Implemented first part of the new MAG mapping
This commit is contained in:
Sandro La Bruzzo
parent
73a67c0e4a
commit
6f3e925cae
|
|
@ -1,7 +1,7 @@
|
|||
package eu.dnetlib.dhp.collection.crossref
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
|
||||
import eu.dnetlib.dhp.actionmanager.ror.GenerateRorActionSetJob
|
||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf._
|
||||
|
|
@ -15,6 +15,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.{
|
|||
}
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import org.apache.commons.lang.StringUtils
|
||||
import org.apache.spark.sql.Row
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.JsonAST._
|
||||
|
|
@ -650,6 +651,33 @@ case object Crossref2Oaf {
|
|||
r
|
||||
}
|
||||
|
||||
def generateAffliation(input: Row): List[String] = {
|
||||
val doi = input.getString(0)
|
||||
val rorId = input.getString(1)
|
||||
|
||||
val pubId = s"50|${PidType.doi.toString.padTo(12, "_")}::${DoiCleaningRule.normalizeDoi(doi)}"
|
||||
val affId = GenerateRorActionSetJob.calculateOpenaireId(rorId)
|
||||
|
||||
val r: Relation = new Relation
|
||||
DoiCleaningRule.clean(doi)
|
||||
r.setSource(pubId)
|
||||
r.setTarget(affId)
|
||||
r.setRelType(ModelConstants.RESULT_ORGANIZATION)
|
||||
r.setRelClass(ModelConstants.HAS_AUTHOR_INSTITUTION)
|
||||
r.setSubRelType(ModelConstants.AFFILIATION)
|
||||
r.setDataInfo(generateDataInfo())
|
||||
r.setCollectedfrom(List(createCrossrefCollectedFrom()).asJava)
|
||||
val r1: Relation = new Relation
|
||||
r1.setTarget(pubId)
|
||||
r1.setSource(affId)
|
||||
r1.setRelType(ModelConstants.RESULT_ORGANIZATION)
|
||||
r1.setRelClass(ModelConstants.IS_AUTHOR_INSTITUTION_OF)
|
||||
r1.setSubRelType(ModelConstants.AFFILIATION)
|
||||
r1.setDataInfo(generateDataInfo())
|
||||
r1.setCollectedfrom(List(createCrossrefCollectedFrom()).asJava)
|
||||
List(mapper.writeValueAsString(r), mapper.writeValueAsString(r1))
|
||||
}
|
||||
|
||||
def convert(input: String, vocabularies: VocabularyGroup, mode: TransformationType): List[Oaf] = {
|
||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||
lazy val json: json4s.JValue = parse(input)
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
|||
import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result, Dataset => OafDataset}
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory
|
||||
import org.apache.spark.sql._
|
||||
import org.apache.spark.sql.functions.{col, lower}
|
||||
import org.apache.spark.sql.functions.{col, explode, lower}
|
||||
import org.apache.spark.sql.types._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
|
|
@ -104,6 +104,22 @@ class SparkMapDumpIntoOAF(propertyPath: String, args: Array[String], log: Logger
|
|||
.mode(SaveMode.Append)
|
||||
.option("compression", "gzip")
|
||||
.text(s"$targetPath")
|
||||
|
||||
// Generate affiliation relations:
|
||||
spark.read
|
||||
.json(sourcePath)
|
||||
.select(col("DOI"), explode(col("author.affiliation")).alias("affiliations"))
|
||||
.select(col("DOI"), explode(col("affiliations.id")).alias("aids"))
|
||||
.where("aids is not null")
|
||||
.select(col("DOI"), explode(col("aids")).alias("aff"))
|
||||
.select(col("DOI"), col("aff.id").alias("id"), col("aff.id-type").alias("idType"))
|
||||
.where(col("idType").like("ROR"))
|
||||
.flatMap(r => Crossref2Oaf.generateAffliation(r))
|
||||
.write
|
||||
.mode(SaveMode.Append)
|
||||
.option("compression", "gzip")
|
||||
.text(s"$targetPath")
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,9 +1,12 @@
|
|||
package eu.dnetlib.dhp.collection.mag
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf.{Author, Journal, Publication}
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, PidType}
|
||||
import eu.dnetlib.dhp.schema.oaf
|
||||
import eu.dnetlib.dhp.schema.oaf.{ Dataset => OafDataset, Author, DataInfo, Instance, Journal, Publication, Qualifier, Result}
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils, PidType}
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils._
|
||||
import eu.dnetlib.dhp.utils
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import org.apache.spark.sql.types._
|
||||
import org.apache.spark.sql.{Dataset, Row, SparkSession}
|
||||
import org.json4s
|
||||
|
|
@ -304,14 +307,15 @@ object MagUtility extends Serializable {
|
|||
def getSchema(streamName: String): StructType = {
|
||||
var schema = new StructType()
|
||||
val d: Seq[String] = stream(streamName)._2
|
||||
d.foreach { case t =>
|
||||
val currentType = t.split(":")
|
||||
val fieldName: String = currentType.head
|
||||
var fieldType: String = currentType.last
|
||||
val nullable: Boolean = fieldType.endsWith("?")
