added workflow to serialize scholix and summary in json
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package eu.dnetlib.dhp.sx.graph
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.sx.scholix.Scholix
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import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
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import org.apache.commons.io.IOUtils
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import org.apache.spark.SparkConf
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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import org.apache.hadoop.io.compress._
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object SparkConvertObjectToJson {
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def main(args: Array[String]): Unit = {
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val log: Logger = LoggerFactory.getLogger(getClass)
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/convert_object_json_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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log.info(s"sourcePath -> $sourcePath")
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val targetPath = parser.get("targetPath")
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log.info(s"targetPath -> $targetPath")
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val objectType = parser.get("objectType")
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log.info(s"objectType -> $objectType")
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implicit val scholixEncoder :Encoder[Scholix]= Encoders.kryo[Scholix]
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implicit val summaryEncoder :Encoder[ScholixSummary]= Encoders.kryo[ScholixSummary]
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val mapper = new ObjectMapper
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objectType.toLowerCase match {
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case "scholix" =>
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log.info("Serialize Scholix")
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val d: Dataset[Scholix] = spark.read.load(sourcePath).as[Scholix]
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d.map(s => mapper.writeValueAsString(s))(Encoders.STRING).rdd.repartition(6000).saveAsTextFile(targetPath, classOf[GzipCodec])
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case "summary" =>
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log.info("Serialize Summary")
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val d: Dataset[ScholixSummary] = spark.read.load(sourcePath).as[ScholixSummary]
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d.map(s => mapper.writeValueAsString(s))(Encoders.STRING).rdd.repartition(1000).saveAsTextFile(targetPath, classOf[GzipCodec])
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}
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}
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}
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@ -0,0 +1,6 @@
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[
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{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
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{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
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{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true},
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{"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true}
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]
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@ -117,6 +117,68 @@
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<arg>--relationPath</arg><arg>${targetPath}/resolved/resolvedRelation</arg>
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<arg>--relationPath</arg><arg>${targetPath}/resolved/resolvedRelation</arg>
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</spark>
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</spark>
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<ok to="DropJSONPath"/>
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<error to="Kill"/>
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</action>
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<action name="DropJSONPath">
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<fs>
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<delete path='${targetPath}/index'/>
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<mkdir path='${targetPath}/index/'/>
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</fs>
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<ok to="SerializeScholix"/>
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<error to="Kill"/>
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</action>
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<action name="SerializeScholix">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Serialize scholix to JSON</name>
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<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.shuffle.partitions=6000
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--master</arg><arg>yarn</arg>
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<arg>--sourcePath</arg><arg>${targetPath}/provision/scholix/scholix</arg>
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<arg>--targetPath</arg><arg>${targetPath}/index/scholix_json</arg>
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<arg>--objectType</arg><arg>scholix</arg>
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</spark>
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<ok to="SerializeSummary"/>
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<error to="Kill"/>
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</action>
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<action name="SerializeSummary">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Serialize summary to JSON</name>
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<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.shuffle.partitions=6000
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--master</arg><arg>yarn</arg>
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<arg>--sourcePath</arg><arg>${targetPath}/provision/summaries_filtered</arg>
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<arg>--targetPath</arg><arg>${targetPath}/index/summaries_json</arg>
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<arg>--objectType</arg><arg>summary</arg>
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</spark>
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<ok to="End"/>
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<ok to="End"/>
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<error to="Kill"/>
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<error to="Kill"/>
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</action>
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</action>
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