292 lines
12 KiB
Scala
292 lines
12 KiB
Scala
package eu.dnetlib.dhp.sx.graph
|
|
|
|
import eu.dnetlib.dhp.application.AbstractScalaApplication
|
|
import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations
|
|
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
|
import eu.dnetlib.dhp.datacite.{DataciteToOAFTransformation, DataciteType}
|
|
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
|
|
import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixResource}
|
|
import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
|
|
import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils
|
|
import eu.dnetlib.dhp.utils.{DHPUtils, ISLookupClientFactory}
|
|
import org.apache.spark.sql.functions.max
|
|
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
|
import org.slf4j.Logger
|
|
|
|
import scala.collection.JavaConverters._
|
|
import java.text.SimpleDateFormat
|
|
|
|
class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:Logger) extends AbstractScalaApplication(propertyPath, args, log:Logger) {
|
|
|
|
val ISO_DATE_PATTERN = "yyyy-MM-dd'T'HH:mm:ssZ"
|
|
val simpleFormatter = new SimpleDateFormat(ISO_DATE_PATTERN)
|
|
|
|
val SCHOLIX_RESOURCE_PATH_NAME = "scholixResource"
|
|
val DATACITE_OAF_PATH_NAME = "dataciteOAFUpdate"
|
|
val PID_MAP_PATH_NAME = "pidMap"
|
|
val RESOLVED_REL_PATH_NAME ="resolvedRelation"
|
|
val SCHOLIX_PATH_NAME = "scholix"
|
|
|
|
|
|
def scholixResourcePath(workingPath:String) = s"$workingPath/$SCHOLIX_RESOURCE_PATH_NAME"
|
|
def dataciteOAFPath(workingPath:String) = s"$workingPath/$DATACITE_OAF_PATH_NAME"
|
|
def pidMapPath(workingPath:String) = s"$workingPath/$PID_MAP_PATH_NAME"
|
|
def resolvedRelationPath(workingPath:String) = s"$workingPath/$RESOLVED_REL_PATH_NAME"
|
|
def scholixPath(workingPath:String) = s"$workingPath/$SCHOLIX_PATH_NAME"
|
|
|
|
|
|
/**
|
|
* Utility to parse Date in ISO8601 to epochMillis
|
|
* @param inputDate The String represents an input date in ISO8601
|
|
* @return The relative epochMillis of parsed date
|
|
*/
|
|
def ISO8601toEpochMillis(inputDate:String):Long = {
|
|
simpleFormatter.parse(inputDate).getTime
|
|
}
|
|
|
|
|
|
/**
|
|
* This method tries to retrieve the last collection date from all datacite
|
|
* records in HDFS.
|
|
* This method should be called before indexing scholexplorer to retrieve
|
|
* the delta of Datacite record to download, since from the generation of
|
|
* raw graph to the generation of Scholexplorer sometimes it takes 20 days
|
|
* @param spark
|
|
* @param entitiesPath
|
|
* @return the last collection date from the current scholexplorer Graph of the datacite records
|
|
*/
|
|
def retrieveLastCollectedFrom(spark:SparkSession, entitiesPath:String):Long = {
|
|
log.info("Retrieve last entities collected From")
|
|
|
|
implicit val oafEncoder:Encoder[Result] = Encoders.kryo[Result]
|
|
import spark.implicits._
|
|
|
|
val entitiesDS = spark.read.load(s"$entitiesPath/*").as[Result]
|
|
|
|
val date = entitiesDS.filter(r => r.getDateofcollection!= null).map(_.getDateofcollection).select(max("value")).first.getString(0)
|
|
|
|
ISO8601toEpochMillis(date)
|
|
}
|
|
|
|
|
|
/**
|
|
* The method of update Datacite relationships on Scholexplorer
|
|
* needs some utilities data structures
|
|
* One is the scholixResource DS that stores all the nodes in the Scholix Graph
|
|
* in format (dnetID, ScholixResource )
|
|
* @param summaryPath the path of the summary in Scholix
|
|
* @param workingPath the working path
|
|
* @param spark the spark session
|
|
*/
|
|
def generateScholixResource(summaryPath:String, workingPath: String, spark:SparkSession) :Unit = {
|
|
implicit val summaryEncoder:Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
|
|
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
|
|
|
|
log.info("Convert All summary to ScholixResource")
|
|
spark.read.load(summaryPath).as[ScholixSummary]
|
|
