Merge branch 'beta' into hierarchical_orgs_relations
commit
d02caef185
@ -1,41 +0,0 @@
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package eu.dnetlib.dhp.actionmanager.datacite
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf.Oaf
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import org.apache.hadoop.io.Text
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import org.apache.hadoop.io.compress.GzipCodec
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import org.apache.hadoop.mapred.SequenceFileOutputFormat
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import org.apache.spark.SparkConf
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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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import scala.io.Source
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object ExportActionSetJobNode {
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val log: Logger = LoggerFactory.getLogger(ExportActionSetJobNode.getClass)
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def main(args: Array[String]): Unit = {
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val conf = new SparkConf
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json")).mkString)
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parser.parseArgument(args)
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val master = parser.get("master")
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val sourcePath = parser.get("sourcePath")
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val targetPath = parser.get("targetPath")
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val spark: SparkSession = SparkSession.builder().config(conf)
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.appName(ExportActionSetJobNode.getClass.getSimpleName)
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.master(master)
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.getOrCreate()
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implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
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implicit val tEncoder:Encoder[(String,String)] = Encoders.tuple(Encoders.STRING,Encoders.STRING)
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spark.read.load(sourcePath).as[Oaf]
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.map(o =>DataciteToOAFTransformation.toActionSet(o))
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.filter(o => o!= null)
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.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
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}
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}
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@ -1,46 +0,0 @@
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package eu.dnetlib.dhp.actionmanager.datacite
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
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import eu.dnetlib.dhp.schema.mdstore.MetadataRecord
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
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import eu.dnetlib.dhp.utils.ISLookupClientFactory
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import org.apache.spark.SparkConf
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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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import scala.io.Source
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object FilterCrossrefEntitiesSpark {
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val log: Logger = LoggerFactory.getLogger(getClass.getClass)
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def main(args: Array[String]): Unit = {
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val conf = new SparkConf
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/filter_crossref_param.json")).mkString)
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parser.parseArgument(args)
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val master = parser.get("master")
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val sourcePath = parser.get("sourcePath")
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log.info("sourcePath: {}", sourcePath)
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val targetPath = parser.get("targetPath")
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log.info("targetPath: {}", targetPath)
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val spark: SparkSession = SparkSession.builder().config(conf)
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.appName(getClass.getSimpleName)
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.master(master)
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.getOrCreate()
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implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
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implicit val resEncoder: Encoder[Result] = Encoders.kryo[Result]
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val d:Dataset[Oaf]= spark.read.load(sourcePath).as[Oaf]
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d.filter(r => r.isInstanceOf[Result]).map(r => r.asInstanceOf[Result]).write.mode(SaveMode.Overwrite).save(targetPath)
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}
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}
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@ -0,0 +1,49 @@
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package eu.dnetlib.dhp.collection
