[scholexplorer]
- implemented generation of scholix of delta update of datacitepull/176/head
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63952018c0
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package eu.dnetlib.dhp.sx.graph
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import eu.dnetlib.dhp.application.AbstractScalaApplication
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import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
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import eu.dnetlib.dhp.datacite.{DataciteToOAFTransformation, DataciteType}
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
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import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixResource}
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import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
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import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils
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import eu.dnetlib.dhp.utils.{DHPUtils, ISLookupClientFactory}
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import org.apache.spark.sql.functions.max
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.slf4j.Logger
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import scala.collection.JavaConverters._
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import java.text.SimpleDateFormat
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class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:Logger) extends AbstractScalaApplication(propertyPath, args, log:Logger) {
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val ISO_DATE_PATTERN = "yyyy-MM-dd'T'HH:mm:ssZ"
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val simpleFormatter = new SimpleDateFormat(ISO_DATE_PATTERN)
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val SCHOLIX_RESOURCE_PATH_NAME = "scholixResource"
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val DATACITE_OAF_PATH_NAME = "dataciteOAFUpdate"
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val PID_MAP_PATH_NAME = "pidMap"
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val RESOLVED_REL_PATH_NAME ="resolvedRelation"
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val SCHOLIX_PATH_NAME = "scholix"
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def scholixResourcePath(workingPath:String) = s"$workingPath/$SCHOLIX_RESOURCE_PATH_NAME"
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def dataciteOAFPath(workingPath:String) = s"$workingPath/$DATACITE_OAF_PATH_NAME"
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def pidMapPath(workingPath:String) = s"$workingPath/$PID_MAP_PATH_NAME"
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def resolvedRelationPath(workingPath:String) = s"$workingPath/$RESOLVED_REL_PATH_NAME"
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def scholixPath(workingPath:String) = s"$workingPath/$SCHOLIX_PATH_NAME"
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/**
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* Utility to parse Date in ISO8601 to epochMillis
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* @param inputDate The String represents an input date in ISO8601
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* @return The relative epochMillis of parsed date
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*/
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def ISO8601toEpochMillis(inputDate:String):Long = {
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simpleFormatter.parse(inputDate).getTime
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}
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/**
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* This method tries to retrieve the last collection date from all datacite
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* records in HDFS.
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* This method should be called before indexing scholexplorer to retrieve
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* the delta of Datacite record to download, since from the generation of
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* raw graph to the generation of Scholexplorer sometimes it takes 20 days
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* @param spark
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* @param entitiesPath
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* @return the last collection date from the current scholexplorer Graph of the datacite records
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*/
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def retrieveLastCollectedFrom(spark:SparkSession, entitiesPath:String):Long = {
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log.info("Retrieve last entities collected From")
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implicit val oafEncoder:Encoder[Result] = Encoders.kryo[Result]
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import spark.implicits._
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val entitiesDS = spark.read.load(s"$entitiesPath/*").as[Result]
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val date = entitiesDS.filter(r => r.getDateofcollection!= null).map(_.getDateofcollection).select(max("value")).first.getString(0)
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ISO8601toEpochMillis(date)
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}
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/**
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* The method of update Datacite relationships on Scholexplorer
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* needs some utilities data structures
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* One is the scholixResource DS that stores all the nodes in the Scholix Graph
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* in format (dnetID, ScholixResource )
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* @param summaryPath the path of the summary in Scholix
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* @param workingPath the working path
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* @param spark the spark session
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*/
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def generateScholixResource(summaryPath:String, workingPath: String, spark:SparkSession) :Unit = {
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implicit val summaryEncoder:Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
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implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
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log.info("Convert All summary to ScholixResource")
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spark.read.load(summaryPath).as[ScholixSummary]
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.map(ScholixUtils.generateScholixResourceFromSummary)
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.filter(r => r.getIdentifier!= null && r.getIdentifier.size>0)
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.map(r=> (r.getIdentifier,r))(Encoders.tuple(Encoders.STRING, scholixResourceEncoder))
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.write.mode(SaveMode.Overwrite).save(scholixResourcePath(workingPath))
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}
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/**
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* This method get and Transform only datacite records with
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* timestamp greater than timestamp
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* @param datacitePath the datacite input Path
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* @param timestamp the timestamp
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* @param workingPath the working path where save the generated Dataset
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* @param spark SparkSession
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* @param vocabularies Vocabularies needed for transformation
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*/
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def getDataciteUpdate(datacitePath:String, timestamp:Long, workingPath:String, spark:SparkSession,vocabularies: VocabularyGroup): Unit = {
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import spark.implicits._
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val ds = spark.read.load(datacitePath).as[DataciteType]
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implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