.map(ScholixUtils.generateScholixResourceFromSummary)
|
|
.filter(r => r.getIdentifier!= null && r.getIdentifier.size>0)
|
|
.map(r=> (r.getIdentifier,r))(Encoders.tuple(Encoders.STRING, scholixResourceEncoder))
|
|
.write.mode(SaveMode.Overwrite).save(scholixResourcePath(workingPath))
|
|
|
|
}
|
|
|
|
|
|
/**
|
|
* This method get and Transform only datacite records with
|
|
* timestamp greater than timestamp
|
|
* @param datacitePath the datacite input Path
|
|
* @param timestamp the timestamp
|
|
* @param workingPath the working path where save the generated Dataset
|
|
* @param spark SparkSession
|
|
* @param vocabularies Vocabularies needed for transformation
|
|
*/
|
|
|
|
def getDataciteUpdate(datacitePath:String, timestamp:Long, workingPath:String, spark:SparkSession,vocabularies: VocabularyGroup): Unit = {
|
|
import spark.implicits._
|
|
val ds = spark.read.load(datacitePath).as[DataciteType]
|
|
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
|
ds.filter(_.timestamp>=timestamp)
|
|
.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks = true))
|
|
.flatMap(i => fixRelations(i)).filter(i => i != null)
|
|
.write.mode(SaveMode.Overwrite).save(dataciteOAFPath(workingPath))
|
|
|
|
}
|
|
|
|
|
|
/**
|
|
* This method convert an Instance of OAF Result into
|
|
* Scholix Resource
|
|
* @param r The input Result
|
|
* @return The Scholix Resource
|
|
*/
|
|
def resultToScholixResource(r:Result):ScholixResource = {
|
|
ScholixUtils.generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
|
|
}
|
|
|
|
|
|
/**
|
|
* After added the new ScholixResource, we need to update the scholix Pid Map
|
|
* to intersected with the new Datacite Relations
|
|
|
|
* @param workingPath The working Path starting from save the new Map
|
|
* @param spark the spark session
|
|
*/
|
|
def generatePidMap(workingPath:String, spark:SparkSession ) :Unit = {
|
|
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
|
|
import spark.implicits._
|
|
spark.read.load(scholixResourcePath(workingPath)).as[(String,ScholixResource)]
|
|
.flatMap(r=>
|
|
r._2.getIdentifier.asScala
|
|
.map(i =>DHPUtils.generateUnresolvedIdentifier(i.getIdentifier, i.getSchema))
|
|
.map((_, r._1))
|
|
)(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
|
.groupByKey(_._1)
|
|
.reduceGroups((a,b) => if (a!= null && a._2!= null) a else b)
|
|
.map(_._2)(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
|
.write.mode(SaveMode.Overwrite).save(pidMapPath(workingPath))
|
|
}
|
|
|
|
/**
|
|
* This method convert the new Datacite Resource into Scholix Resource
|
|
* Needed to fill the source and the type of Scholix Relationships
|
|
* @param workingPath the Working Path
|
|
* @param spark The spark Session
|
|
*/
|
|
def addMissingScholixResource(workingPath:String, spark:SparkSession ) :Unit = {
|
|
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
|
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
|
|
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
|
|
|
|
spark.read.load(dataciteOAFPath(workingPath)).as[Oaf]
|
|
.filter(_.isInstanceOf[Result])
|
|
.map(_.asInstanceOf[Result])
|
|
.map(resultToScholixResource)
|
|
.filter(r => r.getIdentifier!= null && r.getIdentifier.size>0)
|
|
.map(r=> (r.getIdentifier,r))(Encoders.tuple(Encoders.STRING, scholixResourceEncoder))
|
|
.write.mode(SaveMode.Append).save(scholixResourcePath(workingPath))
|
|
}
|
|
|
|
|
|
/**
|
|
* This method resolve the datacite relation and filter the resolved
|
|
* relation
|
|
* @param workingPath the working path
|
|
* @param spark the spark session
|
|
*/
|
|
|
|
def resolveUpdateRelation(workingPath:String, spark:SparkSession) :Unit = {
|
|
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
|
implicit val relationEncoder:Encoder[Relation] = Encoders.kryo[Relation]
|
|
import spark.implicits._
|
|
|
|
val pidMap = spark.read.load(pidMapPath(workingPath)).as[(String,String)]
|
|
|
|
