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Merge branch 'beta' into hierarchical_orgs_relations

This commit is contained in:
Claudio Atzori 2021-11-08 09:40:24 +01:00
parent d02caef185 7bd224f051
commit 9cb8e4ad21
7 changed files with 16 additions and 11 deletions
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3
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala
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@ -75,7 +75,7 @@ object SparkResolveRelation {
if (targetResolved != null && targetResolved._1.nonEmpty)
currentRelation.setTarget(targetResolved._1)
currentRelation
}.filter(r => !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved"))
}
.write
.mode(SaveMode.Overwrite)
.save(s"$workingPath/relation_resolved")
@ -88,6 +88,7 @@ object SparkResolveRelation {
fs.rename(new Path(s"$graphBasePath/relation"), new Path(s"$workingPath/relation"))
spark.read.load(s"$workingPath/relation_resolved").as[Relation]
.filter(r => !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved"))
.map(r => mapper.writeValueAsString(r))
.write
.option("compression", "gzip")

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")
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")

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")
.map { input: ((String, Relation), (String, ScholixSummary)) =>
val rel: Relation = input._1._2
val source: ScholixSummary = input._2._2
(rel.getTarget, ScholixUtils.scholixFromSource(rel, source))
if (input._1!= null && input._2!= null) {
val rel: Relation = input._1._2
val source: ScholixSummary = input._2._2
(rel.getTarget, ScholixUtils.scholixFromSource(rel, source))
}
else null
}(Encoders.tuple(Encoders.STRING, scholixEncoder))
.filter(r => r!= null)
.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))

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala
View File

@ -289,7 +289,7 @@ object ScholixUtils {
if (r.getInstance() == null || r.getInstance().isEmpty)
return List()
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))
.map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2)).distinct.toList
}

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml
View File

@ -24,7 +24,7 @@
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=8000
--conf spark.sql.shuffle.partitions=15000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}

4
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/workflow.xml
View File

@ -54,7 +54,7 @@
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=5000
--conf spark.sql.shuffle.partitions=20000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
@ -79,7 +79,7 @@
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=6000
--conf spark.sql.shuffle.partitions=20000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}

4
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
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@ -65,7 +65,7 @@ FROM ${stats_db_name}.project_tmp p
UPDATE ${stats_db_name}.publication_tmp
SET delayed = 'yes'
WHERE publication_tmp.id IN (SELECT distinct r.id
FROM stats_wf_db_obs.result r,
FROM ${stats_db_name}.result r,
${stats_db_name}.project_results pr,
${stats_db_name}.project_tmp p
WHERE r.id = pr.result
@ -75,7 +75,7 @@ WHERE publication_tmp.id IN (SELECT distinct r.id
UPDATE ${stats_db_name}.dataset_tmp
SET delayed = 'yes'
WHERE dataset_tmp.id IN (SELECT distinct r.id
FROM stats_wf_db_obs.result r,
FROM ${stats_db_name}.result r,
${stats_db_name}.project_results pr,
${stats_db_name}.project_tmp p
WHERE r.id = pr.result