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import eu.dnetlib.dhp.schema.common.ModelSupport
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import eu.dnetlib.dhp.schema.oaf.{Oaf, OafEntity, Relation}
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object CollectionUtils {
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/**
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* This method in pipeline to the transformation phase,
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* generates relations in both verse, typically it should be a phase of flatMap
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*
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* @param i input OAF
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* @return
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* If the input OAF is an entity -> List(i)
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* If the input OAF is a relation -> List(relation, inverseRelation)
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*
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*/
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def fixRelations(i: Oaf): List[Oaf] = {
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if (i.isInstanceOf[OafEntity])
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return List(i)
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else {
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val r: Relation = i.asInstanceOf[Relation]
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val currentRel = ModelSupport.findRelation(r.getRelClass)
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if (currentRel != null) {
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// Cleaning relation
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r.setRelType(currentRel.getRelType)
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r.setSubRelType(currentRel.getSubReltype)
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r.setRelClass(currentRel.getRelClass)
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val inverse = new Relation
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inverse.setSource(r.getTarget)
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inverse.setTarget(r.getSource)
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inverse.setRelType(currentRel.getRelType)
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inverse.setSubRelType(currentRel.getSubReltype)
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inverse.setRelClass(currentRel.getInverseRelClass)
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inverse.setCollectedfrom(r.getCollectedfrom)
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inverse.setDataInfo(r.getDataInfo)
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inverse.setProperties(r.getProperties)
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inverse.setLastupdatetimestamp(r.getLastupdatetimestamp)
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inverse.setValidated(r.getValidated)
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inverse.setValidationDate(r.getValidationDate)
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return List(r, inverse)
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}
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}
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List()
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}
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}
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@ -1,12 +1,10 @@
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package eu.dnetlib.dhp.actionmanager.datacite
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package eu.dnetlib.dhp.datacite
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import org.apache.commons.io.IOUtils
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import org.apache.http.client.config.RequestConfig
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import org.apache.http.client.methods.{HttpGet, HttpPost, HttpRequestBase, HttpUriRequest}
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import org.apache.http.client.methods.{HttpGet, HttpPost, HttpUriRequest}
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import org.apache.http.entity.StringEntity
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import org.apache.http.impl.client.{HttpClientBuilder, HttpClients}
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import java.io.IOException
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import org.apache.http.impl.client.HttpClientBuilder
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abstract class AbstractRestClient extends Iterator[String] {
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@ -1,7 +1,7 @@
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package eu.dnetlib.dhp.actionmanager.datacite
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package eu.dnetlib.dhp.datacite
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import org.json4s.{DefaultFormats, JValue}
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import org.json4s.jackson.JsonMethods.{compact, parse, render}
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import org.json4s.{DefaultFormats, JValue}
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class DataciteAPIImporter(timestamp: Long = 0, blocks: Long = 10, until:Long = -1) extends AbstractRestClient {
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@ -1,81 +0,0 @@
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<workflow-app name="Import_Datacite_and_transform_to_OAF" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>mainPath</name>
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<description>the working path of Datacite stores</description>
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</property>
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<property>
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<name>isLookupUrl</name>
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<description>The IS lookUp service endopoint</description>
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</property>
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<property>
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<name>blocksize</name>
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<value>100</value>
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<description>The request block size</description>
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</property>
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</parameters>
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<start to="ImportDatacite"/>
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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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</kill>
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<action name="ImportDatacite">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>ImportDatacite</name>
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<class>eu.dnetlib.dhp.actionmanager.datacite.ImportDatacite</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--targetPath</arg><arg>${mainPath}/datacite_update</arg>
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<arg>--dataciteDumpPath</arg><arg>${mainPath}/datacite_dump</arg>
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<arg>--namenode</arg><arg>${nameNode}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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<arg>--blocksize</arg><arg>${blocksize}</arg>
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</spark>
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<ok to="TransformJob"/>
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<error to="Kill"/>
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</action>
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<action name="TransformJob">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>TransformJob</name>
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<class>eu.dnetlib.dhp.actionmanager.datacite.GenerateDataciteDatasetSpark</class>
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<jar>dhp-aggregation-${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=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${spark2ExtraListeners}
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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>--sourcePath</arg><arg>${mainPath}/datacite_dump</arg>
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<arg>--targetPath</arg><arg>${mainPath}/datacite_oaf</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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<arg>--exportLinks</arg><arg>false</arg>
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<arg>--master</arg><arg>yarn-cluster</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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<end name="End"/>
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</workflow-app>
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@ -1,23 +0,0 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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</configuration>
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@ -1,84 +0,0 @@
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<workflow-app name="Generate_Datacite_and_Crossref_dump_for_Scholexplorer" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>datacitePath</name>
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<description>the path of Datacite spark dataset</description>
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</property>
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<property>
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<name>isLookupUrl</name>
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<description>The IS lookUp service endopoint</description>
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</property>
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<property>
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<name>crossrefPath</name>
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<description>the path of Crossref spark dataset</description>
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</property>
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<property>
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<name>targetPath</name>
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<description>the path of Crossref spark dataset</description>
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</property>
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</parameters>
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<start to="ImportDatacite"/>
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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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</kill>
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<action name="ImportDatacite">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>ImportDatacite</name>
