Fixed workflow generation of delta in datacite
This commit is contained in:
parent
b881ee5ef8
commit
3920d68992
|
@ -12,7 +12,7 @@ import org.json4s.jackson.JsonMethods.parse
|
||||||
import scala.collection.JavaConverters._
|
import scala.collection.JavaConverters._
|
||||||
import scala.io.Source
|
import scala.io.Source
|
||||||
|
|
||||||
object ScholixUtils {
|
object ScholixUtils extends Serializable {
|
||||||
|
|
||||||
|
|
||||||
val DNET_IDENTIFIER_SCHEMA: String = "DNET Identifier"
|
val DNET_IDENTIFIER_SCHEMA: String = "DNET Identifier"
|
||||||
|
@ -24,7 +24,7 @@ object ScholixUtils {
|
||||||
case class RelatedEntities(id: String, relatedDataset: Long, relatedPublication: Long) {}
|
case class RelatedEntities(id: String, relatedDataset: Long, relatedPublication: Long) {}
|
||||||
|
|
||||||
val relations: Map[String, RelationVocabulary] = {
|
val relations: Map[String, RelationVocabulary] = {
|
||||||
val input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/relations.json")).mkString
|
val input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/scholexplorer/relation/relations.json")).mkString
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||||
|
|
||||||
lazy val json: json4s.JValue = parse(input)
|
lazy val json: json4s.JValue = parse(input)
|
||||||
|
@ -62,6 +62,11 @@ object ScholixUtils {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
def generateScholixResourceFromResult(r:Result) :ScholixResource = {
|
||||||
|
generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] = new Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] with Serializable {
|
val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] = new Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] with Serializable {
|
||||||
override def zero: RelatedEntities = null
|
override def zero: RelatedEntities = null
|
||||||
|
|
||||||
|
@ -184,6 +189,19 @@ object ScholixUtils {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
def generateCompleteScholix(scholix: Scholix, target: ScholixResource): Scholix = {
|
||||||
|
val s = new Scholix
|
||||||
|
s.setPublicationDate(scholix.getPublicationDate)
|
||||||
|
s.setPublisher(scholix.getPublisher)
|
||||||
|
s.setLinkprovider(scholix.getLinkprovider)
|
||||||
|
s.setRelationship(scholix.getRelationship)
|
||||||
|
s.setSource(scholix.getSource)
|
||||||
|
s.setTarget(target)
|
||||||
|
s.setIdentifier(DHPUtils.md5(s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}"))
|
||||||
|
s
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
def generateScholixResourceFromSummary(summaryObject: ScholixSummary): ScholixResource = {
|
def generateScholixResourceFromSummary(summaryObject: ScholixSummary): ScholixResource = {
|
||||||
val r = new ScholixResource
|
val r = new ScholixResource
|
||||||
r.setIdentifier(summaryObject.getLocalIdentifier)
|
r.setIdentifier(summaryObject.getLocalIdentifier)
|
||||||
|
|
|
@ -0,0 +1,19 @@
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>jobTracker</name>
|
||||||
|
<value>yarnRM</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>nameNode</name>
|
||||||
|
<value>hdfs://nameservice1</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.use.system.libpath</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.action.sharelib.for.spark</name>
|
||||||
|
<value>spark2</value>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
</configuration>
|
|
@ -0,0 +1,62 @@
|
||||||
|
<workflow-app name="Retrieve Scholix Update" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>sourcePath</name>
|
||||||
|
<description>the source path of scholix graph</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>datacitePath</name>
|
||||||
|
<description>the datacite native path</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>workingSupportPath</name>
|
||||||
|
<description>the working Support path</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>isLookupUrl</name>
|
||||||
|
<description>The IS lookUp service endopoint</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>updateDS</name>
|
||||||
|
<value>false</value>
|
||||||
|
<description>The transformation Rule to apply</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<start to="RetrieveDeltaDatacite"/>
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
<action name="RetrieveDeltaDatacite">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>New Update from Datacite to Scholix</name>
|
||||||
|