|
||||
if (nullable)
|
||||
fieldType = fieldType.replace("?", "")
|
||||
schema = schema.add(StructField(fieldName, datatypedict(fieldType), nullable))
|
||||
d.foreach {
|
||||
case t =>
|
||||
val currentType = t.split(":")
|
||||
val fieldName: String = currentType.head
|
||||
var fieldType: String = currentType.last
|
||||
val nullable: Boolean = fieldType.endsWith("?")
|
||||
if (nullable)
|
||||
fieldType = fieldType.replace("?", "")
|
||||
schema = schema.add(StructField(fieldName, datatypedict(fieldType), nullable))
|
||||
}
|
||||
schema
|
||||
}
|
||||
|
|
@ -331,12 +335,152 @@ object MagUtility extends Serializable {
|
|||
|
||||
}
|
||||
|
||||
def getInstanceType(magType: Option[String], source: Option[String]): Result = {
|
||||
|
||||
|
||||
|
||||
var result:Result = null
|
||||
val di = new DataInfo
|
||||
di.setDeletedbyinference(false)
|
||||
di.setInferred(false)
|
||||
di.setInvisible(false)
|
||||
di.setTrust("0.9")
|
||||
di.setProvenanceaction(
|
||||
OafMapperUtils.qualifier(
|
||||
ModelConstants.SYSIMPORT_ACTIONSET,
|
||||
ModelConstants.SYSIMPORT_ACTIONSET,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS
|
||||
)
|
||||
)
|
||||
if (magType== null) {
|
||||
result = new Publication
|
||||
result.setDataInfo(di)
|
||||
val i =new Instance
|
||||
i.setInstancetype(qualifier(
|
||||
"0038",
|
||||
"Other literature type",
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE
|
||||
))
|
||||
|
||||
result.setInstance(List(i).asJava)
|
||||
return result
|
||||
}
|
||||
|
||||
val currentType: String = magType.get
|
||||
|
||||
val tp = currentType.toLowerCase match {
|
||||
case "book" =>
|
||||
result = new Publication
|
||||
qualifier("0002", "Book", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)
|
||||
case "bookchapter" =>
|
||||
result = new Publication
|
||||
qualifier(
|
||||
"00013",
|
||||
"Part of book or chapter of book",
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE
|
||||
)
|
||||
case "journal" =>
|
||||
result = new Publication
|
||||
qualifier("0043", "Journal", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)
|
||||
case "patent" =>
|
||||
if (source.nonEmpty) {
|
||||
val s = source.get.toLowerCase
|
||||
if (s.contains("patent") || s.contains("brevet")) {
|
||||
result = new Publication
|
||||
qualifier(
|
||||
"0019",
|
||||
"Patent",
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE
|
||||
)
|
||||
} else if (s.contains("journal of")) {
|
||||
result = new Publication
|
||||
qualifier(
|
||||
"0043",
|
||||
"Journal",
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE
|
||||
)
|
||||
} else if (s.contains("proceedings") || s.contains("conference") || s.contains("workshop") || s.contains(
|
||||
"symposium"
|
||||
)) {
|
||||
result = new Publication
|
||||
qualifier(
|
||||
"0001",
|
||||
"Article",
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE
|
||||
)
|
||||
} else null
|
||||
} else null
|
||||
|
||||
case "repository" =>
|
||||
result = new Publication()
|
||||
di.setInvisible(true)
|
||||
qualifier(
|
||||
"0038",
|
||||
"Other literature type",
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE
|
||||
)
|
||||
|
||||
case "thesis" =>
|
||||
result = new Publication
|
||||
qualifier(
|
||||
"0044",
|
||||
"Thesis",
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE
|
||||
)
|
||||
case "dataset" =>
|
||||
result = new OafDataset
|
||||
qualifier(
|
||||
"0021",
|
||||
"Dataset",
