forked from D-Net/dnet-hadoop
Implemented first part of the new MAG mapping
This commit is contained in:
Sandro La Bruzzo
parent
73a67c0e4a
commit
6f3e925cae
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@ -1,7 +1,7 @@
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package eu.dnetlib.dhp.collection.crossref
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.actionmanager.ror.GenerateRorActionSetJob
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.oaf._
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@ -15,6 +15,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.{
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}
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import eu.dnetlib.dhp.utils.DHPUtils
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import org.apache.commons.lang.StringUtils
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import org.apache.spark.sql.Row
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import org.json4s
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import org.json4s.DefaultFormats
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import org.json4s.JsonAST._
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@ -650,6 +651,33 @@ case object Crossref2Oaf {
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r
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}
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def generateAffliation(input: Row): List[String] = {
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val doi = input.getString(0)
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val rorId = input.getString(1)
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val pubId = s"50|${PidType.doi.toString.padTo(12, "_")}::${DoiCleaningRule.normalizeDoi(doi)}"
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val affId = GenerateRorActionSetJob.calculateOpenaireId(rorId)
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val r: Relation = new Relation
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DoiCleaningRule.clean(doi)
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r.setSource(pubId)
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r.setTarget(affId)
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r.setRelType(ModelConstants.RESULT_ORGANIZATION)
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r.setRelClass(ModelConstants.HAS_AUTHOR_INSTITUTION)
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r.setSubRelType(ModelConstants.AFFILIATION)
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r.setDataInfo(generateDataInfo())
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r.setCollectedfrom(List(createCrossrefCollectedFrom()).asJava)
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val r1: Relation = new Relation
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r1.setTarget(pubId)
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r1.setSource(affId)
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r1.setRelType(ModelConstants.RESULT_ORGANIZATION)
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r1.setRelClass(ModelConstants.IS_AUTHOR_INSTITUTION_OF)
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r1.setSubRelType(ModelConstants.AFFILIATION)
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r1.setDataInfo(generateDataInfo())
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r1.setCollectedfrom(List(createCrossrefCollectedFrom()).asJava)
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List(mapper.writeValueAsString(r), mapper.writeValueAsString(r1))
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}
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def convert(input: String, vocabularies: VocabularyGroup, mode: TransformationType): List[Oaf] = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: json4s.JValue = parse(input)
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@ -7,7 +7,7 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result, Dataset => OafDataset}
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import eu.dnetlib.dhp.utils.ISLookupClientFactory
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import org.apache.spark.sql._
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import org.apache.spark.sql.functions.{col, lower}
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import org.apache.spark.sql.functions.{col, explode, lower}
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import org.apache.spark.sql.types._
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import org.slf4j.{Logger, LoggerFactory}
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@ -104,6 +104,22 @@ class SparkMapDumpIntoOAF(propertyPath: String, args: Array[String], log: Logger
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.mode(SaveMode.Append)
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.option("compression", "gzip")
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.text(s"$targetPath")
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// Generate affiliation relations:
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spark.read
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.json(sourcePath)
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.select(col("DOI"), explode(col("author.affiliation")).alias("affiliations"))
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.select(col("DOI"), explode(col("affiliations.id")).alias("aids"))
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.where("aids is not null")
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.select(col("DOI"), explode(col("aids")).alias("aff"))
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.select(col("DOI"), col("aff.id").alias("id"), col("aff.id-type").alias("idType"))
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.where(col("idType").like("ROR"))
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.flatMap(r => Crossref2Oaf.generateAffliation(r))
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.write
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.mode(SaveMode.Append)
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.option("compression", "gzip")
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.text(s"$targetPath")
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}
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}
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@ -1,9 +1,12 @@
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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
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import eu.dnetlib.dhp.schema.oaf.{ Dataset => OafDataset, Author, DataInfo, Instance, Journal, Publication, Qualifier, Result}
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import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils, PidType}
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils._
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import eu.dnetlib.dhp.utils
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import eu.dnetlib.dhp.utils.DHPUtils
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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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@ -304,14 +307,15 @@ object MagUtility extends Serializable {
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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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d.foreach {
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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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@ -331,12 +335,152 @@ object MagUtility extends Serializable {
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}
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def getInstanceType(magType: Option[String], source: Option[String]): Result = {
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var result:Result = null
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val di = new DataInfo
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di.setDeletedbyinference(false)
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di.setInferred(false)
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di.setInvisible(false)
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di.setTrust("0.9")
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di.setProvenanceaction(
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OafMapperUtils.qualifier(
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ModelConstants.SYSIMPORT_ACTIONSET,
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ModelConstants.SYSIMPORT_ACTIONSET,