<class>eu.dnetlib.dhp.sx.graph.SparkRetrieveDataciteDelta</class>
|
||||||
|
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.shuffle.partitions=6000
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||||
|
<arg>--datacitePath</arg><arg>${datacitePath}</arg>
|
||||||
|
<arg>--master</arg><arg>yarn</arg>
|
||||||
|
<arg>--workingSupportPath</arg><arg>${workingSupportPath}</arg>
|
||||||
|
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||||
|
<arg>--updateDS</arg><arg>${updateDS}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
|
|
||||||
|
</workflow-app>
|
|
@ -0,0 +1,41 @@
|
||||||
|
[
|
||||||
|
{
|
||||||
|
"paramName": "s",
|
||||||
|
"paramLongName": "sourcePath",
|
||||||
|
"paramDescription": "the source mdstore path",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
|
||||||
|
{
|
||||||
|
"paramName": "d",
|
||||||
|
"paramLongName": "datacitePath",
|
||||||
|
"paramDescription": "the datacite native path",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
|
||||||
|
{
|
||||||
|
"paramName": "w",
|
||||||
|
"paramLongName": "workingSupportPath",
|
||||||
|
"paramDescription": "the working Support path",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "i",
|
||||||
|
"paramLongName": "isLookupUrl",
|
||||||
|
"paramDescription": "the isLookup URL",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "m",
|
||||||
|
"paramLongName": "master",
|
||||||
|
"paramDescription": "the master name",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "u",
|
||||||
|
"paramLongName": "updateDS",
|
||||||
|
"paramDescription": "Need to regenerate all support Dataset",
|
||||||
|
"paramRequired": false
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
|
@ -9,9 +9,10 @@ import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixResource}
|
||||||
import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
|
import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
|
||||||
import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils
|
import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils
|
||||||
import eu.dnetlib.dhp.utils.{DHPUtils, ISLookupClientFactory}
|
import eu.dnetlib.dhp.utils.{DHPUtils, ISLookupClientFactory}
|
||||||
|
import org.apache.hadoop.fs.{FileSystem, Path}
|
||||||
import org.apache.spark.sql.functions.max
|
import org.apache.spark.sql.functions.max
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||||
import org.slf4j.Logger
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
import scala.collection.JavaConverters._
|
import scala.collection.JavaConverters._
|
||||||
import java.text.SimpleDateFormat
|
import java.text.SimpleDateFormat
|
||||||
|
@ -58,14 +59,15 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
|
||||||
def retrieveLastCollectedFrom(spark:SparkSession, entitiesPath:String):Long = {
|
def retrieveLastCollectedFrom(spark:SparkSession, entitiesPath:String):Long = {
|
||||||
log.info("Retrieve last entities collected From")
|
log.info("Retrieve last entities collected From")
|
||||||
|
|
||||||
implicit val oafEncoder:Encoder[Result] = Encoders.kryo[Result]
|
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||||
|
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
|
|
||||||
val entitiesDS = spark.read.load(s"$entitiesPath/*").as[Result]
|
val entitiesDS = spark.read.load(s"$entitiesPath/*").as[Oaf].filter(o =>o.isInstanceOf[Result]).map(r => r.asInstanceOf[Result])
|
||||||
|
|
||||||
val date = entitiesDS.filter(r => r.getDateofcollection!= null).map(_.getDateofcollection).select(max("value")).first.getString(0)
|
val date = entitiesDS.filter(r => r.getDateofcollection!= null).map(_.getDateofcollection).select(max("value")).first.getString(0)
|
||||||
|
|
||||||
ISO8601toEpochMillis(date)
|
ISO8601toEpochMillis(date) / 1000
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
@ -73,7 +75,7 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
|
||||||
* The method of update Datacite relationships on Scholexplorer
|
* The method of update Datacite relationships on Scholexplorer
|
||||||
* needs some utilities data structures
|
* needs some utilities data structures
|
||||||
* One is the scholixResource DS that stores all the nodes in the Scholix Graph
|
* One is the scholixResource DS that stores all the nodes in the Scholix Graph
|
||||||
* in format (dnetID, ScholixResource )
|
* in format ScholixResource
|
||||||
* @param summaryPath the path of the summary in Scholix
|