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE
|
||||
)
|
||||
case "conference" =>
|
||||
result = new Publication
|
||||
qualifier(
|
||||
"0001",
|
||||
"Article",
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE
|
||||
)
|
||||
}
|
||||
|
||||
if (result != null) {
|
||||
result.setDataInfo(di)
|
||||
val i =new Instance
|
||||
i.setInstancetype(tp)
|
||||
result.setInstance(List(i).asJava)
|
||||
}
|
||||
result
|
||||
|
||||
}
|
||||
|
||||
def convertMAGtoOAF(paper: MAGPaper): Publication = {
|
||||
val pub = new Publication
|
||||
|
||||
val magPid = structuredProperty(
|
||||
paper.doi.get,
|
||||
qualifier(
|
||||
PidType.mag_id.toString,
|
||||
PidType.mag_id.toString,
|
||||
ModelConstants.DNET_PID_TYPES,
|
||||
ModelConstants.DNET_PID_TYPES
|
||||
),
|
||||
null
|
||||
)
|
||||
|
||||
if (paper.doi.isDefined) {
|
||||
val pub = new Publication
|
||||
pub.setPid(
|
||||
List(
|
||||
magPid,
|
||||
structuredProperty(
|
||||
paper.doi.get,
|
||||
qualifier(
|
||||
|
|
@ -349,76 +493,65 @@ object MagUtility extends Serializable {
|
|||
)
|
||||
).asJava
|
||||
)
|
||||
|
||||
pub.setOriginalId(List(paper.paperId.get.toString, paper.doi.get).asJava)
|
||||
} else {
|
||||
pub.setPid(
|
||||
List(
|
||||
magPid
|
||||
).asJava
|
||||
)
|
||||
pub.setOriginalId(List(paper.paperId.get.toString).asJava)
|
||||
}
|
||||
|
||||
//IMPORTANT
|
||||
//The old method result.setId(generateIdentifier(result, doi))
|
||||
//will be replaced using IdentifierFactory
|
||||
pub.setId(IdentifierFactory.createDOIBoostIdentifier(pub))
|
||||
pub.setId(s"50|mag_________::${DHPUtils.md5(paper.paperId.get.toString)}")
|
||||
|
||||
val mainTitles = structuredProperty(paper.originalTitle.get, ModelConstants.MAIN_TITLE_QUALIFIER, null)
|
||||
val mainTitles = structuredProperty(paper.originalTitle.get, ModelConstants.MAIN_TITLE_QUALIFIER, null)
|
||||
|
||||
val originalTitles = structuredProperty(paper.paperTitle.get, ModelConstants.ALTERNATIVE_TITLE_QUALIFIER, null)
|
||||
val originalTitles = structuredProperty(paper.paperTitle.get, ModelConstants.ALTERNATIVE_TITLE_QUALIFIER, null)
|
||||
|
||||
pub.setTitle(List(mainTitles, originalTitles).asJava)
|
||||
pub.setTitle(List(mainTitles, originalTitles).asJava)
|
||||
|
||||
if (paper.bookTitle.isDefined)
|
||||
pub.setSource(List(field[String](paper.bookTitle.get, null)).asJava)
|
||||
if (paper.abstractText.isDefined)
|
||||
pub.setDescription(List(field(paper.abstractText.get, null)).asJava)
|
||||
if (paper.authors.isDefined && paper.authors.get.nonEmpty) {
|
||||
pub.setAuthor(
|
||||
paper.authors.get
|
||||
.filter(a => a.AuthorName.isDefined)
|
||||
.map(a => {
|
||||
val author = new Author
|
||||
author.setFullname(a.AuthorName.get)
|
||||
if (a.AffiliationName.isDefined)
|
||||
author.setAffiliation(List(field(a.AffiliationName.get, null)).asJava)
|
||||
author.setPid(
|
||||
List(
|
||||
structuredProperty(
|
||||
s"https://academic.microsoft.com/#/detail/${a.AuthorId.get}",
|
||||
qualifier("url", "url", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES),
|
||||
null
|
||||
)
|
||||
).asJava
|
||||
)
|
||||
author
|
||||
})
|
||||
.asJava
|
||||
)
|
||||
if (paper.bookTitle.isDefined)
|
||||
pub.setSource(List(field[String](paper.bookTitle.get, null)).asJava)
|
||||
if (paper.abstractText.isDefined)
|
||||
pub.setDescription(List(field(paper.abstractText.get, null)).asJava)
|
||||
if (paper.authors.isDefined && paper.authors.get.nonEmpty) {
|
||||