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<class>eu.dnetlib.dhp.actionmanager.datacite.GenerateDataciteDatasetSpark</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${datacitePath}</arg>
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<arg>--targetPath</arg><arg>${targetPath}/datacite_oaf</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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<arg>--exportLinks</arg><arg>true</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="FilterCrossrefEntities"/>
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<error to="Kill"/>
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</action>
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<action name="FilterCrossrefEntities">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>FilterCrossrefEntities</name>
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<class>eu.dnetlib.dhp.actionmanager.datacite.FilterCrossrefEntitiesSpark</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
|
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${crossrefPath}</arg>
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<arg>--targetPath</arg><arg>${targetPath}/crossref_oaf</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
|
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</spark>
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<ok to="End"/>
|
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<error to="Kill"/>
|
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</action>
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<end name="End"/>
|
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</workflow-app>
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@ -1,46 +1,52 @@
|
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<workflow-app name="Datacite_to_ActionSet_Workflow" xmlns="uri:oozie:workflow:0.5">
|
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<workflow-app name="Collect_Datacite" xmlns="uri:oozie:workflow:0.5">
|
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<parameters>
|
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<property>
|
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<name>sourcePath</name>
|
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<name>mainPath</name>
|
||||
<description>the working path of Datacite stores</description>
|
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</property>
|
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<property>
|
||||
<name>outputPath</name>
|
||||
<description>the path of Datacite ActionSet</description>
|
||||
<name>isLookupUrl</name>
|
||||
<description>The IS lookUp service endopoint</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>blocksize</name>
|
||||
<value>100</value>
|
||||
<description>The request block size</description>
|
||||
</property>
|
||||
|
||||
</parameters>
|
||||
|
||||
<start to="ExportDataset"/>
|
||||
<start to="ImportDatacite"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
|
||||
<action name="ExportDataset">
|
||||
<action name="ImportDatacite">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>ExportDataset</name>
|
||||
<class>eu.dnetlib.dhp.actionmanager.datacite.ExportActionSetJobNode</class>
|
||||
<name>ImportDatacite</name>
|
||||
<class>eu.dnetlib.dhp.datacite.ImportDatacite</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||
<arg>--targetPath</arg><arg>${outputPath}</arg>
|
||||
<arg>--targetPath</arg><arg>${mainPath}/datacite_update</arg>
|
||||
<arg>--dataciteDumpPath</arg><arg>${mainPath}/datacite_dump</arg>
|
||||
<arg>--namenode</arg><arg>${nameNode}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
<arg>--blocksize</arg><arg>${blocksize}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
@ -0,0 +1,126 @@
|
||||
<workflow-app name="transform_Datacite" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>mainPath</name>
|
||||
<description>the working path of Datacite stores</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>isLookupUrl</name>
|
||||
<description>The IS lookUp service endopoint</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>mdStoreOutputId</name>
|
||||
<description>the identifier of the cleaned MDStore</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>mdStoreManagerURI</name>
|
||||
<description>the path of the cleaned mdstore</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="StartTransaction"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="StartTransaction">
|
||||
<java>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
</configuration>
|
||||
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
|
||||
<arg>--action</arg><arg>NEW_VERSION</arg>
|
||||
<arg>--mdStoreID</arg><arg>${mdStoreOutputId}</arg>
|
||||
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
|
||||
<capture-output/>
|
||||
</java>
|
||||
<ok to="TransformJob"/>
|
||||
<error to="EndReadRollBack"/>
|
||||
</action>
|
||||
|
||||
<action name="TransformJob">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>TransformJob</name>
|
||||
<class>eu.dnetlib.dhp.datacite.GenerateDataciteDatasetSpark</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${mainPath}/datacite_dump</arg>
|
||||
<arg>--mdstoreOutputVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
<arg>--exportLinks</arg><arg>true</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="CommitVersion"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="CommitVersion">
|
||||
<java>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
</configuration>
|
||||
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
|
||||
<arg>--action</arg><arg>COMMIT</arg>
|
||||
<arg>--namenode</arg><arg>${nameNode}</arg>
|
||||
<arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
|
||||
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
|
||||
</java>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="EndReadRollBack">
|
||||
<java>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
</configuration>
|
||||
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
|
||||
<arg>--action</arg><arg>READ_UNLOCK</arg>
|
||||
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
|
||||
<arg>--readMDStoreId</arg><arg>${wf:actionData('BeginRead')['mdStoreReadLockVersion']}</arg>
|
||||
<capture-output/>
|
||||
</java>
|
||||
<ok to="RollBack"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="RollBack">
|
||||
<java>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
</configuration>
|
||||
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
|
||||
<arg>--action</arg><arg>ROLLBACK</arg>
|
||||
<arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
|
||||
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
|
||||
</java>
|
||||
<ok to="Kill"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
@ -1,8 +1,7 @@
|
||||
package eu.dnetlib.dhp.actionmanager.datacite
|
||||
package eu.dnetlib.dhp.datacite
|
||||
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import com.fasterxml.jackson.databind.SerializationFeature
|
||||
import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature}
|
||||
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
@ -1,136 +0,0 @@
|
||||
|
||||
package eu.dnetlib.dhp.oa.graph.raw;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.FlatMapFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.clearspring.analytics.util.Lists;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
|
||||
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
|
||||
import eu.dnetlib.dhp.schema.common.EntityType;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
|
||||
public class CopyHdfsOafApplication extends AbstractMigrationApplication {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(CopyHdfsOafApplication.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void main(final String[] args) throws Exception {
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
CopyHdfsOafApplication.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
final Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
final String mdstoreManagerUrl = parser.get("mdstoreManagerUrl");
|
||||
log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl);
|
||||
|
||||
final String mdFormat = parser.get("mdFormat");
|
||||
log.info("mdFormat: {}", mdFormat);
|
||||
|
||||
final String mdLayout = parser.get("mdLayout");
|
||||
log.info("mdLayout: {}", mdLayout);
|
||||
|
||||
final String mdInterpretation = parser.get("mdInterpretation");
|
||||
log.info("mdInterpretation: {}", mdInterpretation);
|
||||
|
||||
final String hdfsPath = parser.get("hdfsPath");
|
||||
log.info("hdfsPath: {}", hdfsPath);
|
||||
|
||||
final String isLookupUrl = parser.get("isLookupUrl");
|
||||
log.info("isLookupUrl: {}", isLookupUrl);
|
||||
|
||||
final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
|
||||
final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService);
|
||||
|
||||
final Set<String> paths = mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation);
|
||||
|
||||
final SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(conf, isSparkSessionManaged, spark -> processPaths(spark, vocs, hdfsPath, paths));
|
||||
}
|
||||
|
||||
public static void processPaths(final SparkSession spark,
|
||||
final VocabularyGroup vocs,
|
||||
final String outputPath,
|
||||
final Set<String> paths) {
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
log.info("Found {} mdstores", paths.size());
|
||||
paths.forEach(log::info);
|
||||
|
||||
final String[] validPaths = paths
|
||||
.stream()
|
||||
.filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration()))
|
||||
.toArray(String[]::new);
|
||||
log.info("Non empty mdstores {}", validPaths.length);
|
||||
|
||||
if (validPaths.length > 0) {
|
||||
// load the dataset
|
||||
Dataset<Oaf> oaf = spark
|
||||
.read()
|
||||
.load(validPaths)
|
||||
.as(Encoders.kryo(Oaf.class));
|
||||
|
||||
// dispatch each entity type individually in the respective graph subdirectory in append mode
|
||||
for (Map.Entry<String, Class> e : ModelSupport.oafTypes.entrySet()) {
|
||||
oaf
|
||||
.filter((FilterFunction<Oaf>) o -> o.getClass().getSimpleName().toLowerCase().equals(e.getKey()))
|
||||
.map((MapFunction<Oaf, String>) OBJECT_MAPPER::writeValueAsString, Encoders.bean(e.getValue()))
|
||||
.write()
|
||||
.option("compression", "gzip")
|
||||
.mode(SaveMode.Append)
|
||||
.text(outputPath + "/" + e.getKey());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private static Relation getInverse(Relation rel, VocabularyGroup vocs) {
|
||||
final Relation inverse = new Relation();
|
||||
|
||||
inverse.setProperties(rel.getProperties());
|
||||
inverse.setValidated(rel.getValidated());
|
||||
inverse.setValidationDate(rel.getValidationDate());
|
||||
inverse.setCollectedfrom(rel.getCollectedfrom());
|
||||
inverse.setDataInfo(rel.getDataInfo());
|
||||
inverse.setLastupdatetimestamp(rel.getLastupdatetimestamp());
|
||||
|
||||
inverse.setSource(rel.getTarget());
|
||||
inverse.setTarget(rel.getSource());
|
||||
inverse.setRelType(rel.getRelType());
|
||||
inverse.setSubRelType(rel.getSubRelType());
|
||||
|
||||
return inverse;