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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ModelConstants.DNET_PROVENANCE_ACTIONS
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)
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)
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if (magType== null) {
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result = new Publication
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result.setDataInfo(di)
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val i =new Instance
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i.setInstancetype(qualifier(
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"0038",
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"Other literature type",
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ModelConstants.DNET_PUBLICATION_RESOURCE,
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ModelConstants.DNET_PUBLICATION_RESOURCE
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))
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result.setInstance(List(i).asJava)
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return result
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}
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val currentType: String = magType.get
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val tp = currentType.toLowerCase match {
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case "book" =>
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result = new Publication
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qualifier("0002", "Book", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)
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case "bookchapter" =>
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result = new Publication
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qualifier(
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"00013",
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"Part of book or chapter of book",
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ModelConstants.DNET_PUBLICATION_RESOURCE,
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ModelConstants.DNET_PUBLICATION_RESOURCE
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)
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case "journal" =>
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result = new Publication
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qualifier("0043", "Journal", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)
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case "patent" =>
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if (source.nonEmpty) {
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val s = source.get.toLowerCase
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if (s.contains("patent") || s.contains("brevet")) {
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result = new Publication
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qualifier(
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"0019",
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"Patent",
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ModelConstants.DNET_PUBLICATION_RESOURCE,
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ModelConstants.DNET_PUBLICATION_RESOURCE
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)
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} else if (s.contains("journal of")) {
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result = new Publication
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qualifier(
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"0043",
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"Journal",
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ModelConstants.DNET_PUBLICATION_RESOURCE,
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ModelConstants.DNET_PUBLICATION_RESOURCE
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)
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} else if (s.contains("proceedings") || s.contains("conference") || s.contains("workshop") || s.contains(
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"symposium"
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)) {
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result = new Publication
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qualifier(
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"0001",
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"Article",
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ModelConstants.DNET_PUBLICATION_RESOURCE,
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ModelConstants.DNET_PUBLICATION_RESOURCE
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)
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} else null
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} else null
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case "repository" =>
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result = new Publication()
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di.setInvisible(true)
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qualifier(
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"0038",
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"Other literature type",
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ModelConstants.DNET_PUBLICATION_RESOURCE,
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ModelConstants.DNET_PUBLICATION_RESOURCE
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)
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case "thesis" =>
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result = new Publication
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qualifier(
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"0044",
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"Thesis",
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ModelConstants.DNET_PUBLICATION_RESOURCE,
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ModelConstants.DNET_PUBLICATION_RESOURCE
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)
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case "dataset" =>
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result = new OafDataset
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qualifier(
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"0021",
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"Dataset",
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ModelConstants.DNET_PUBLICATION_RESOURCE,
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ModelConstants.DNET_PUBLICATION_RESOURCE
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)
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case "conference" =>
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result = new Publication
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qualifier(
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"0001",
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"Article",
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ModelConstants.DNET_PUBLICATION_RESOURCE,
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ModelConstants.DNET_PUBLICATION_RESOURCE
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)
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}
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if (result != null) {
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result.setDataInfo(di)
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val i =new Instance
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i.setInstancetype(tp)
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result.setInstance(List(i).asJava)
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}
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result
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}
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def convertMAGtoOAF(paper: MAGPaper): Publication = {
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val pub = new Publication
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val magPid = structuredProperty(
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paper.doi.get,
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qualifier(
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PidType.mag_id.toString,
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PidType.mag_id.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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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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magPid,