pub.setAuthor(
|
||||
paper.authors.get
|
||||
.filter(a => a.AuthorName.isDefined)
|
||||
.map(a => {
|
||||
val author = new Author
|
||||
author.setFullname(a.AuthorName.get)
|
||||
author
|
||||
})
|
||||
.asJava
|
||||
)
|
||||
}
|
||||
|
||||
}
|
||||
if (paper.date.isDefined)
|
||||
pub.setDateofacceptance(field(paper.date.get, null))
|
||||
|
||||
if (paper.date.isDefined)
|
||||
pub.setDateofacceptance(field(paper.date.get, null))
|
||||
if (paper.publisher.isDefined)
|
||||
pub.setPublisher(field(paper.publisher.get, null))
|
||||
|
||||
if (paper.journalId.isDefined && paper.journalName.isDefined) {
|
||||
val j = new Journal
|
||||
|
||||
j.setName(paper.journalName.get)
|
||||
j.setSp(paper.firstPage.orNull)
|
||||
j.setEp(paper.lastPage.orNull)
|
||||
if (paper.publisher.isDefined)
|
||||
pub.setPublisher(field(paper.publisher.get, null))
|
||||
|
||||
if (paper.journalId.isDefined && paper.journalName.isDefined) {
|
||||
val j = new Journal
|
||||
|
||||
j.setName(paper.journalName.get)
|
||||
j.setSp(paper.firstPage.orNull)
|
||||
j.setEp(paper.lastPage.orNull)
|
||||
if (paper.publisher.isDefined)
|
||||
pub.setPublisher(field(paper.publisher.get, null))
|
||||
j.setIssnPrinted(paper.journalIssn.orNull)
|
||||
j.setVol(paper.volume.orNull)
|
||||
j.setIss(paper.issue.orNull)
|
||||
j.setConferenceplace(paper.conferenceLocation.orNull)
|
||||
j.setEdition(paper.conferenceName.orNull)
|
||||
pub.setJournal(j)
|
||||
}
|
||||
|
||||
pub
|
||||
} else {
|
||||
null
|
||||
j.setIssnPrinted(paper.journalIssn.orNull)
|
||||
j.setVol(paper.volume.orNull)
|
||||
j.setIss(paper.issue.orNull)
|
||||
j.setConferenceplace(paper.conferenceLocation.orNull)
|
||||
j.setEdition(paper.conferenceName.orNull)
|
||||
pub.setJournal(j)
|
||||
}
|
||||
|
||||
pub
|
||||
|
||||
}
|
||||
|
||||
def convertInvertedIndexString(json_input: String): String = {
|
||||
|
|
|
|||
|
|
@ -2,13 +2,11 @@ package eu.dnetlib.dhp.collection.crossref
|
|||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
|
||||
import org.apache.spark.sql.SparkSession
|
||||
import org.junit.jupiter.api.{BeforeEach, Test}
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.io.Source
|
||||
|
||||
@ExtendWith(Array(classOf[MockitoExtension]))
|
||||
class CrossrefMappingTest extends AbstractVocabularyTest {
|
||||
|
|
@ -21,21 +19,6 @@ class CrossrefMappingTest extends AbstractVocabularyTest {
|
|||
super.setUpVocabulary()
|
||||
}
|
||||
|
||||
def testMapping(): Unit = {
|
||||
val spark = SparkSession.builder().master("local[*]").appName("TransformCrossref").getOrCreate()
|
||||
|
||||
val s = new SparkMapDumpIntoOAF(null, null, null)
|
||||
import spark.implicits._
|
||||
|
||||
s.transformCrossref(
|
||||
spark,
|
||||
sourcePath = "/home/sandro/Downloads/crossref",
|
||||
targetPath = "/home/sandro/Downloads/crossref_transformed",
|
||||
unpaywallPath = null,
|
||||
vocabularies = vocabularies
|
||||
)
|
||||
|
||||
print(spark.read.text("/home/sandro/Downloads/crossref_transformed").count)
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,15 +1,19 @@
|
|||
package eu.dnetlib.dhp.collection.mag
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.schema.oaf.{Dataset, Publication, Result}
|
||||
import org.apache.spark.sql.SparkSession
|
||||
import org.apache.spark.sql.functions.col
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.Assertions._
|
||||
|
||||
|
||||
|
||||
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