val unresolvedRelations:Dataset[(String,Relation)] = spark.read.load(dataciteOAFPath(workingPath)).as[Oaf]
|
|
.filter(_.isInstanceOf[Relation])
|
|
.map(_.asInstanceOf[Relation])
|
|
.map { r =>
|
|
if (r.getSource.startsWith("unresolved"))
|
|
(r.getSource, r)
|
|
else
|
|
(r.getTarget, r)
|
|
}(Encoders.tuple(Encoders.STRING, relationEncoder))
|
|
|
|
unresolvedRelations
|
|
.joinWith(pidMap, unresolvedRelations("_1").equalTo(pidMap("_1")))
|
|
.map(t => {
|
|
val r =t._1._2
|
|
val resolvedIdentifier = t._2._2
|
|
if (r.getSource.startsWith("unresolved"))
|
|
r.setSource(resolvedIdentifier)
|
|
else
|
|
r.setTarget(resolvedIdentifier)
|
|
r
|
|
})(relationEncoder)
|
|
.filter(r => !(r.getSource.startsWith("unresolved") || r.getTarget.startsWith("unresolved") ))
|
|
.write.mode(SaveMode.Overwrite)
|
|
.save(resolvedRelationPath(workingPath))
|
|
}
|
|
|
|
|
|
|
|
/**
|
|
* This method generate scholix starting from resolved relation
|
|
*
|
|
*
|
|
* @param workingPath
|
|
* @param spark
|
|
*/
|
|
def generateScholixUpdate(workingPath:String, spark:SparkSession) :Unit = {
|
|
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
|
implicit val scholixEncoder:Encoder[Scholix] = Encoders.kryo[Scholix]
|
|
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
|
|
implicit val relationEncoder:Encoder[Relation] = Encoders.kryo[Relation]
|
|
import spark.implicits._
|
|
|
|
val relationss:Dataset[(String, Relation)] = spark.read.load(s"$workingPath/ResolvedRelation").as[Relation].map(r =>(r.getSource,r))(Encoders.tuple(Encoders.STRING, relationEncoder))
|
|
|
|
val id_summary:Dataset[(String,ScholixResource)] = spark.read.load(scholixResourcePath(workingPath)).as[(String,ScholixResource)]
|
|
|
|
relationss.joinWith(id_summary, relationss("_1").equalTo(id_summary("_1")),"inner")
|
|
.map(t => (t._1._2.getTarget,ScholixUtils.scholixFromSource(t._1._2, t._2._2)))(Encoders.tuple(Encoders.STRING, scholixEncoder))
|
|
.write.mode(SaveMode.Overwrite)
|
|
.save(s"$workingPath/scholix_one_verse")
|
|
|
|
val source_scholix:Dataset[(String,Scholix)] = spark.read.load(s"$workingPath/scholix_one_verse").as[(String,Scholix)]
|
|
|
|
source_scholix.joinWith(id_summary, source_scholix("_1").equalTo(id_summary("_1")),"inner")
|
|
.map(t => {
|
|
val target = t._2._2
|
|
val scholix = t._1._2
|
|
scholix.setTarget(target)
|
|
scholix
|
|
})(scholixEncoder).write.mode(SaveMode.Overwrite).save(s"$workingPath/scholix")
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
/**
|
|
* Here all the spark applications runs this method
|
|
* where the whole logic of the spark node is defined
|
|
*/
|
|
override def run(): Unit = {
|
|
val sourcePath = parser.get("sourcePath")
|
|
log.info(s"SourcePath is '$sourcePath'")
|
|
|
|
val datacitePath = parser.get("datacitePath")
|
|
log.info(s"DatacitePath is '$datacitePath'")
|
|
|
|
val workingPath = parser.get("workingPath")
|
|
log.info(s"workingPath is '$workingPath'")
|
|
|
|
val isLookupUrl: String = parser.get("isLookupUrl")
|
|
log.info("isLookupUrl: {}", isLookupUrl)
|
|
|
|
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
|
|
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
|
|
require(vocabularies != null)
|
|
|
|
|
|
val updateDS:Boolean = "true".equalsIgnoreCase(parser.get("updateDS"))
|
|
log.info(s"updateDS is '$updateDS'")
|
|
|
|
var lastCollectionDate = 0L
|
|
if (updateDS) {
|
|
generateScholixResource(s"$sourcePath/provision/summaries", workingPath, spark)
|
|
log.info("Retrieve last entities collected From starting from scholix Graph")
|
|
lastCollectionDate = retrieveLastCollectedFrom(spark, s"$sourcePath/entities")
|
|
}
|
|
|
|
getDataciteUpdate(datacitePath, lastCollectionDate, workingPath, spark, vocabularies)
|
|
addMissingScholixResource(workingPath,spark)
|
|
generatePidMap(workingPath, spark)
|
|
resolveUpdateRelation(workingPath,spark)
|
|
generateScholixUpdate(workingPath, spark)
|
|
|
|
|
|
}
|
|
}
|