forked from antonis.lempesis/dnet-hadoop
added scholix generation
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4c54bd8742
commit
8535506c22
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@ -4,9 +4,10 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf.Relation
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import eu.dnetlib.dhp.schema.sx.scholix.Scholix
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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 org.apache.commons.io.IOUtils
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import org.apache.spark.SparkConf
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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object SparkCreateScholix {
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@ -31,40 +32,45 @@ object SparkCreateScholix {
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log.info(s"targetPath -> $targetPath")
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implicit val relEncoder:Encoder[Relation] = Encoders.kryo[Relation]
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implicit val summaryEncoder :Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
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implicit val scholixEncoder :Encoder[Scholix] = Encoders.kryo[Scholix]
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implicit val relEncoder: Encoder[Relation] = Encoders.kryo[Relation]
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implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
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implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
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import spark.implicits._
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val relationDS:Dataset[(String, Relation)] = spark.read.load(relationPath).as[Relation]
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.map(r => (r.getSource, r))(Encoders.tuple(Encoders.STRING, relEncoder))
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val summaryDS:Dataset[(String, ScholixSummary)] = spark.read.load(summaryPath).as[ScholixSummary]
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.map(r => (r.getId, r))(Encoders.tuple(Encoders.STRING, summaryEncoder))
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val res: Array[((String, Relation), (String, ScholixSummary))] =relationDS.joinWith(summaryDS, relationDS("_1").equalTo(summaryDS("_1")), "left").take(10)
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res.foreach(r =>println(r._1._2))
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// relationDS.joinWith(summaryDS, relationDS("_1").equalTo(summaryDS("_1")), "left")
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// .map {input:((String,Relation), (String, ScholixSummary)) =>
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// val rel:Relation = input._1._2
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// val source:ScholixSummary = input._2._2
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//
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//
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// val s = new Scholix
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//
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//
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// }
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val relationDS: Dataset[(String, Relation)] = spark.read.load(relationPath).as[Relation]
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.map(r => (r.getSource, r))(Encoders.tuple(Encoders.STRING, relEncoder))
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val summaryDS: Dataset[(String, ScholixSummary)] = spark.read.load(summaryPath).as[ScholixSummary]
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.map(r => (r.getId, r))(Encoders.tuple(Encoders.STRING, summaryEncoder))
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relationDS.joinWith(summaryDS, relationDS("_1").equalTo(summaryDS("_1")), "left")
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.map { input: ((String, Relation), (String, ScholixSummary)) =>
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val rel: Relation = input._1._2
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val source: ScholixSummary = input._2._2
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(rel.getTarget, ScholixUtils.scholixFromSource(rel, source))
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}(Encoders.tuple(Encoders.STRING, scholixEncoder))
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.write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_from_source")
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val scholixSource: Dataset[(String, Scholix)] = spark.read.load(s"$targetPath/scholix_from_source").as[(String, Scholix)](Encoders.tuple(Encoders.STRING, scholixEncoder))
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scholixSource.joinWith(summaryDS, scholixSource("_1").equalTo(summaryDS("_1")), "left")
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.map { input: ((String, Scholix), (String, ScholixSummary)) =>
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val s: Scholix = input._1._2
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val target: ScholixSummary = input._2._2
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ScholixUtils.generateCompleteScholix(s, target)
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}.write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_one_verse")
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val scholix_o_v: Dataset[Scholix] = spark.read.load(s"$targetPath/scholix_one_verse").as[Scholix]
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scholix_o_v.flatMap(s => List(s, ScholixUtils.createInverseScholixRelation(s))).groupByKey(_.getIdentifier).reduceGroups { (x, y) =>
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if (x != null)
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x
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else
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y
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}.write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix")
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}
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}
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@ -4,6 +4,7 @@ package eu.dnetlib.dhp.sx.graph.scholix
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import eu.dnetlib.dhp.schema.oaf.{Dataset, Relation, Result, StructuredProperty}
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import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixCollectedFrom, ScholixEntityId, ScholixIdentifier, ScholixRelationship, ScholixResource}
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import eu.dnetlib.dhp.schema.sx.summary.{CollectedFromType, SchemeValue, ScholixSummary, Typology}
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import eu.dnetlib.dhp.utils.DHPUtils
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import org.json4s
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import org.json4s.DefaultFormats
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import org.json4s.jackson.JsonMethods.parse
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@ -45,13 +46,35 @@ object ScholixUtils {
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def extractRelationDate(summary: ScholixSummary):String = {
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if(summary.getDate== null && !summary.getDate.isEmpty)
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if(summary.getDate== null || summary.getDate.isEmpty)
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null
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else {
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summary.getDate.get(0)
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}
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}
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def inverseRelationShip(rel:ScholixRelationship):ScholixRelationship = {
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new ScholixRelationship(rel.getInverse, rel.getSchema, rel.getName)
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}
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def createInverseScholixRelation(scholix: Scholix):Scholix = {
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val s = new Scholix
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s.setPublicationDate(scholix.getPublicationDate)
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s.setPublisher(scholix.getPublisher)
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s.setLinkprovider(scholix.getLinkprovider)
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s.setRelationship(inverseRelationShip(scholix.getRelationship))
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s.setSource(scholix.getTarget)
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s.setTarget(scholix.getSource)
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s.setIdentifier(DHPUtils.md5(s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}"))
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s
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}
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@ -78,6 +101,19 @@ object ScholixUtils {
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}
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def generateCompleteScholix(scholix: Scholix, target:ScholixSummary): Scholix = {
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val s = new Scholix
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s.setPublicationDate(scholix.getPublicationDate)
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s.setPublisher(scholix.getPublisher)
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s.setLinkprovider(scholix.getLinkprovider)
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s.setRelationship(scholix.getRelationship)
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s.setSource(scholix.getSource)
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s.setTarget(generateScholixResourceFromSummary(target))
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s.setIdentifier(DHPUtils.md5(s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}"))
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s
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}
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def generateScholixResourceFromSummary(summaryObject: ScholixSummary): ScholixResource = {
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val r = new ScholixResource
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r.setIdentifier(summaryObject.getLocalIdentifier)
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@ -0,0 +1,6 @@
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[
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{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
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{"paramName":"r", "paramLongName":"relationPath", "paramDescription": "the relation resolved Path", "paramRequired": true},
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{"paramName":"s", "paramLongName":"summaryPath", "paramDescription": "the summary Path", "paramRequired": true},
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{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the target base path of the scholix", "paramRequired": true}
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]
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@ -10,7 +10,7 @@
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</property>
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</parameters>
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<start to="CreateSummaries"/>
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<start to="CreateScholix"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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@ -90,6 +90,33 @@
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<arg>--sourcePath</arg><arg>${targetPath}/dedup</arg>
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<arg>--targetPath</arg><arg>${targetPath}/provision/summaries</arg>
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</spark>
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<ok to="CreateScholix"/>
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<error to="Kill"/>
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</action>
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<action name="CreateScholix">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Generate Scholix Dataset</name>
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<class>eu.dnetlib.dhp.sx.graph.SparkCreateScholix</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.shuffle.partitions=6000
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--master</arg><arg>yarn</arg>
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<arg>--summaryPath</arg><arg>${targetPath}/provision/summaries</arg>
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<arg>--targetPath</arg><arg>${targetPath}/provision/scholix</arg>
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<arg>--relationPath</arg><arg>${targetPath}/resolved/resolvedRelation</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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