forked from D-Net/dnet-hadoop
imported changes in stable_id into master
This commit is contained in:
parent
8c96a82a03
commit
7dc824fc23
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@ -12,31 +12,10 @@ import org.slf4j.{Logger, LoggerFactory}
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object SparkConvertORCIDToOAF {
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val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)
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def run(spark:SparkSession,sourcePath:String,workingPath:String, targetPath:String):Unit = {
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def run(spark:SparkSession,workingPath:String, targetPath:String):Unit = {
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import spark.implicits._
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implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
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val inputRDD:RDD[OrcidAuthor] = spark.sparkContext.textFile(s"$sourcePath/authors").map(s => ORCIDToOAF.convertORCIDAuthor(s)).filter(s => s!= null).filter(s => ORCIDToOAF.authorValid(s))
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spark.createDataset(inputRDD).as[OrcidAuthor].write.mode(SaveMode.Overwrite).save(s"$workingPath/author")
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val res = spark.sparkContext.textFile(s"$sourcePath/works").flatMap(s => ORCIDToOAF.extractDOIWorks(s)).filter(s => s!= null)
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spark.createDataset(res).as[OrcidWork].write.mode(SaveMode.Overwrite).save(s"$workingPath/works")
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val authors :Dataset[OrcidAuthor] = spark.read.load(s"$workingPath/author").as[OrcidAuthor]
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val works :Dataset[OrcidWork] = spark.read.load(s"$workingPath/works").as[OrcidWork]
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works.joinWith(authors, authors("oid").equalTo(works("oid")))
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.map(i =>{
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val doi = i._1.doi
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val author = i._2
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(doi, author)
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}).groupBy(col("_1").alias("doi"))
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.agg(collect_list(col("_2")).alias("authors"))
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.write.mode(SaveMode.Overwrite).save(s"$workingPath/orcidworksWithAuthor")
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val dataset: Dataset[ORCIDItem] =spark.read.load(s"$workingPath/orcidworksWithAuthor").as[ORCIDItem]
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logger.info("Converting ORCID to OAF")
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@ -55,10 +34,10 @@ object SparkConvertORCIDToOAF {
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.master(parser.get("master")).getOrCreate()
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val sourcePath = parser.get("sourcePath")
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val workingPath = parser.get("workingPath")
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val targetPath = parser.get("targetPath")
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run(spark, sourcePath, workingPath, targetPath)
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run(spark, workingPath, targetPath)
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}
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@ -0,0 +1,56 @@
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package eu.dnetlib.doiboost.orcid
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf.Publication
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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.rdd.RDD
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.apache.spark.sql.functions.{col, collect_list}
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import org.slf4j.{Logger, LoggerFactory}
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class SparkPreprocessORCID {
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val logger: Logger = LoggerFactory.getLogger(getClass)
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def run(spark:SparkSession,sourcePath:String,workingPath:String):Unit = {
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import spark.implicits._
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val inputRDD:RDD[OrcidAuthor] = spark.sparkContext.textFile(s"$sourcePath/authors").map(s => ORCIDToOAF.convertORCIDAuthor(s)).filter(s => s!= null).filter(s => ORCIDToOAF.authorValid(s))
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spark.createDataset(inputRDD).as[OrcidAuthor].write.mode(SaveMode.Overwrite).save(s"$workingPath/author")
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val res = spark.sparkContext.textFile(s"$sourcePath/works").flatMap(s => ORCIDToOAF.extractDOIWorks(s)).filter(s => s!= null)
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spark.createDataset(res).as[OrcidWork].write.mode(SaveMode.Overwrite).save(s"$workingPath/works")
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val authors :Dataset[OrcidAuthor] = spark.read.load(s"$workingPath/author").as[OrcidAuthor]
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val works :Dataset[OrcidWork] = spark.read.load(s"$workingPath/works").as[OrcidWork]
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works.joinWith(authors, authors("oid").equalTo(works("oid")))
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.map(i =>{
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val doi = i._1.doi
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val author = i._2
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(doi, author)
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}).groupBy(col("_1").alias("doi"))
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.agg(collect_list(col("_2")).alias("authors"))
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.write.mode(SaveMode.Overwrite).save(s"$workingPath/orcidworksWithAuthor")
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}
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def main(args: Array[String]): Unit = {
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/preprocess_orcid_params.json")))
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parser.parseArgument(args)
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val spark: SparkSession =
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SparkSession
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.builder()
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.config(conf)
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.appName(getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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val sourcePath = parser.get("sourcePath")
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val workingPath = parser.get("workingPath")
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run(spark, sourcePath, workingPath)
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}
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}
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@ -1,6 +1,6 @@
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[
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{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