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,74 @@
|
||||
package eu.dnetlib.dhp.oa.graph.raw
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.common.HdfsSupport
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport
|
||||
import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.commons.lang3.StringUtils
|
||||
import org.apache.http.client.methods.HttpGet
|
||||
import org.apache.http.impl.client.HttpClients
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.{SparkConf, SparkContext}
|
||||
import org.slf4j.LoggerFactory
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
import scala.io.Source
|
||||
|
||||
object CopyHdfsOafSparkApplication {
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
val log = LoggerFactory.getLogger(getClass)
|
||||
val conf = new SparkConf()
|
||||
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json")).mkString)
|
||||
parser.parseArgument(args)
|
||||
|
||||
val spark =
|
||||
SparkSession
|
||||
.builder()
|
||||
.config(conf)
|
||||
.appName(getClass.getSimpleName)
|
||||
.master(parser.get("master")).getOrCreate()
|
||||
|
||||
val sc: SparkContext = spark.sparkContext
|
||||
|
||||
val mdstoreManagerUrl = parser.get("mdstoreManagerUrl")
|
||||
log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl)
|
||||
|
||||
val mdFormat = parser.get("mdFormat")
|
||||
log.info("mdFormat: {}", mdFormat)
|
||||
|
||||
val mdLayout = parser.get("mdLayout")
|
||||
log.info("mdLayout: {}", mdLayout)
|
||||
|
||||
val mdInterpretation = parser.get("mdInterpretation")
|
||||
log.info("mdInterpretation: {}", mdInterpretation)
|
||||
|
||||
val hdfsPath = parser.get("hdfsPath")
|
||||
log.info("hdfsPath: {}", hdfsPath)
|
||||
|
||||
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||
|
||||
val paths = DHPUtils.mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation, true).asScala
|
||||
|
||||
val validPaths: List[String] = paths.filter(p => HdfsSupport.exists(p, sc.hadoopConfiguration)).toList
|
||||
|
||||
if (validPaths.nonEmpty) {
|
||||
val oaf = spark.read.load(validPaths: _*).as[Oaf]
|
||||
val mapper = new ObjectMapper()
|
||||
val l =ModelSupport.oafTypes.entrySet.asScala.map(e => e.getKey).toList
|
||||
l.foreach(
|
||||
e =>
|
||||
oaf.filter(o => o.getClass.getSimpleName.equalsIgnoreCase(e))
|
||||
.map(s => mapper.writeValueAsString(s))(Encoders.STRING)
|
||||
.write
|
||||
.option("compression", "gzip")
|
||||
.mode(SaveMode.Append)
|
||||
.text(s"$hdfsPath/${e}")
|
||||
)
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,152 @@
|
||||
package eu.dnetlib.dhp.oa.graph.resolution
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.common.HdfsSupport
|
||||
import eu.dnetlib.dhp.schema.oaf.{Relation, Result}
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.fs.{FileSystem, Path}
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.sql._
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.JsonAST.{JField, JObject, JString}
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
object SparkResolveRelation {
|
||||
def main(args: Array[String]): Unit = {
|
||||
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||
val conf: SparkConf = new SparkConf()
|
||||
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/resolution/resolve_relations_params.json")))
|
||||
parser.parseArgument(args)
|
||||
val spark: SparkSession =
|
||||
SparkSession
|
||||
.builder()
|
||||
.config(conf)
|
||||
.appName(getClass.getSimpleName)
|
||||
.master(parser.get("master")).getOrCreate()
|
||||
|
||||
|
||||
val graphBasePath = parser.get("graphBasePath")
|
||||
log.info(s"graphBasePath -> $graphBasePath")
|
||||
val workingPath = parser.get("workingPath")
|
||||
log.info(s"workingPath -> $workingPath")
|
||||
|
||||
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
|
||||
import spark.implicits._
|
||||
|
||||
|
||||
//CLEANING TEMPORARY FOLDER
|
||||
HdfsSupport.remove(workingPath, spark.sparkContext.hadoopConfiguration)
|
||||
val fs = FileSystem.get(spark.sparkContext.hadoopConfiguration)
|
||||
fs.mkdirs(new Path(workingPath))
|
||||
|
||||
extractPidResolvedTableFromJsonRDD(spark, graphBasePath, workingPath)
|
||||
|
||||
val mapper: ObjectMapper = new ObjectMapper()
|
||||
|
||||
val rPid: Dataset[(String, String)] = spark.read.load(s"$workingPath/relationResolvedPid").as[(String, String)]
|
||||
|
||||
val relationDs: Dataset[(String, Relation)] = spark.read.text(s"$graphBasePath/relation").as[String]
|
||||
.map(s => mapper.readValue(s, classOf[Relation])).as[Relation]
|
||||
.map(r => (r.getSource.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
|
||||
|
||||
relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_2")), "left").map {
|
||||
m =>
|
||||
val sourceResolved = m._2
|
||||
val currentRelation = m._1._2
|
||||
if (sourceResolved != null && sourceResolved._1 != null && sourceResolved._1.nonEmpty)
|
||||
currentRelation.setSource(sourceResolved._1)
|
||||
currentRelation
|
||||
}.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$workingPath/relationResolvedSource")
|
||||
|
||||
|
||||
val relationSourceResolved: Dataset[(String, Relation)] = spark.read.load(s"$workingPath/relationResolvedSource").as[Relation]
|
||||
.map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
|
||||
relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_2")), "left").map {
|
||||
m =>
|
||||
val targetResolved = m._2
|
||||
val currentRelation = m._1._2
|
||||
if (targetResolved != null && targetResolved._1.nonEmpty)
|
||||
currentRelation.setTarget(targetResolved._1)
|
||||
currentRelation
|
||||
}.filter(r => !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved"))
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$workingPath/relation_resolved")
|
||||
|
||||
|
||||
// TO BE conservative we keep the original relation in the working dir
|
||||
// and save the relation resolved on the graphBasePath
|
||||
//In future this two line of code should be removed
|
||||
|
||||
fs.rename(new Path(s"$graphBasePath/relation"), new Path(s"$workingPath/relation"))
|
||||
|
||||
spark.read.load(s"$workingPath/relation_resolved").as[Relation]
|
||||
.map(r => mapper.writeValueAsString(r))
|
||||
.write
|
||||
.option("compression", "gzip")
|
||||
.mode(SaveMode.Overwrite)
|
||||
.text(s"$graphBasePath/relation")
|
||||
}
|
||||
|
||||
|
||||
def extractPidsFromRecord(input: String): (String, List[(String, String)]) = {
|
||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||
lazy val json: json4s.JValue = parse(input)
|
||||
val id: String = (json \ "id").extract[String]
|
||||
val result: List[(String, String)] = for {
|
||||
JObject(pids) <- json \\ "instance" \ "pid"
|
||||
JField("value", JString(pidValue)) <- pids
|
||||
JField("qualifier", JObject(qualifier)) <- pids
|
||||
JField("classid", JString(pidType)) <- qualifier
|
||||
} yield (pidValue, pidType)
|
||||
|
||||
val alternateIds: List[(String, String)] = for {
|
||||
JObject(pids) <- json \\ "alternateIdentifier"
|
||||
JField("value", JString(pidValue)) <- pids
|
||||
JField("qualifier", JObject(qualifier)) <- pids
|
||||
JField("classid", JString(pidType)) <- qualifier
|
||||
} yield (pidValue, pidType)
|
||||
|
||||
(id, result ::: alternateIds)
|
||||
}
|
||||
|
||||
|
||||
private def isRelation(input: String): Boolean = {
|
||||
|
||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||
lazy val json: json4s.JValue = parse(input)
|
||||
val source = (json \ "source").extractOrElse[String](null)
|
||||
|
||||
source != null
|
||||
}
|
||||
|
||||
private def extractPidResolvedTableFromJsonRDD(spark: SparkSession, graphPath: String, workingPath: String) = {
|
||||
import spark.implicits._
|
||||
|
||||
val d: RDD[(String, String)] = spark.sparkContext.textFile(s"$graphPath/*")
|
||||
.filter(i => !isRelation(i))
|
||||
.map(i => extractPidsFromRecord(i))
|
||||
.filter(s => s != null && s._1 != null && s._2 != null && s._2.nonEmpty)
|
||||
.flatMap { p =>
|
||||
p._2.map(pid =>
|
||||
(p._1, DHPUtils.generateUnresolvedIdentifier(pid._1, pid._2))
|
||||
)
|
||||
}.filter(r => r._1 != null || r._2 != null)
|
||||
|
||||
spark.createDataset(d)
|
||||
.groupByKey(_._2)
|
||||
.reduceGroups((x, y) => if (x._1.startsWith("50|doi") || x._1.startsWith("50|pmid")) x else y)
|
||||
.map(s => s._2)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$workingPath/relationResolvedPid")
|
||||
}
|
||||
|
||||
}
|
||||
@ -1,154 +0,0 @@
|
||||
package eu.dnetlib.dhp.sx.graph
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.{Relation, Result}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.io.compress.GzipCodec
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.sql._
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.JsonAST.{JField, JObject, JString}
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
object SparkResolveRelation {
|
||||
def main(args: Array[String]): Unit = {
|
||||
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||
val conf: SparkConf = new SparkConf()
|
||||
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/resolve_relations_params.json")))
|
||||
parser.parseArgument(args)
|
||||
val spark: SparkSession =
|
||||
SparkSession
|
||||
.builder()
|
||||
.config(conf)
|
||||
.appName(getClass.getSimpleName)
|
||||
.master(parser.get("master")).getOrCreate()
|
||||
|
||||
|
||||
val relationPath = parser.get("relationPath")
|
||||
log.info(s"sourcePath -> $relationPath")
|
||||
val entityPath = parser.get("entityPath")
|
||||
log.info(s"entityPath -> $entityPath")
|
||||
val workingPath = parser.get("workingPath")
|
||||
log.info(s"workingPath -> $workingPath")
|
||||
|
||||
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
|
||||
import spark.implicits._
|
||||
|
||||
|
||||
extractPidResolvedTableFromJsonRDD(spark, entityPath, workingPath)
|
||||
|
||||
val mappper = new ObjectMapper()
|
||||
|
||||
val rPid:Dataset[(String,String)] = spark.read.load(s"$workingPath/relationResolvedPid").as[(String,String)]
|
||||
|
||||
val relationDs:Dataset[(String,Relation)] = spark.read.load(relationPath).as[Relation].map(r => (r.getSource.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
|
||||
|
||||
relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_2")), "left").map{
|
||||
m =>
|
||||
val sourceResolved = m._2
|
||||
val currentRelation = m._1._2
|
||||
if (sourceResolved!=null && sourceResolved._1!=null && sourceResolved._1.nonEmpty)
|
||||
currentRelation.setSource(sourceResolved._1)
|
||||
currentRelation
|
||||
}.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$workingPath/relationResolvedSource")
|
||||
|
||||
|
||||
val relationSourceResolved:Dataset[(String,Relation)] = spark.read.load(s"$workingPath/relationResolvedSource").as[Relation].map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
|
||||
relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_2")), "left").map{
|
||||
m =>
|
||||
val targetResolved = m._2
|
||||
val currentRelation = m._1._2
|
||||
if (targetResolved!=null && targetResolved._1.nonEmpty)
|
||||
currentRelation.setTarget(targetResolved._1)
|
||||
currentRelation
|
||||
}.filter(r => r.getSource.startsWith("50")&& r.getTarget.startsWith("50"))
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$workingPath/relation_resolved")
