(List(field(a.AffiliationName.get, null)).asJava)
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author.setPid(
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List(
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structuredProperty(
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s"https://academic.microsoft.com/#/detail/${a.AuthorId.get}",
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qualifier("url", "url", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES),
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null
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)
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).asJava
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)
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author
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})
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.asJava
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)
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}
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if (paper.date.isDefined)
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pub.setDateofacceptance(field(paper.date.get, null))
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if (paper.publisher.isDefined)
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pub.setPublisher(field(paper.publisher.get, null))
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if (paper.journalId.isDefined && paper.journalName.isDefined) {
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val j = new Journal
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j.setName(paper.journalName.get)
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j.setSp(paper.firstPage.orNull)
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j.setEp(paper.lastPage.orNull)
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if (paper.publisher.isDefined)
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pub.setPublisher(field(paper.publisher.get, null))
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j.setIssnPrinted(paper.journalIssn.orNull)
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j.setVol(paper.volume.orNull)
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j.setIss(paper.issue.orNull)
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j.setConferenceplace(paper.conferenceLocation.orNull)
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j.setEdition(paper.conferenceName.orNull)
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pub.setJournal(j)
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}
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pub
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} else {
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null
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}
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}
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def convertInvertedIndexString(json_input: String): String = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: json4s.JValue = parse(json_input)
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val idl = (json \ "IndexLength").extract[Int]
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if (idl > 0) {
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val res = Array.ofDim[String](idl)
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val iid = (json \ "InvertedIndex").extract[Map[String, List[Int]]]
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for { (k: String, v: List[Int]) <- iid } {
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v.foreach(item => res(item) = k)
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}
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(0 until idl).foreach(i => {
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if (res(i) == null)
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res(i) = ""
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})
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return res.mkString(" ")
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}
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""
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}
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}
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