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ds.filter(_.timestamp>=timestamp)
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.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks = true))
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.flatMap(i => fixRelations(i)).filter(i => i != null)
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.write.mode(SaveMode.Overwrite).save(dataciteOAFPath(workingPath))
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}
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/**
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* This method convert an Instance of OAF Result into
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* Scholix Resource
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* @param r The input Result
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* @return The Scholix Resource
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*/
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def resultToScholixResource(r:Result):ScholixResource = {
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ScholixUtils.generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
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}
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/**
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* After added the new ScholixResource, we need to update the scholix Pid Map
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* to intersected with the new Datacite Relations
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* @param workingPath The working Path starting from save the new Map
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* @param spark the spark session
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*/
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def generatePidMap(workingPath:String, spark:SparkSession ) :Unit = {
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implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
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import spark.implicits._
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spark.read.load(scholixResourcePath(workingPath)).as[(String,ScholixResource)]
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.flatMap(r=>
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r._2.getIdentifier.asScala
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.map(i =>DHPUtils.generateUnresolvedIdentifier(i.getIdentifier, i.getSchema))
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.map((_, r._1))
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)(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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.groupByKey(_._1)
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.reduceGroups((a,b) => if (a!= null && a._2!= null) a else b)
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.map(_._2)(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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.write.mode(SaveMode.Overwrite).save(pidMapPath(workingPath))
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}
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/**
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* This method convert the new Datacite Resource into Scholix Resource
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* Needed to fill the source and the type of Scholix Relationships
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* @param workingPath the Working Path
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* @param spark The spark Session
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*/
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def addMissingScholixResource(workingPath:String, spark:SparkSession ) :Unit = {
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implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
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implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
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implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
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spark.read.load(dataciteOAFPath(workingPath)).as[Oaf]
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.filter(_.isInstanceOf[Result])
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.map(_.asInstanceOf[Result])
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.map(resultToScholixResource)
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.filter(r => r.getIdentifier!= null && r.getIdentifier.size>0)
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.map(r=> (r.getIdentifier,r))(Encoders.tuple(Encoders.STRING, scholixResourceEncoder))
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.write.mode(SaveMode.Append).save(scholixResourcePath(workingPath))
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}
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/**
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* This method resolve the datacite relation and filter the resolved
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* relation
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* @param workingPath the working path
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* @param spark the spark session
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*/
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def resolveUpdateRelation(workingPath:String, spark:SparkSession) :Unit = {
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implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
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implicit val relationEncoder:Encoder[Relation] = Encoders.kryo[Relation]
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import spark.implicits._
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val pidMap = spark.read.load(pidMapPath(workingPath)).as[(String,String)]
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val unresolvedRelations:Dataset[(String,Relation)] = spark.read.load(dataciteOAFPath(workingPath)).as[Oaf]
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.filter(_.isInstanceOf[Relation])
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.map(_.asInstanceOf[Relation])
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.map { r =>
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if (r.getSource.startsWith("unresolved"))
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(r.getSource, r)
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else
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(r.getTarget, r)
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}(Encoders.tuple(Encoders.STRING, relationEncoder))
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unresolvedRelations
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.joinWith(pidMap, unresolvedRelations("_1").equalTo(pidMap("_1")))
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.map(t => {
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val r =t._1._2
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val resolvedIdentifier = t._2._2
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if (r.getSource.startsWith("unresolved"))
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r.setSource(resolvedIdentifier)
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else
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r.setTarget(resolvedIdentifier)
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r
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})(relationEncoder)
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.filter(r => !(r.getSource.startsWith("unresolved") || r.getTarget.startsWith("unresolved") ))
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.write.mode(SaveMode.Overwrite)
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.save(resolvedRelationPath(workingPath))
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}
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/**
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* This method generate scholix starting from resolved relation
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*
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*
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* @param workingPath
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* @param spark
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*/
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def generateScholixUpdate(workingPath:String, spark:SparkSession) :Unit = {
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implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
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implicit val scholixEncoder:Encoder[Scholix] = Encoders.kryo[Scholix]
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implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
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implicit val relationEncoder:Encoder[Relation] = Encoders.kryo[Relation]
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import spark.implicits._
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val relationss:Dataset[(String, Relation)] = spark.read.load(s"$workingPath/ResolvedRelation").as[Relation].map(r =>(r.getSource,r))(Encoders.tuple(Encoders.STRING, relationEncoder))
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val id_summary:Dataset[(String,ScholixResource)] = spark.read.load(scholixResourcePath(workingPath)).as[(String,ScholixResource)]
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relationss.joinWith(id_summary, relationss("_1").equalTo(id_summary("_1")),"inner")
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.map(t => (t._1._2.getTarget,ScholixUtils.scholixFromSource(t._1._2, t._2._2)))(Encoders.tuple(Encoders.STRING, scholixEncoder))
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.write.mode(SaveMode.Overwrite)
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.save(s"$workingPath/scholix_one_verse")
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val source_scholix:Dataset[(String,Scholix)] = spark.read.load(s"$workingPath/scholix_one_verse").as[(String,Scholix)]
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source_scholix.joinWith(id_summary, source_scholix("_1").equalTo(id_summary("_1")),"inner")
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.map(t => {
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val target = t._2._2
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val scholix = t._1._2
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scholix.setTarget(target)
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scholix
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})(scholixEncoder).write.mode(SaveMode.Overwrite).save(s"$workingPath/scholix")
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}
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/**
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* Here all the spark applications runs this method
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* where the whole logic of the spark node is defined
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*/
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override def run(): Unit = {
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val sourcePath = parser.get("sourcePath")
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log.info(s"SourcePath is '$sourcePath'")
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val datacitePath = parser.get("datacitePath")
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log.info(s"DatacitePath is '$datacitePath'")
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val workingPath = parser.get("workingPath")
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log.info(s"workingPath is '$workingPath'")
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val isLookupUrl: String = parser.get("isLookupUrl")
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log.info("isLookupUrl: {}", isLookupUrl)
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val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
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val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
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require(vocabularies != null)
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val updateDS:Boolean = "true".equalsIgnoreCase(parser.get("updateDS"))
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log.info(s"updateDS is '$updateDS'")
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var lastCollectionDate = 0L
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if (updateDS) {
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generateScholixResource(s"$sourcePath/provision/summaries", workingPath, spark)
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log.info("Retrieve last entities collected From starting from scholix Graph")
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lastCollectionDate = retrieveLastCollectedFrom(spark, s"$sourcePath/entities")
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}
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getDataciteUpdate(datacitePath, lastCollectionDate, workingPath, spark, vocabularies)
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addMissingScholixResource(workingPath,spark)
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generatePidMap(workingPath, spark)
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resolveUpdateRelation(workingPath,spark)
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generateScholixUpdate(workingPath, spark)
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}
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}
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@ -1,54 +0,0 @@
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package eu.dnetlib.dhp.sx.graph
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import eu.dnetlib.dhp.application.AbstractScalaApplication
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import eu.dnetlib.dhp.schema.oaf.Result
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import org.apache.spark.sql.functions.max
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import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
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import org.slf4j.Logger
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class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:Logger) extends AbstractScalaApplication(propertyPath, args, log:Logger) {
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def retrieveLastCollectedFrom(spark:SparkSession, entitiesPath:String):String = {
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log.info("Retrieve last entities collected From")
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implicit val oafEncoder:Encoder[Result] = Encoders.kryo[Result]
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import spark.implicits._
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val entitiesDS = spark.read.load(s"$entitiesPath/*").as[Result]
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entitiesDS.filter(r => r.getDateofcollection!= null).map(_.getDateofcollection).select(max("value")).first.getString(0)
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}
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/**
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* Here all the spark applications runs this method
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* where the whole logic of the spark node is defined
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*/
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override def run(): Unit = {
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val sourcePath = parser.get("sourcePath")
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log.info(s"SourcePath is '$sourcePath'")
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val datacitePath = parser.get("datacitePath")
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log.info(s"DatacitePath is '$datacitePath'")
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log.info("Retrieve last entities collected From")
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implicit val oafEncoder:Encoder[Result] = Encoders.kryo[Result]
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val lastCollectionDate = retrieveLastCollectedFrom(spark, s"$sourcePath/entities")
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}
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}
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@ -0,0 +1,26 @@
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package eu.dnetlib.dhp.sx.graph
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import org.junit.jupiter.api.Test
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import java.text.SimpleDateFormat
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class RetrieveDataciteDeltaTest {
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@Test
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def testParsingDate(): Unit = {
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val inputDate = "2021-12-02T11:17:36+0000"
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val t = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ").parse(inputDate).getTime
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println(t)
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}
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}
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