|
||||
|
||||
spark.read.load(s"$workingPath/relation_resolved").as[Relation]
|
||||
.map(r => mappper.writeValueAsString(r))
|
||||
.rdd.saveAsTextFile(s"$workingPath/relation", classOf[GzipCodec])
|
||||
|
||||
}
|
||||
|
||||
|
||||
def extractPidsFromRecord(input:String):(String,List[(String,String)]) = {
|
||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||
lazy val json: json4s.JValue = parse(input)
|
||||
val id:String = (json \ "id").extract[String]
|
||||
val result: List[(String,String)] = for {
|
||||
JObject(pids) <- json \ "pid"
|
||||
JField("value", JString(pidValue)) <- pids
|
||||
JField("qualifier", JObject(qualifier)) <- pids
|
||||
JField("classname", JString(pidType)) <- qualifier
|
||||
} yield (pidValue, pidType)
|
||||
|
||||
val alternateIds: List[(String,String)] = for {
|
||||
JObject(pids) <- json \\ "alternateIdentifier"
|
||||
JField("value", JString(pidValue)) <- pids
|
||||
JField("qualifier", JObject(qualifier)) <- pids
|
||||
JField("classname", JString(pidType)) <- qualifier
|
||||
} yield (pidValue, pidType)
|
||||
|
||||
(id,result:::alternateIds)
|
||||
}
|
||||
|
||||
private def extractPidResolvedTableFromJsonRDD(spark: SparkSession, entityPath: String, workingPath: String) = {
|
||||
import spark.implicits._
|
||||
|
||||
val d: RDD[(String,String)] = spark.sparkContext.textFile(s"$entityPath/*")
|
||||
.map(i => extractPidsFromRecord(i))
|
||||
.filter(s => s != null && s._1!= null && s._2!=null && s._2.nonEmpty)
|
||||
.flatMap{ p =>
|
||||
p._2.map(pid =>
|
||||
(p._1, convertPidToDNETIdentifier(pid._1, pid._2))
|
||||
)
|
||||
}.filter(r =>r._1 != null || r._2 != null)
|
||||
|
||||
spark.createDataset(d)
|
||||
.groupByKey(_._2)
|
||||
.reduceGroups((x, y) => if (x._1.startsWith("50|doi") || x._1.startsWith("50|pmid")) x else y)
|
||||
.map(s => s._2)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$workingPath/relationResolvedPid")
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
This method should be used once we finally convert everythings in Kryo dataset
|
||||
instead of using rdd of json
|
||||
*/
|
||||
private def extractPidResolvedTableFromKryo(spark: SparkSession, entityPath: String, workingPath: String) = {
|
||||
import spark.implicits._
|
||||
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
||||
val entities: Dataset[Result] = spark.read.load(s"$entityPath/*").as[Result]
|
||||
entities.flatMap(e => e.getPid.asScala
|
||||
.map(p =>
|
||||
convertPidToDNETIdentifier(p.getValue, p.getQualifier.getClassid))
|
||||
.filter(s => s != null)
|
||||
.map(s => (s, e.getId))
|
||||
).groupByKey(_._1)
|
||||
.reduceGroups((x, y) => if (x._2.startsWith("50|doi") || x._2.startsWith("50|pmid")) x else y)
|
||||
.map(s => s._2)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$workingPath/relationResolvedPid")
|
||||
}
|
||||
|
||||
def convertPidToDNETIdentifier(pid:String, pidType: String):String = {
|
||||
if (pid==null || pid.isEmpty || pidType== null || pidType.isEmpty)
|
||||
null
|
||||
else
|
||||
s"unresolved::${pid.toLowerCase}::${pidType.toLowerCase}"
|
||||
}
|
||||
|
||||
}
|
||||
@ -1,59 +1,37 @@
|
||||
<workflow-app name="Resolve Relation" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>entityPath</name>
|
||||
<description>the path of deduplicate Entities</description>
|
||||
<name>graphBasePath</name>
|
||||
<description>the path of the graph</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>relationPath</name>
|
||||
<description>the path of relation unresolved</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>targetPath</name>
|
||||
<description>the path of relation unresolved</description>
|
||||
</property>
|
||||
|
||||
</parameters>
|
||||
|
||||
<start to="DropRelFolder"/>
|
||||
<start to="ResolveRelations"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
|
||||
<action name="DropRelFolder">
|
||||
<fs>
|
||||
<delete path='${targetPath}/relation'/>
|
||||
<delete path='${targetPath}/relation_resolved'/>
|
||||
<delete path='${targetPath}/resolvedSource'/>
|
||||
<delete path='${targetPath}/resolvedPid'/>
|
||||
|
||||
</fs>
|
||||
<ok to="ResolveRelations"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<action name="ResolveRelations">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Resolve Relations in raw graph</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkResolveRelation</class>
|
||||
<class>eu.dnetlib.dhp.oa.graph.resolution.SparkResolveRelation</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=3000
|
||||
--conf spark.sql.shuffle.partitions=8000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--relationPath</arg><arg>${relationPath}</arg>
|
||||
<arg>--workingPath</arg><arg>${targetPath}</arg>
|
||||
<arg>--entityPath</arg><arg>${entityPath}</arg>
|
||||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingDir}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
@ -1,6 +1,5 @@
|
||||
[
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"r", "paramLongName":"relationPath", "paramDescription": "the source Path", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the source Path", "paramRequired": true},
|
||||
{"paramName":"e", "paramLongName":"entityPath", "paramDescription": "the path of the raw graph", "paramRequired": true}
|
||||
{"paramName":"g", "paramLongName":"graphBasePath", "paramDescription": "the path of the raw graph", "paramRequired": true}
|
||||
]
|
||||
@ -1,4 +1,4 @@
|
||||
#!/usr/bin/env bash
|
||||
|
||||
curl --request GET $1/cache/updateCache
|
||||
sleep 20h
|
||||
sleep 6h
|
||||
Loading…
Reference in New Issue