* @param summaryPath the path of the summary in Scholix
|
||||||
* @param workingPath the working path
|
* @param workingPath the working path
|
||||||
* @param spark the spark session
|
* @param spark the spark session
|
||||||
|
@ -84,11 +86,37 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
|
||||||
|
|
||||||
log.info("Convert All summary to ScholixResource")
|
log.info("Convert All summary to ScholixResource")
|
||||||
spark.read.load(summaryPath).as[ScholixSummary]
|
spark.read.load(summaryPath).as[ScholixSummary]
|
||||||
.map(ScholixUtils.generateScholixResourceFromSummary)
|
.map(ScholixUtils.generateScholixResourceFromSummary)(scholixResourceEncoder)
|
||||||
.filter(r => r.getIdentifier!= null && r.getIdentifier.size>0)
|
.filter(r => r.getIdentifier!= null && r.getIdentifier.size>0)
|
||||||
.map(r=> (r.getIdentifier,r))(Encoders.tuple(Encoders.STRING, scholixResourceEncoder))
|
.write.mode(SaveMode.Overwrite).save(s"${scholixResourcePath(workingPath)}_native")
|
||||||
.write.mode(SaveMode.Overwrite).save(scholixResourcePath(workingPath))
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* This method convert the new Datacite Resource into Scholix Resource
|
||||||
|
* Needed to fill the source and the type of Scholix Relationships
|
||||||
|
* @param workingPath the Working Path
|
||||||
|
* @param spark The spark Session
|
||||||
|
*/
|
||||||
|
def addMissingScholixResource(workingPath:String, spark:SparkSession ) :Unit = {
|
||||||
|
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||||
|
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
|
||||||
|
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
|
||||||
|
import spark.implicits._
|
||||||
|
|
||||||
|
spark.read.load(dataciteOAFPath(workingPath)).as[Oaf]
|
||||||
|
.filter(_.isInstanceOf[Result])
|
||||||
|
.map(_.asInstanceOf[Result])
|
||||||
|
.map(ScholixUtils.generateScholixResourceFromResult)
|
||||||
|
.filter(r => r.getIdentifier!= null && r.getIdentifier.size>0)
|
||||||
|
.write.mode(SaveMode.Overwrite).save(s"${scholixResourcePath(workingPath)}_update")
|
||||||
|
|
||||||
|
val update = spark.read.load(s"${scholixResourcePath(workingPath)}_update").as[ScholixResource]
|
||||||
|
val native = spark.read.load(s"${scholixResourcePath(workingPath)}_native").as[ScholixResource]
|
||||||
|
val graph = update.union(native)
|
||||||
|
.groupByKey(_.getDnetIdentifier)
|
||||||
|
.reduceGroups((a,b) => if (a!= null && a.getDnetIdentifier!= null) a else b)
|
||||||
|
.map(_._2)
|
||||||
|
graph.write.mode(SaveMode.Overwrite).save(s"${scholixResourcePath(workingPath)}_graph")
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
@ -102,29 +130,20 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
|
||||||
* @param vocabularies Vocabularies needed for transformation
|
* @param vocabularies Vocabularies needed for transformation
|
||||||
*/
|
*/
|
||||||
|
|
||||||
def getDataciteUpdate(datacitePath:String, timestamp:Long, workingPath:String, spark:SparkSession,vocabularies: VocabularyGroup): Unit = {
|
def getDataciteUpdate(datacitePath:String, timestamp:Long, workingPath:String, spark:SparkSession,vocabularies: VocabularyGroup): Long = {
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
val ds = spark.read.load(datacitePath).as[DataciteType]
|
val ds = spark.read.load(datacitePath).as[DataciteType]
|
||||||
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||||
|
val total = ds.filter(_.timestamp>=timestamp).count()
|
||||||
|
if (total >0) {
|
||||||
ds.filter(_.timestamp >= timestamp)
|
ds.filter(_.timestamp >= timestamp)
|
||||||
.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks = true))
|
.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks = true))
|
||||||
.flatMap(i => fixRelations(i)).filter(i => i != null)
|
.flatMap(i => fixRelations(i)).filter(i => i != null)
|
||||||
.write.mode(SaveMode.Overwrite).save(dataciteOAFPath(workingPath))
|
.write.mode(SaveMode.Overwrite).save(dataciteOAFPath(workingPath))
|
||||||
|
|
||||||
}
|
}
|
||||||
|
total
|
||||||
|
|
||||||
/**
|
|
||||||
* 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
|
* After added the new ScholixResource, we need to update the scholix Pid Map
|
||||||
* to intersected with the new Datacite Relations
|
* to intersected with the new Datacite Relations
|
||||||
|
@ -135,11 +154,11 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
|
||||||
def generatePidMap(workingPath:String, spark:SparkSession ) :Unit = {
|
def generatePidMap(workingPath:String, spark:SparkSession ) :Unit = {
|
||||||
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
|
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
|
||||||
import spark.implicits._
|
import spark.implicits._
|
||||||
spark.read.load(scholixResourcePath(workingPath)).as[(String,ScholixResource)]
|
spark.read.load(s"${scholixResourcePath(workingPath)}_graph").as[ScholixResource]
|
||||||
.flatMap(r=>
|
.flatMap(r=>
|
||||||
r._2.getIdentifier.asScala
|
r.getIdentifier.asScala
|
||||||
.map(i =>DHPUtils.generateUnresolvedIdentifier(i.getIdentifier, i.getSchema))
|
.map(i =>DHPUtils.generateUnresolvedIdentifier(i.getIdentifier, i.getSchema))
|
||||||
.map((_, r._1))
|
.map(t =>(t, r.getDnetIdentifier))
|
||||||
)(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
)(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
||||||
.groupByKey(_._1)
|
.groupByKey(_._1)
|
||||||
.reduceGroups((a,b) => if (a!= null && a._2!= null) a else b)
|
.reduceGroups((a,b) => if (a!= null && a._2!= null) a else b)
|
||||||
|
@ -147,27 +166,6 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
|
||||||
.write.mode(SaveMode.Overwrite).save(pidMapPath(workingPath))
|
.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
|
* This method resolve the datacite relation and filter the resolved
|
||||||
* relation
|
* relation
|
||||||
|
@ -222,25 +220,26 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
|
||||||
implicit val scholixEncoder:Encoder[Scholix] = Encoders.kryo[Scholix]
|
implicit val scholixEncoder:Encoder[Scholix] = Encoders.kryo[Scholix]
|
||||||
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
|
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
|
||||||
implicit val relationEncoder:Encoder[Relation] = Encoders.kryo[Relation]
|
implicit val relationEncoder:Encoder[Relation] = Encoders.kryo[Relation]
|
||||||
import spark.implicits._
|
implicit val intermediateEncoder :Encoder[(String,Scholix)] = Encoders.tuple(Encoders.STRING, scholixEncoder)
|
||||||
|
|
||||||
val relationss:Dataset[(String, Relation)] = spark.read.load(s"$workingPath/ResolvedRelation").as[Relation].map(r =>(r.getSource,r))(Encoders.tuple(Encoders.STRING, relationEncoder))
|
|
||||||
|
|
||||||
val id_summary:Dataset[(String,ScholixResource)] = spark.read.load(scholixResourcePath(workingPath)).as[(String,ScholixResource)]
|
val relations:Dataset[(String, Relation)] = spark.read.load(resolvedRelationPath(workingPath)).as[Relation].map(r =>(r.getSource,r))(Encoders.tuple(Encoders.STRING, relationEncoder))
|
||||||
|
|
||||||
relationss.joinWith(id_summary, relationss("_1").equalTo(id_summary("_1")),"inner")
|
val id_summary:Dataset[(String,ScholixResource)] = spark.read.load(s"${scholixResourcePath(workingPath)}_graph").as[ScholixResource].map(r => (r.getDnetIdentifier,r))(Encoders.tuple(Encoders.STRING, scholixResourceEncoder))
|
||||||
.map(t => (t._1._2.getTarget,ScholixUtils.scholixFromSource(t._1._2, t._2._2)))(Encoders.tuple(Encoders.STRING, scholixEncoder))
|
|
||||||
.write.mode(SaveMode.Overwrite)
|
id_summary.cache()
|
||||||
.save(s"$workingPath/scholix_one_verse")
|
|
||||||
|
relations.joinWith(id_summary, relations("_1").equalTo(id_summary("_1")),"inner")
|
||||||
|
.map(t => (t._1._2.getTarget,ScholixUtils.scholixFromSource(t._1._2, t._2._2)))
|
||||||
|
.write.mode(SaveMode.Overwrite).save(s"$workingPath/scholix_one_verse")
|
||||||
|
|
||||||
val source_scholix:Dataset[(String, Scholix)] =spark.read.load(s"$workingPath/scholix_one_verse").as[(String,Scholix)]
|
val source_scholix:Dataset[(String, Scholix)] =spark.read.load(s"$workingPath/scholix_one_verse").as[(String,Scholix)]
|
||||||
|
|
||||||
source_scholix.joinWith(id_summary, source_scholix("_1").equalTo(id_summary("_1")),"inner")
|
source_scholix.joinWith(id_summary, source_scholix("_1").equalTo(id_summary("_1")),"inner")
|
||||||
.map(t => {
|
.map(t => {
|
||||||
val target = t._2._2
|
val target:ScholixResource =t._2._2
|
||||||
val scholix = t._1._2
|
val scholix:Scholix = t._1._2
|
||||||
scholix.setTarget(target)
|
ScholixUtils.generateCompleteScholix(scholix,target)
|
||||||
scholix
|
|
||||||
})(scholixEncoder).write.mode(SaveMode.Overwrite).save(s"$workingPath/scholix")
|
})(scholixEncoder).write.mode(SaveMode.Overwrite).save(s"$workingPath/scholix")
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -259,7 +258,7 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
|
||||||
val datacitePath = parser.get("datacitePath")
|
val datacitePath = parser.get("datacitePath")
|
||||||
log.info(s"DatacitePath is '$datacitePath'")
|
log.info(s"DatacitePath is '$datacitePath'")
|
||||||
|
|
||||||
val workingPath = parser.get("workingPath")
|
val workingPath = parser.get("workingSupportPath")
|
||||||
log.info(s"workingPath is '$workingPath'")
|
log.info(s"workingPath is '$workingPath'")
|
||||||
|
|
||||||
val isLookupUrl: String = parser.get("isLookupUrl")
|
val isLookupUrl: String = parser.get("isLookupUrl")
|
||||||
|
@ -279,13 +278,28 @@ class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:L
|
||||||
log.info("Retrieve last entities collected From starting from scholix Graph")
|
log.info("Retrieve last entities collected From starting from scholix Graph")
|
||||||
lastCollectionDate = retrieveLastCollectedFrom(spark, s"$sourcePath/entities")
|
lastCollectionDate = retrieveLastCollectedFrom(spark, s"$sourcePath/entities")
|
||||||
}
|
}
|
||||||
|
else {
|
||||||
|
val fs = FileSystem.get(spark.sparkContext.hadoopConfiguration)
|
||||||
|
fs.delete(new Path(s"${scholixResourcePath(workingPath)}_native"), true)
|
||||||
|
fs.rename(new Path(s"${scholixResourcePath(workingPath)}_graph"), new Path(s"${scholixResourcePath(workingPath)}_native"))
|
||||||
|
lastCollectionDate = retrieveLastCollectedFrom(spark, dataciteOAFPath(workingPath))
|
||||||
|
}
|
||||||
|
|
||||||
getDataciteUpdate(datacitePath, lastCollectionDate, workingPath, spark, vocabularies)
|
val numRecords = getDataciteUpdate(datacitePath, lastCollectionDate, workingPath, spark, vocabularies)
|
||||||
|
if (numRecords>0) {
|
||||||
addMissingScholixResource(workingPath,spark)
|
addMissingScholixResource(workingPath,spark)
|
||||||
generatePidMap(workingPath, spark)
|
generatePidMap(workingPath, spark)
|
||||||
resolveUpdateRelation(workingPath,spark)
|
resolveUpdateRelation(workingPath,spark)
|
||||||
generateScholixUpdate(workingPath, spark)
|
generateScholixUpdate(workingPath, spark)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
object SparkRetrieveDataciteDelta {
|
||||||
|
val log: Logger = LoggerFactory.getLogger(SparkRetrieveDataciteDelta.getClass)
|
||||||
|
|
||||||
|
def main(args: Array[String]): Unit = {
|
||||||
|
new SparkRetrieveDataciteDelta("/eu/dnetlib/dhp/sx/graph/retrieve_datacite_delta_params.json", args, log).initialize().run()
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
|
@ -33,7 +33,8 @@ public class PrepareInfo implements Serializable {
|
||||||
private static final Logger log = LoggerFactory.getLogger(PrepareInfo.class);
|
private static final Logger log = LoggerFactory.getLogger(PrepareInfo.class);
|
||||||
|
|
||||||
// associate orgs with all their parent
|
// associate orgs with all their parent
|
||||||
private static final String ORGANIZATION_ORGANIZATION_QUERY = "SELECT target key, collect_set(source) as valueSet " +
|
private static final String ORGANIZATION_ORGANIZATION_QUERY = "SELECT target key, collect_set(source) as valueSet "
|
||||||
|
+
|
||||||
"FROM relation " +
|
"FROM relation " +
|
||||||
"WHERE lower(relclass) = '" + ModelConstants.IS_PARENT_OF.toLowerCase() +
|
"WHERE lower(relclass) = '" + ModelConstants.IS_PARENT_OF.toLowerCase() +
|
||||||
"' and datainfo.deletedbyinference = false " +
|
"' and datainfo.deletedbyinference = false " +
|
||||||
|
|
|
@ -2,7 +2,6 @@
|
||||||
package eu.dnetlib.dhp.resulttoorganizationfromsemrel;
|
package eu.dnetlib.dhp.resulttoorganizationfromsemrel;
|
||||||
|
|
||||||
import static eu.dnetlib.dhp.PropagationConstant.*;
|
import static eu.dnetlib.dhp.PropagationConstant.*;
|
||||||
|
|
||||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
||||||
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
|
@ -22,13 +21,11 @@ import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.KeyValueSet;
|
import eu.dnetlib.dhp.KeyValueSet;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
import eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob;
|
import eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob;
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
|
||||||
|
|
||||||
public class SparkResultToOrganizationFromSemRel implements Serializable {
|
public class SparkResultToOrganizationFromSemRel implements Serializable {
|
||||||
private static final Logger log = LoggerFactory.getLogger(SparkResultToOrganizationFromSemRel.class);
|
private static final Logger log = LoggerFactory.getLogger(SparkResultToOrganizationFromSemRel.class);
|
||||||
private static final int MAX_ITERATION = 5;
|
private static final int MAX_ITERATION = 5;
|
||||||
|
@ -201,6 +198,4 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
|
||||||
.json(outputPath);
|
.json(outputPath);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
@ -179,7 +179,6 @@ public class StepActions implements Serializable {
|
||||||
"GROUP BY resId")
|
"GROUP BY resId")
|
||||||
.as(Encoders.bean(KeyValueSet.class));
|
.as(Encoders.bean(KeyValueSet.class));
|
||||||
|
|
||||||
|
|
||||||
// create new relations from result to organization for each result linked to a leaf
|
// create new relations from result to organization for each result linked to a leaf
|
||||||
return resultParent
|
return resultParent
|
||||||
.flatMap(
|
.flatMap(
|
||||||
|
@ -200,7 +199,6 @@ public class StepActions implements Serializable {
|
||||||
.iterator(),
|
.iterator(),
|
||||||
Encoders.bean(Relation.class));
|
Encoders.bean(Relation.class));
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
@ -363,6 +363,7 @@ public class PrepareInfoJobTest {
|
||||||
Assertions.assertEquals(7, verificationDs.count());
|
Assertions.assertEquals(7, verificationDs.count());
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
public void resultOrganizationTest1() throws Exception {
|
public void resultOrganizationTest1() throws Exception {
|
||||||
|
|
||||||
|
|
|
@ -1,6 +1,7 @@
|
||||||
[
|
[
|
||||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||||
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
|
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
|
||||||
|
{"paramName":"su", "paramLongName":"scholixUpdatePath", "paramDescription": "the scholix updated Path", "paramRequired": false},
|
||||||
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true},
|
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true},
|
||||||
{"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true}
|
{"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true}
|
||||||
]
|
]
|
|
@ -90,68 +90,6 @@
|
||||||
<arg>--relationPath</arg><arg>${targetPath}/relation</arg>
|
<arg>--relationPath</arg><arg>${targetPath}/relation</arg>
|
||||||
|
|
||||||
</spark>
|
</spark>
|
||||||
<ok to="DropJSONPath"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="DropJSONPath">
|
|
||||||
<fs>
|
|
||||||
<delete path='${targetPath}/index'/>
|
|
||||||
<mkdir path='${targetPath}/index/'/>
|
|
||||||
</fs>
|
|
||||||
<ok to="SerializeScholix"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="SerializeScholix">
|
|
||||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
|
||||||
<master>yarn</master>
|
|
||||||
<mode>cluster</mode>
|
|
||||||
<name>Serialize scholix to JSON</name>
|
|
||||||
<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
|
|
||||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
|
||||||
<spark-opts>
|
|
||||||
--executor-memory=${sparkExecutorMemory}
|
|
||||||
--executor-cores=${sparkExecutorCores}
|
|
||||||
--driver-memory=${sparkDriverMemory}
|
|
||||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
|
||||||
--conf spark.sql.shuffle.partitions=6000
|
|
||||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
|
||||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
|
||||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
|
||||||
</spark-opts>
|
|
||||||
<arg>--master</arg><arg>yarn</arg>
|
|
||||||
<arg>--sourcePath</arg><arg>${targetPath}/provision/scholix/scholix</arg>
|
|
||||||
<arg>--targetPath</arg><arg>${targetPath}/index/scholix_json</arg>
|
|
||||||
<arg>--objectType</arg><arg>scholix</arg>
|
|
||||||
|
|
||||||
</spark>
|
|
||||||
<ok to="SerializeSummary"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="SerializeSummary">
|
|
||||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
|
||||||
<master>yarn</master>
|
|
||||||
<mode>cluster</mode>
|
|
||||||
<name>Serialize summary to JSON</name>
|
|
||||||
<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
|
|
||||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
|
||||||
<spark-opts>
|
|
||||||
--executor-memory=${sparkExecutorMemory}
|
|
||||||
--executor-cores=${sparkExecutorCores}
|
|
||||||
--driver-memory=${sparkDriverMemory}
|
|
||||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
|
||||||
--conf spark.sql.shuffle.partitions=6000
|
|
||||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
|
||||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