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structuredProperty(
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paper.doi.get,
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qualifier(
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@ -349,76 +493,65 @@ object MagUtility extends Serializable {
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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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} else {
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pub.setPid(
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List(
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magPid
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).asJava
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)
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pub.setOriginalId(List(paper.paperId.get.toString).asJava)
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}
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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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pub.setId(s"50|mag_________::${DHPUtils.md5(paper.paperId.get.toString)}")
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val mainTitles = structuredProperty(paper.originalTitle.get, ModelConstants.MAIN_TITLE_QUALIFIER, null)
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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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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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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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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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author
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})
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.asJava
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)
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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.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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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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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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}
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def convertInvertedIndexString(json_input: String): String = {
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|
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@ -2,13 +2,11 @@ package eu.dnetlib.dhp.collection.crossref
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
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import org.apache.spark.sql.SparkSession
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import org.junit.jupiter.api.{BeforeEach, Test}
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import org.junit.jupiter.api.BeforeEach
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import org.junit.jupiter.api.extension.ExtendWith
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import org.mockito.junit.jupiter.MockitoExtension
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import org.slf4j.{Logger, LoggerFactory}
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import scala.io.Source
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@ExtendWith(Array(classOf[MockitoExtension]))
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class CrossrefMappingTest extends AbstractVocabularyTest {
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@ -21,21 +19,6 @@ class CrossrefMappingTest extends AbstractVocabularyTest {
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super.setUpVocabulary()
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}
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def testMapping(): Unit = {
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val spark = SparkSession.builder().master("local[*]").appName("TransformCrossref").getOrCreate()
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val s = new SparkMapDumpIntoOAF(null, null, null)
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import spark.implicits._
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s.transformCrossref(
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spark,
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sourcePath = "/home/sandro/Downloads/crossref",
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targetPath = "/home/sandro/Downloads/crossref_transformed",
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unpaywallPath = null,
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vocabularies = vocabularies
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)
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print(spark.read.text("/home/sandro/Downloads/crossref_transformed").count)
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}
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}
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|
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@ -1,15 +1,19 @@
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package eu.dnetlib.dhp.collection.mag
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.schema.oaf.{Dataset, Publication, Result}
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import org.apache.spark.sql.SparkSession
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import org.apache.spark.sql.functions.col
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import org.junit.jupiter.api.Test
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import org.junit.jupiter.api.Assertions._
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|
||||
|
||||
|
||||
class MAGMappingTest {
|
||||
|
||||
val mapper = new ObjectMapper()
|
||||
|
||||
@Test
|
||||
|
||||
def mappingTest(): Unit = {
|
||||
|
||||
val spark = SparkSession
|
||||
|
|
@ -28,4 +32,60 @@ class MAGMappingTest {
|
|||
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Test
|
||||
def mappingMagType(): Unit = {
|
||||
/*
|
||||
+-----------+--------+
|
||||
| docType| count|
|
||||
+-----------+--------+
|
||||
| null|79939635|
|
||||
|BookChapter| 2431452|
|
||||
| Dataset| 123923|
|
||||
| Repository| 5044165|
|
||||
| Thesis| 5525681|
|
||||
| Conference| 5196866|
|
||||
| Journal|89452763|
|
||||
| Book| 4460017|
|
||||
| Patent|64631955|
|
||||
+-----------+--------+
|
||||
|
||||
"instancetype":{
|
||||
"classid":"0001",
|
||||
"classname":"Article",
|
||||
"schemeid":"dnet:publication_resource",
|
||||
"schemename":"dnet:publication_resource"},"instanceTypeMapping":[{"originalType":"journal-article","typeCode":null,"typeLabel":null,"vocabularyName":"openaire::coar_resource_types_3_1"}
|
||||
|
||||
*/
|
||||
|
||||
checkResult[Publication](MagUtility.getInstanceType(null, null), invisible = false,"Other literature type")
|
||||
checkResult[Publication](MagUtility.getInstanceType(Some("BookChapter"), null), invisible = false,"Part of book or chapter of book")
|
||||
checkResult[Publication](MagUtility.getInstanceType(Some("Book"), null), invisible = false,"Book")
|
||||
checkResult[Publication](MagUtility.getInstanceType(Some("Repository"), null), invisible = true,"Other literature type")
|
||||
checkResult[Publication](MagUtility.getInstanceType(Some("Thesis"), null), invisible = false,"Thesis")
|
||||
checkResult[Publication](MagUtility.getInstanceType(Some("Conference"), null), invisible = false,"Article")
|
||||
checkResult[Publication](MagUtility.getInstanceType(Some("Journal"), null), invisible = false,"Journal")
|
||||
checkResult[Dataset](MagUtility.getInstanceType(Some("Dataset"), null), invisible = false,"Dataset")
|
||||
checkResult[Publication](MagUtility.getInstanceType(Some("Patent"), Some("Patent Department of the Navy")), invisible = false,"Patent")
|
||||
checkResult[Dataset](MagUtility.getInstanceType(Some("Dataset"), null), invisible = false,"Dataset")
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
def checkResult[T](r:Result, invisible:Boolean, typeName:String): Unit = {
|
||||
|
||||
assertNotNull(r)
|
||||
assertTrue(r.isInstanceOf[T])
|
||||
assertNotNull(r.getDataInfo)
|
||||
assertEquals( invisible ,r.getDataInfo.getInvisible)
|
||||
assertNotNull(r.getInstance())
|
||||
assertTrue(r.getInstance().size()>0)
|
||||
assertNotNull(r.getInstance().get(0).getInstancetype)
|
||||
assertEquals(typeName, r.getInstance().get(0).getInstancetype.getClassname)
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue