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implement first version of scholexplorer integration for the generation of final graph

This commit is contained in:
Sandro La Bruzzo 2021-11-02 15:58:15 +01:00
parent 7fa49f6956
commit 7bd224f051
4 changed files with 11 additions and 7 deletions
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2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala
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@ -59,7 +59,7 @@ object SparkConvertRDDtoDataset {
log.info("Converting Relation") log.info("Converting Relation")
val rddRelation =spark.sparkContext.textFile(s"$sourcePath/relation").map(s => mapper.readValue(s, classOf[Relation])) val rddRelation =spark.sparkContext.textFile(s"$sourcePath/relation").map(s => mapper.readValue(s, classOf[Relation])).filter(r=> r.getSource.startsWith("50") && r.getTarget.startsWith("50"))
spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath")

10
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala
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@ -51,10 +51,14 @@ object SparkCreateScholix {
relationDS.joinWith(summaryDS, relationDS("_1").equalTo(summaryDS("_1")), "left") relationDS.joinWith(summaryDS, relationDS("_1").equalTo(summaryDS("_1")), "left")
.map { input: ((String, Relation), (String, ScholixSummary)) => .map { input: ((String, Relation), (String, ScholixSummary)) =>
val rel: Relation = input._1._2 if (input._1!= null && input._2!= null) {
val source: ScholixSummary = input._2._2 val rel: Relation = input._1._2
(rel.getTarget, ScholixUtils.scholixFromSource(rel, source)) val source: ScholixSummary = input._2._2
(rel.getTarget, ScholixUtils.scholixFromSource(rel, source))
}
else null
}(Encoders.tuple(Encoders.STRING, scholixEncoder)) }(Encoders.tuple(Encoders.STRING, scholixEncoder))
.filter(r => r!= null)
.write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_from_source") .write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_from_source")
val scholixSource: Dataset[(String, Scholix)] = spark.read.load(s"$targetPath/scholix_from_source").as[(String, Scholix)](Encoders.tuple(Encoders.STRING, scholixEncoder)) val scholixSource: Dataset[(String, Scholix)] = spark.read.load(s"$targetPath/scholix_from_source").as[(String, Scholix)](Encoders.tuple(Encoders.STRING, scholixEncoder))

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala
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@ -289,7 +289,7 @@ object ScholixUtils {
if (r.getInstance() == null || r.getInstance().isEmpty) if (r.getInstance() == null || r.getInstance().isEmpty)
return List() return List()
r.getInstance().asScala.filter(i => i.getUrl!= null && !i.getUrl.isEmpty) r.getInstance().asScala.filter(i => i.getUrl!= null && !i.getUrl.isEmpty)
.filter(i => i.getPid!= null && i.getUrl != null)
.flatMap(i => findURLForPID(i.getPid.asScala.toList, i.getUrl.asScala.toList)) .flatMap(i => findURLForPID(i.getPid.asScala.toList, i.getUrl.asScala.toList))
.map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2)).distinct.toList .map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2)).distinct.toList
} }

4
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/workflow.xml
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@ -54,7 +54,7 @@
--executor-cores=${sparkExecutorCores} --executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory} --driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=5000 --conf spark.sql.shuffle.partitions=20000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
@ -79,7 +79,7 @@
--executor-cores=${sparkExecutorCores} --executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory} --driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=6000 --conf spark.sql.shuffle.partitions=20000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}