|
||||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
|
||||||
</spark-opts>
|
|
||||||
<arg>--master</arg><arg>yarn</arg>
|
|
||||||
<arg>--sourcePath</arg><arg>${targetPath}/provision/summaries_filtered</arg>
|
|
||||||
<arg>--targetPath</arg><arg>${targetPath}/index/summaries_json</arg>
|
|
||||||
<arg>--objectType</arg><arg>summary</arg>
|
|
||||||
</spark>
|
|
||||||
<ok to="End"/>
|
<ok to="End"/>
|
||||||
<error to="Kill"/>
|
<error to="Kill"/>
|
||||||
</action>
|
</action>
|
||||||
|
|
|
@ -1,158 +0,0 @@
|
||||||
{
|
|
||||||
"cites":{
|
|
||||||
"original":"Cites",
|
|
||||||
"inverse":"IsCitedBy"
|
|
||||||
},
|
|
||||||
"compiles":{
|
|
||||||
"original":"Compiles",
|
|
||||||
"inverse":"IsCompiledBy"
|
|
||||||
},
|
|
||||||
"continues":{
|
|
||||||
"original":"Continues",
|
|
||||||
"inverse":"IsContinuedBy"
|
|
||||||
},
|
|
||||||
"derives":{
|
|
||||||
"original":"IsSourceOf",
|
|
||||||
"inverse":"IsDerivedFrom"
|
|
||||||
},
|
|
||||||
"describes":{
|
|
||||||
"original":"Describes",
|
|
||||||
"inverse":"IsDescribedBy"
|
|
||||||
},
|
|
||||||
"documents":{
|
|
||||||
"original":"Documents",
|
|
||||||
"inverse":"IsDocumentedBy"
|
|
||||||
},
|
|
||||||
"hasmetadata":{
|
|
||||||
"original":"HasMetadata",
|
|
||||||
"inverse":"IsMetadataOf"
|
|
||||||
},
|
|
||||||
"hasassociationwith":{
|
|
||||||
"original":"HasAssociationWith",
|
|
||||||
"inverse":"HasAssociationWith"
|
|
||||||
},
|
|
||||||
"haspart":{
|
|
||||||
"original":"HasPart",
|
|
||||||
"inverse":"IsPartOf"
|
|
||||||
},
|
|
||||||
"hasversion":{
|
|
||||||
"original":"HasVersion",
|
|
||||||
"inverse":"IsVersionOf"
|
|
||||||
},
|
|
||||||
"iscitedby":{
|
|
||||||
"original":"IsCitedBy",
|
|
||||||
"inverse":"Cites"
|
|
||||||
},
|
|
||||||
"iscompiledby":{
|
|
||||||
"original":"IsCompiledBy",
|
|
||||||
"inverse":"Compiles"
|
|
||||||
},
|
|
||||||
"iscontinuedby":{
|
|
||||||
"original":"IsContinuedBy",
|
|
||||||
"inverse":"Continues"
|
|
||||||
},
|
|
||||||
"isderivedfrom":{
|
|
||||||
"original":"IsDerivedFrom",
|
|
||||||
"inverse":"IsSourceOf"
|
|
||||||
},
|
|
||||||
"isdescribedby":{
|
|
||||||
"original":"IsDescribedBy",
|
|
||||||
"inverse":"Describes"
|
|
||||||
},
|
|
||||||
"isdocumentedby":{
|
|
||||||
"original":"IsDocumentedBy",
|
|
||||||
"inverse":"Documents"
|
|
||||||
},
|
|
||||||
"isidenticalto":{
|
|
||||||
"original":"IsIdenticalTo",
|
|
||||||
"inverse":"IsIdenticalTo"
|
|
||||||
},
|
|
||||||
"ismetadatafor":{
|
|
||||||
"original":"IsMetadataFor",
|
|
||||||
"inverse":"IsMetadataOf"
|
|
||||||
},
|
|
||||||
"ismetadataof":{
|
|
||||||
"original":"IsMetadataOf",
|
|
||||||
"inverse":"IsMetadataFor"
|
|
||||||
},
|
|
||||||
"isnewversionof":{
|
|
||||||
"original":"IsNewVersionOf",
|
|
||||||
"inverse":"IsPreviousVersionOf"
|
|
||||||
},
|
|
||||||
"isobsoletedby":{
|
|
||||||
"original":"IsObsoletedBy",
|
|
||||||
"inverse":"Obsoletes"
|
|
||||||
},
|
|
||||||
"isoriginalformof":{
|
|
||||||
"original":"IsOriginalFormOf",
|
|
||||||
"inverse":"IsVariantFormOf"
|
|
||||||
},
|
|
||||||
"ispartof":{
|
|
||||||
"original":"IsPartOf",
|
|
||||||
"inverse":"HasPart"
|
|
||||||
},
|
|
||||||
"ispreviousversionof":{
|
|
||||||
"original":"IsPreviousVersionOf",
|
|
||||||
"inverse":"IsNewVersionOf"
|
|
||||||
},
|
|
||||||
"isreferencedby":{
|
|
||||||
"original":"IsReferencedBy",
|
|
||||||
"inverse":"References"
|
|
||||||
},
|
|
||||||
"isrelatedto":{
|
|
||||||
"original":"IsRelatedTo",
|
|
||||||
"inverse":"IsRelatedTo"
|
|
||||||
},
|
|
||||||
"isrequiredby":{
|
|
||||||
"original":"IsRequiredBy",
|
|
||||||
"inverse":"Requires"
|
|
||||||
},
|
|
||||||
"isreviewedby":{
|
|
||||||
"original":"IsReviewedBy",
|
|
||||||
"inverse":"Reviews"
|
|
||||||
},
|
|
||||||
"issourceof":{
|
|
||||||
"original":"IsSourceOf",
|
|
||||||
"inverse":"IsDerivedFrom"
|
|
||||||
},
|
|
||||||
"issupplementedby":{
|
|
||||||
"original":"IsSupplementedBy",
|
|
||||||
"inverse":"IsSupplementTo"
|
|
||||||
},
|
|
||||||
"issupplementto":{
|
|
||||||
"original":"IsSupplementTo",
|
|
||||||
"inverse":"IsSupplementedBy"
|
|
||||||
},
|
|
||||||
"isvariantformof":{
|
|
||||||
"original":"IsVariantFormOf",
|
|
||||||
"inverse":"IsOriginalFormOf"
|
|
||||||
},
|
|
||||||
"isversionof":{
|
|
||||||
"original":"IsVersionOf",
|
|
||||||
"inverse":"HasVersion"
|
|
||||||
},
|
|
||||||
"obsoletes":{
|
|
||||||
"original":"Obsoletes",
|
|
||||||
"inverse":"IsObsoletedBy"
|
|
||||||
},
|
|
||||||
"references":{
|
|
||||||
"original":"References",
|
|
||||||
"inverse":"IsReferencedBy"
|
|
||||||
},
|
|
||||||
"requires":{
|
|
||||||
"original":"Requires",
|
|
||||||
"inverse":"IsRequiredBy"
|
|
||||||
},
|
|
||||||
"related":{
|
|
||||||
"original":"IsRelatedTo",
|
|
||||||
"inverse":"IsRelatedTo"
|
|
||||||
},
|
|
||||||
"reviews":{
|
|
||||||
"original":"Reviews",
|
|
||||||
"inverse":"IsReviewedBy"
|
|
||||||
},
|
|
||||||
"unknown":{
|
|
||||||
"original":"Unknown",
|
|
||||||
"inverse":"Unknown"
|
|
||||||
}
|
|
||||||
}
|
|
|
@ -0,0 +1,10 @@
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>oozie.use.system.libpath</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.action.sharelib.for.spark</name>
|
||||||
|
<value>spark2</value>
|
||||||
|
</property>
|
||||||
|
</configuration>
|
|
@ -0,0 +1,83 @@
|
||||||
|
<workflow-app name="Create Scholix final Graph" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>scholixUpdatePath</name>
|
||||||
|
<description>the working dir base path of the scholix updated</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>targetPath</name>
|
||||||
|
<description>the final graph path</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<start to="DropJSONPath"/>
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
|
||||||
|
<action name="DropJSONPath">
|
||||||
|
<fs>
|
||||||
|
<delete path='${targetPath}/index'/>
|
||||||
|
<mkdir path='${targetPath}/index/'/>
|
||||||
|
</fs>
|
||||||
|
<ok to="SerializeScholix"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="SerializeScholix">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Serialize scholix to JSON</name>
|
||||||
|
<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.shuffle.partitions=6000
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--master</arg><arg>yarn</arg>
|
||||||
|
<arg>--sourcePath</arg><arg>${targetPath}/provision/scholix/scholix</arg>
|
||||||
|
<arg>--targetPath</arg><arg>${targetPath}/index/scholix_json</arg>
|
||||||
|
<arg>--scholixUpdatePath</arg><arg>${scholixUpdatePath}</arg>
|
||||||
|
<arg>--objectType</arg><arg>scholix</arg>
|
||||||
|
|
||||||
|
</spark>
|
||||||
|
<ok to="SerializeSummary"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="SerializeSummary">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Serialize summary to JSON</name>
|
||||||
|
<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.shuffle.partitions=6000
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--master</arg><arg>yarn</arg>
|
||||||
|
<arg>--sourcePath</arg><arg>${targetPath}/provision/summaries_filtered</arg>
|
||||||
|
<arg>--targetPath</arg><arg>${targetPath}/index/summaries_json</arg>
|
||||||
|
<arg>--objectType</arg><arg>summary</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
<end name="End"/>
|
||||||
|
</workflow-app>
|
|
@ -30,6 +30,9 @@ object SparkConvertObjectToJson {
|
||||||
log.info(s"targetPath -> $targetPath")
|
log.info(s"targetPath -> $targetPath")
|
||||||
val objectType = parser.get("objectType")
|
val objectType = parser.get("objectType")
|
||||||
log.info(s"objectType -> $objectType")
|
log.info(s"objectType -> $objectType")
|
||||||
|
val scholixUpdatePath = parser.get("scholixUpdatePath")
|
||||||
|
log.info(s"scholixUpdatePath -> $scholixUpdatePath")
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
|
implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
|
||||||
|
@ -42,7 +45,8 @@ object SparkConvertObjectToJson {
|
||||||
case "scholix" =>
|
case "scholix" =>
|
||||||
log.info("Serialize Scholix")
|
log.info("Serialize Scholix")
|
||||||
val d: Dataset[Scholix] = spark.read.load(sourcePath).as[Scholix]
|
val d: Dataset[Scholix] = spark.read.load(sourcePath).as[Scholix]
|
||||||
d.map(s => mapper.writeValueAsString(s))(Encoders.STRING).rdd.repartition(6000).saveAsTextFile(targetPath, classOf[GzipCodec])
|
val u :Dataset[Scholix]= spark.read.load(s"$scholixUpdatePath/scholix").as[Scholix]
|
||||||
|
d.union(u).repartition(8000).map(s => mapper.writeValueAsString(s))(Encoders.STRING).rdd.saveAsTextFile(targetPath, classOf[GzipCodec])
|
||||||
case "summary" =>
|
case "summary" =>
|
||||||
log.info("Serialize Summary")
|
log.info("Serialize Summary")
|
||||||
val d: Dataset[ScholixSummary] = spark.read.load(sourcePath).as[ScholixSummary]
|
val d: Dataset[ScholixSummary] = spark.read.load(sourcePath).as[ScholixSummary]
|
||||||
|
|
Loading…
Reference in New Issue