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{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the working dir path", "paramRequired": true},
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{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working dir path", "paramRequired": true},
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{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the target dir path", "paramRequired": true},
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{"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true}
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]
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@ -1,101 +0,0 @@
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<workflow-app name="import Crossref from index into HDFS" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>workingPath</name>
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<description>the working dir base path</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>timestamp</name>
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<description>Timestamp for incremental Harvesting</description>
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</property>
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</parameters>
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<start to="ImportCrossRef"/>
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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="ImportCrossRef">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>
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<arg>-t</arg><arg>${workingPath}/input/crossref/index_update</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-ts</arg><arg>${timestamp}</arg>
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</java>
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<ok to="GenerateDataset"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateDataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>ExtractCrossrefToOAF</name>
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<class>eu.dnetlib.doiboost.crossref.CrossrefDataset</class>
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<jar>dhp-doiboost-${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=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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${sparkExtraOPT}
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</spark-opts>
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<arg>--workingPath</arg><arg>/data/doiboost/input/crossref</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="RenameDataset"/>
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<error to="Kill"/>
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</action>
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<action name="RenameDataset">
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<fs>
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<delete path='${workingPath}/input/crossref/crossref_ds'/>
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<move source="${workingPath}/input/crossref/crossref_ds_updated"
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target="${workingPath}/input/crossref/crossref_ds"/>
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</fs>
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<ok to="ConvertCrossrefToOAF"/>
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<error to="Kill"/>
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</action>
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<action name="ConvertCrossrefToOAF">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>ConvertCrossrefToOAF</name>
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<class>eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF</class>
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<jar>dhp-doiboost-${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=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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${sparkExtraOPT}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${workingPath}/input/crossref/crossref_ds</arg>
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<arg>--targetPath</arg><arg>${workingPath}/process/</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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@ -1,38 +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>hive_metastore_uris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<value>/user/spark/spark2ApplicationHistory</value>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
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</property>
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</configuration>
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@ -1,96 +0,0 @@
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<workflow-app name="Create DOIBoostActionSet" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>hostedByMapPath</name>
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<description>the Hosted By Map Path</description>
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</property>
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<property>
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<name>affiliationPath</name>
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<description>the Affliation Path</description>
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</property>
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<property>
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<name>paperAffiliationPath</name>
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<description>the paperAffiliation Path</description>
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</property>
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<property>
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<name>workingDirPath</name>
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<description>the Working Path</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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</parameters>
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<start to="CreateDOIBoost"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="CreateDOIBoost">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Create DOIBoost Infospace</name>
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<class>eu.dnetlib.doiboost.SparkGenerateDoiBoost</class>
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<jar>dhp-doiboost-${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=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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${sparkExtraOPT}
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</spark-opts>
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<arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
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<arg>--affiliationPath</arg><arg>${affiliationPath}</arg>
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<arg>--paperAffiliationPath</arg><arg>${paperAffiliationPath}</arg>
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<arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="GenerateActionSet"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateActionSet">
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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>Generate DOIBoost ActionSet</name>
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<class>eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${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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${sparkExtraOPT}
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</spark-opts>
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<arg>--dbPublicationPath</arg><arg>${workingDirPath}/doiBoostPublicationFiltered</arg>
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<arg>--dbDatasetPath</arg><arg>${workingDirPath}/crossrefDataset</arg>
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<arg>--crossRefRelation</arg><arg>${workingDirPath}/crossrefRelation</arg>
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<arg>--dbaffiliationRelationPath</arg><arg>${workingDirPath}/doiBoostPublicationAffiliation</arg>
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<arg>-do</arg><arg>${workingDirPath}/doiBoostOrganization</arg>
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<arg>--targetPath</arg><arg>${workingDirPath}/actionDataSet</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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@ -1,92 +0,0 @@
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<workflow-app name="import MAG into HDFS" 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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<description>the working dir base path</description>
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</property>
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<property>
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<name>targetPath</name>
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<description>the working dir base path</description>
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</property>
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<property>
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<name>workingPath</name>
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<description>the working dir base path</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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</parameters>
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<start to="ResetWorkingPath"/>
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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="ResetWorkingPath">
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<fs>
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<delete path='${workingPath}'/>
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<mkdir path='${workingPath}'/>
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</fs>
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<ok to="ConvertMagToDataset"/>
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<error to="Kill"/>
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</action>
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<action name="ConvertMagToDataset">
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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>Convert Mag to Dataset</name>
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<class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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${sparkExtraOPT}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--targetPath</arg><arg>${workingPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="PreprocessMag"/>
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<error to="Kill"/>
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</action>
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<action name="PreprocessMag">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Convert Mag to OAF Dataset</name>
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<class>eu.dnetlib.doiboost.mag.SparkPreProcessMAG</class>
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<jar>dhp-doiboost-${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}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
${sparkExtraOPT}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${workingPath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}/process</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -0,0 +1,194 @@
|
|||
<workflow-app name="preprocess DOIBoost ActionSet" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorIntersectionMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
<!-- Crossref Parameters -->
|
||||
<property>
|
||||
<name>inputPathCrossref</name>
|
||||
<description>the Crossref input path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>crossrefTimestamp</name>
|
||||
<description>Timestamp for the Crossref incremental Harvesting</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>esServer</name>
|
||||
<description>elasticsearch server url for the Crossref Harvesting</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>esIndex</name>
|
||||
<description>elasticsearch index name for the Crossref Harvesting</description>
|
||||
</property>
|
||||
<!-- MAG Parameters -->
|
||||
<property>
|
||||
<name>MAGDumpPath</name>
|
||||
<description>the MAG dump working path</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>inputPathMAG</name>
|
||||
<description>the MAG working path</description>
|
||||
</property>
|
||||
<!-- ORCID Parameters -->
|
||||
<property>
|
||||
<name>inputPathOrcid</name>
|
||||
<description>the ORCID input path</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>workingPathOrcid</name>
|
||||
<description>the ORCID working path</description>
|
||||
</property>
|
||||
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="ImportCrossRef"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="ImportCrossRef">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>
|
||||
<arg>--targetPath</arg><arg>${inputPathCrossref}/index_update</arg>
|
||||
<arg>--namenode</arg><arg>${nameNode}</arg>
|
||||
<arg>--esServer</arg><arg>${esServer}</arg>
|
||||
<arg>--esIndex</arg><arg>${esIndex}</arg>
|
||||
<arg>--timestamp</arg><arg>${crossrefTimestamp}</arg>
|
||||
</java>
|
||||
<ok to="GenerateCrossrefDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
<!-- CROSSREF SECTION -->
|
||||
|
||||
<action name="GenerateCrossrefDataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>GenerateCrossrefDataset</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.CrossrefDataset</class>
|
||||
<jar>dhp-doiboost-${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>--workingPath</arg><arg>${inputPathCrossref}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="RenameDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="RenameDataset">
|
||||
<fs>
|
||||
<delete path="${inputPathCrossref}/crossref_ds"/>
|
||||
<move source="${inputPathCrossref}/crossref_ds_updated"
|
||||
target="${inputPathCrossref}/crossref_ds"/>
|
||||
</fs>
|
||||
<ok to="ResetMagWorkingPath"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
|
||||
<!-- MAG SECTION -->
|
||||
<action name="ResetMagWorkingPath">
|
||||
<fs>
|
||||
<delete path="${inputPathMAG}/dataset"/>
|
||||
<delete path="${inputPathMAG}/process"/>
|
||||
</fs>
|
||||
<ok to="ConvertMagToDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ConvertMagToDataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert Mag to Dataset</name>
|
||||
<class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${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}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${MAGDumpPath}</arg>
|
||||
<arg>--targetPath</arg><arg>${inputPathMAG}/dataset</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="PreprocessORCID"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
|
||||
<!-- ORCID SECTION -->
|
||||
<action name="PreprocessORCID">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert ORCID to Dataset</name>
|
||||
<class>eu.dnetlib.doiboost.orcid.SparkPreprocessORCID</class>
|
||||
<jar>dhp-doiboost-${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>${inputPathOrcid}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPathOrcid}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -0,0 +1,6 @@
|
|||
[
|
||||
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working dir path", "paramRequired": true},
|
||||
{"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true}
|
||||
|
||||
]
|
||||
|
|
@ -16,8 +16,8 @@
|
|||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.wf.rerun.failnodes</name>
|
||||
<value>false</value>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
|
|
@ -0,0 +1,262 @@
|
|||
<workflow-app name="Generate DOIBoost ActionSet" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorIntersectionMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
<!-- Itersection Parameters -->
|
||||
<property>
|
||||
<name>workingPath</name>
|
||||
<description>the working Path</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>hostedByMapPath</name>
|
||||
<description>the hostedByMap Path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>outputPath</name>
|
||||
<description>the Path of the sequence file action set</description>
|
||||
</property>
|
||||
|
||||
|
||||
<!-- Crossref Parameters -->
|
||||
<property>
|
||||
<name>inputPathCrossref</name>
|
||||
<description>the Crossref input path</description>
|
||||
</property>
|
||||
|
||||
<!-- MAG Parameters -->
|
||||
<property>
|
||||
<name>inputPathMAG</name>
|
||||
<description>the MAG working path</description>
|
||||
</property>
|
||||
|
||||
|
||||
<!-- UnpayWall Parameters -->
|
||||
<property>
|
||||
<name>inputPathUnpayWall</name>
|
||||
<description>the UnpayWall working path</description>
|
||||
</property>
|
||||
|
||||
<!-- ORCID Parameters -->
|
||||
<property>
|
||||
<name>inputPathOrcid</name>
|
||||
<description>the ORCID input path</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>workingPathOrcid</name>
|
||||
<description>the ORCID working path</description>
|
||||
</property>
|
||||
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="resume_from"/>
|
||||
|
||||
<decision name="resume_from">
|
||||
<switch>
|
||||
<case to="ProcessMAG">${wf:conf('resumeFrom') eq 'PreprocessMag'}</case>
|
||||
<case to="ProcessUW">${wf:conf('resumeFrom') eq 'PreprocessUW'}</case>
|
||||
<case to="ProcessORCID">${wf:conf('resumeFrom') eq 'PreprocessORCID'}</case>
|
||||
<case to="CreateDOIBoost">${wf:conf('resumeFrom') eq 'CreateDOIBoost'}</case>
|
||||
<case to="GenerateActionSet">${wf:conf('resumeFrom') eq 'GenerateActionSet'}</case>
|
||||
<default to="ConvertCrossrefToOAF"/>
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="ConvertCrossrefToOAF">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>ConvertCrossrefToOAF</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF</class>
|
||||
<jar>dhp-doiboost-${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>${inputPathCrossref}/crossref_ds</arg>
|
||||
<arg>--targetPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="ProcessMAG"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ProcessMAG">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert Mag to OAF Dataset</name>
|
||||
<class>eu.dnetlib.doiboost.mag.SparkProcessMAG</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorIntersectionMemory}
|
||||
--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}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${inputPathMAG}/dataset</arg>
|
||||
<arg>--workingPath</arg><arg>${inputPathMAG}/process_p</arg>
|
||||
<arg>--targetPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="ProcessUW"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<!-- UnpayWall SECTION -->
|
||||
|
||||
<action name="ProcessUW">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert UnpayWall to Dataset</name>
|
||||
<class>eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--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}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${inputPathUnpayWall}/uw_extracted</arg>
|
||||
<arg>--targetPath</arg><arg>${workingPath}/uwPublication</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="ProcessORCID"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<!-- ORCID SECTION -->
|
||||
<action name="ProcessORCID">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert ORCID to Dataset</name>
|
||||
<class>eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF</class>
|
||||
<jar>dhp-doiboost-${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>--workingPath</arg><arg>${workingPathOrcid}</arg>
|
||||
<arg>--targetPath</arg><arg>${workingPath}/orcidPublication</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="CreateDOIBoost"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<!-- INTERSECTION SECTION-->
|
||||
<action name="CreateDOIBoost">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Create DOIBoost Infospace</name>
|
||||
<class>eu.dnetlib.doiboost.SparkGenerateDoiBoost</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorIntersectionMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--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}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
|
||||
<arg>--affiliationPath</arg><arg>${inputPathMAG}/dataset/Affiliations</arg>
|
||||
<arg>--paperAffiliationPath</arg><arg>${inputPathMAG}/dataset/PaperAuthorAffiliations</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="GenerateActionSet"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
<action name="GenerateActionSet">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Generate DOIBoost ActionSet</name>
|
||||
<class>eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet</class>
|
||||
<jar>dhp-doiboost-${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>--dbPublicationPath</arg><arg>${workingPath}/doiBoostPublicationFiltered</arg>
|
||||
<arg>--dbDatasetPath</arg><arg>${workingPath}/crossrefDataset</arg>
|
||||
<arg>--crossRefRelation</arg><arg>${workingPath}/crossrefRelation</arg>
|
||||
<arg>--dbaffiliationRelationPath</arg><arg>${workingPath}/doiBoostPublicationAffiliation</arg>
|
||||
<arg>--dbOrganizationPath</arg><arg>${workingPath}/doiBoostOrganization</arg>
|
||||
<arg>--targetPath</arg><arg>${workingPath}/actionDataSet</arg>
|
||||
<arg>--sFilePath</arg><arg>${outputPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -1,38 +0,0 @@
|
|||
<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>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<value>/user/spark/spark2ApplicationHistory</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2ExtraListeners</name>
|
||||
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2SqlQueryExecutionListeners</name>
|
||||
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -1,55 +0,0 @@
|
|||
<workflow-app name="import UnpayWall into HDFS" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sourcePath</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>targetPath</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="PreprocessUW"/>
|
||||
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="PreprocessUW">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert UnpayWall to Dataset</name>
|
||||
<class>eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
${sparkExtraOPT}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/uw_extracted</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
Loading…
Reference in New Issue