forked from D-Net/dnet-hadoop
changed the workflow to extract info from the dump
This commit is contained in:
parent
d6e21bb6ea
commit
f7379255b6
|
@ -1,54 +0,0 @@
|
|||
package eu.dnetlib.doiboost.crossref
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import org.apache.hadoop.io.compress.GzipCodec
|
||||
import org.apache.spark.{SparkConf, SparkContext}
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.JsonAST._
|
||||
import org.json4s.jackson.JsonMethods._
|
||||
|
||||
import scala.io.Source
|
||||
|
||||
object UnpackCrossrefDumpEntries {
|
||||
|
||||
|
||||
val log: Logger = LoggerFactory.getLogger(UnpackCrossrefDumpEntries.getClass)
|
||||
|
||||
|
||||
|
||||
def extractDump(input:String):List[String] = {
|
||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||
lazy val json: json4s.JValue = parse(input)
|
||||
|
||||
val a = (json \ "items").extract[JArray]
|
||||
a.arr.map(s => compact(render(s)))
|
||||
}
|
||||
|
||||
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
val conf = new SparkConf
|
||||
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json")).mkString)
|
||||
parser.parseArgument(args)
|
||||
val master = parser.get("master")
|
||||
val sourcePath = parser.get("sourcePath")
|
||||
val targetPath = parser.get("targetPath")
|
||||
|
||||
val spark: SparkSession = SparkSession.builder().config(conf)
|
||||
.appName(UnpackCrossrefDumpEntries.getClass.getSimpleName)
|
||||
.master(master)
|
||||
.getOrCreate()
|
||||
|
||||
|
||||
val sc: SparkContext = spark.sparkContext
|
||||
|
||||
|
||||
sc.wholeTextFiles(sourcePath,6000).flatMap(d =>extractDump(d._2))
|
||||
.saveAsTextFile(targetPath, classOf[GzipCodec]);
|
||||
|
||||
|
||||
}
|
||||
}
|
|
@ -1,9 +1,13 @@
|
|||
<workflow-app name="read Crossref dump from HDFS" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<!-- <property>-->
|
||||
<!-- <name>workingPath</name>-->
|
||||
<!-- <description>the working dir base path</description>-->
|
||||
<!-- </property>-->
|
||||
<property>
|
||||
<name>crossrefDumpPath</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>inputPathCrossref</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
|
@ -14,25 +18,27 @@
|
|||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<value>2</value>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
|
||||
</parameters>
|
||||
|
||||
<start to="generateCrossrefDataset"/>
|
||||
<start to="ImportCrossRef"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="ReadCrossRefDump">
|
||||
<action name="ImportCrossRef">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords</main-class>
|
||||
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
|
||||
<arg>--workingPath</arg><arg>/data/doiboost/crossref/</arg>
|
||||
<arg>--crossrefFileNameTarGz</arg><arg>crossref.tar.gz</arg>
|
||||
<arg>--crossrefFileNameTarGz</arg><arg>${crossrefDumpPath}/crossref.tar.gz</arg>
|
||||
<arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/files/</arg>
|
||||
</java>
|
||||
<ok to="generateCrossrefDataset"/>
|
||||
<error to="Kill"/>
|
||||
|
@ -42,24 +48,42 @@
|
|||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>SparkCreateCrossredDataset</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.GenerateCrossrefDatasetSpark</class>
|
||||
<name>SparkGenerateCrossrefDataset</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--conf spark.dynamicAllocation.enabled=true
|
||||
--conf spark.dynamicAllocation.maxExecutors=20
|
||||
--executor-memory=6G
|
||||
--driver-memory=7G
|
||||
--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}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>/data/doiboost/crossref/filess</arg>
|
||||
<arg>--targetPath</arg><arg>/tmp/miriam/crossref/crossrefDataset</arg>
|
||||
<arg>--sourcePath</arg><arg>${workingDir}/files</arg>
|
||||
<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds_updated</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="removeFiles"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="removeFiles">
|
||||
<fs>
|
||||
<delete path="${workingDir}/files"/>
|
||||
</fs>
|
||||
<ok to="renameDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="renameDataset">
|
||||
<fs>
|
||||
<delete path="${inputPathCrossref}/crossref_ds"/>
|
||||
<move source="${inputPathCrossref}/crossref_ds_updated"
|
||||
target="${inputPathCrossref}/crossref_ds"/>
|
||||
</fs>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
|
|
@ -41,17 +41,21 @@
|
|||
<description>the Crossref input path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>crossrefTimestamp</name>
|
||||
<description>Timestamp for the Crossref incremental Harvesting</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>esServer</name>
|
||||
<description>elasticsearch server url for the Crossref Harvesting</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>esIndex</name>
|
||||
<description>elasticsearch index name for the Crossref Harvesting</description>
|
||||
<name>crossrefDumpPath</name>
|
||||
<description>the Crossref dump path</description>
|
||||
</property>
|
||||
<!-- <property>-->
|
||||
<!-- <name>crossrefTimestamp</name>-->
|
||||
<!-- <description>Timestamp for the Crossref incremental Harvesting</description>-->
|
||||
<!-- </property>-->
|
||||
<!-- <property>-->
|
||||
<!-- <name>esServer</name>-->
|
||||
<!-- <description>elasticsearch server url for the Crossref Harvesting</description>-->
|
||||
<!-- </property>-->
|
||||
<!-- <property>-->
|
||||
<!-- <name>esIndex</name>-->
|
||||
<!-- <description>elasticsearch index name for the Crossref Harvesting</description>-->
|
||||
<!-- </property>-->
|
||||
|
||||
<!-- MAG Parameters -->
|
||||
<property>
|
||||
|
@ -114,28 +118,39 @@
|
|||
<message>Action failed, error message[${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>${crossrefTimestamp}</arg>-->
|
||||
<!-- </java>-->
|
||||
<!-- <ok to="GenerateCrossrefDataset"/>-->
|
||||
<!-- <error to="Kill"/>-->
|
||||
<!-- </action>-->
|
||||
|
||||
<action name="ImportCrossRef">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>
|
||||
<arg>--targetPath</arg><arg>${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>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords</main-class>
|
||||
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
|
||||
<arg>--crossrefFileNameTarGz</arg><arg>${crossrefDumpPath}/crossref.tar.gz</arg>
|
||||
<arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/files</arg>
|
||||
</java>
|
||||
<ok to="GenerateCrossrefDataset"/>
|
||||
<ok to="generateCrossrefDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
<!-- CROSSREF SECTION -->
|
||||
|
||||
<action name="GenerateCrossrefDataset">
|
||||
<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>
|
||||
<name>SparkGenerateCrossrefDataset</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
|
@ -147,18 +162,18 @@
|
|||
--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>
|
||||
<arg>--sourcePath</arg><arg>${workingDir}/files/</arg>
|
||||
<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds_updated</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="RenameDataset"/>
|
||||
<ok to="removeFiles"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="RenameDataset">
|
||||
<action name="removeFiles">
|
||||
<fs>
|
||||
<delete path="${inputPathCrossref}/crossref_ds"/>
|
||||
<move source="${inputPathCrossref}/crossref_ds_updated"
|
||||
target="${inputPathCrossref}/crossref_ds"/>
|
||||
<delete path="${workingDir}/files"/>
|
||||
</fs>
|
||||
<ok to="ResetMagWorkingPath"/>
|
||||
<error to="Kill"/>
|
||||
|
@ -166,6 +181,44 @@
|
|||
|
||||
|
||||
|
||||
<!-- 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>
|
||||
|
|
Loading…
Reference in New Issue