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added first implementation of Pangaea Mapping

This commit is contained in:
Sandro La Bruzzo 2021-04-27 11:30:37 +02:00
parent c25238480c
commit 7f8848ecdd
7 changed files with 237 additions and 10 deletions
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21
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
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@ -73,7 +73,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
.load(DedupUtility.createMergeRelPath(workingPath, "*", "*"))
.as(Encoders.bean(Relation.class));
//<mergedObjectID, dedupID>
// <mergedObjectID, dedupID>
Dataset<Tuple2<String, String>> mergedIds = mergeRels
.where(col("relClass").equalTo(ModelConstants.MERGES))
.select(col("source"), col("target"))
@ -116,31 +116,32 @@ public class SparkPropagateRelation extends AbstractSparkAction {
.map((MapFunction<Tuple2<String, Relation>, Relation>) t -> t._2(), Encoders.bean(Relation.class));
}
//redirect the relations to the dedupID
// redirect the relations to the dedupID
private static Dataset<Relation> createNewRels(
Dataset<Relation> rels, //all the relations to be redirected
Dataset<Tuple2<String, String>> mergedIds, //merge rels: <mergedObjectID, dedupID>
Dataset<Relation> rels, // all the relations to be redirected
Dataset<Tuple2<String, String>> mergedIds, // merge rels: <mergedObjectID, dedupID>
MapFunction<Tuple2<Tuple2<Tuple3<String, Relation, String>, Tuple2<String, String>>, Tuple2<String, String>>, Relation> mapRel) {
//<sourceID, relation, targetID>
// <sourceID, relation, targetID>
Dataset<Tuple3<String, Relation, String>> mapped = rels
.map(
(MapFunction<Relation, Tuple3<String, Relation, String>>) r -> new Tuple3<>(getId(r, FieldType.SOURCE),
r, getId(r, FieldType.TARGET)),
Encoders.tuple(Encoders.STRING(), Encoders.kryo(Relation.class), Encoders.STRING()));
//< <sourceID, relation, target>, <sourceID, dedupID> >
// < <sourceID, relation, target>, <sourceID, dedupID> >
Dataset<Tuple2<Tuple3<String, Relation, String>, Tuple2<String, String>>> relSource = mapped
.joinWith(mergedIds, mapped.col("_1").equalTo(mergedIds.col("_1")), "left_outer");
//< <<sourceID, relation, targetID>, <sourceID, dedupID>>, <targetID, dedupID> >
// < <<sourceID, relation, targetID>, <sourceID, dedupID>>, <targetID, dedupID> >
Dataset<Tuple2<Tuple2<Tuple3<String, Relation, String>, Tuple2<String, String>>, Tuple2<String, String>>> relSourceTarget = relSource
.joinWith(mergedIds, relSource.col("_1._3").equalTo(mergedIds.col("_1")), "left_outer");
.joinWith(mergedIds, relSource.col("_1._3").equalTo(mergedIds.col("_1")), "left_outer");
return relSourceTarget
.filter(
(FilterFunction<Tuple2<Tuple2<Tuple3<String, Relation, String>, Tuple2<String, String>>, Tuple2<String, String>>>)
r -> r._1()._1() != null || r._2() != null)
(FilterFunction<Tuple2<Tuple2<Tuple3<String, Relation, String>, Tuple2<String, String>>, Tuple2<String, String>>>) r -> r
._1()
._1() != null || r._2() != null)
.map(mapRel, Encoders.bean(Relation.class))
.distinct();
}

85
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/sx/pangaea/PangaeaUtils.scala Normal file
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@ -0,0 +1,85 @@
package eu.dnetlib.sx.pangaea
import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql.{Encoder, Encoders}
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import java.text.SimpleDateFormat
import java.util.Date
case class PangaeaDataModel(datestamp:String, identifier:String, xml:String) {}
object PangaeaUtils {
def toDataset(input:String):PangaeaDataModel = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
val d = new Date()
val s:String = s"${new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSS")format(d)}Z"
val ds = (json \ "internal-datestamp").extractOrElse[String](s)
val identifier= (json \ "metadatalink").extractOrElse[String]()
val xml= (json \ "xml").extract[String]
PangaeaDataModel(ds, identifier,xml)
}
def getDatasetAggregator(): Aggregator[(String, PangaeaDataModel), PangaeaDataModel, PangaeaDataModel] = new Aggregator[(String, PangaeaDataModel), PangaeaDataModel, PangaeaDataModel]{
override def zero: PangaeaDataModel = null
override def reduce(b: PangaeaDataModel, a: (String, PangaeaDataModel)): PangaeaDataModel = {
if (b == null)
a._2
else {
if (a == null)
b
else {
val ts1 = b.datestamp
val ts2 = a._2.datestamp
if (ts1 > ts2)
b
else
a._2
}
}
}
override def merge(b1: PangaeaDataModel, b2: PangaeaDataModel): PangaeaDataModel = {
if (b1 == null)
b2
else {
if (b2 == null)
b1
else {
val ts1 = b1.datestamp
val ts2 = b2.datestamp
if (ts1 > ts2)
b1
else
b2
}
}
}
override def finish(reduction: PangaeaDataModel): PangaeaDataModel = reduction
override def bufferEncoder: Encoder[PangaeaDataModel] = Encoders.kryo[PangaeaDataModel]
override def outputEncoder: Encoder[PangaeaDataModel] = Encoders.kryo[PangaeaDataModel]
}
}

53
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/sx/pangaea/SparkGeneratePanagaeaDataset.scala Normal file
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@ -0,0 +1,53 @@
package eu.dnetlib.sx.pangaea
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.sx.ebi.SparkCreateEBIDataFrame
import org.apache.spark.rdd.RDD
import org.apache.spark.{SparkConf, SparkContext}
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import scala.io.Source
object SparkGeneratePanagaeaDataset {
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/pangaea/pangaea_to_dataset.json")).mkString)
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(SparkCreateEBIDataFrame.getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
parser.getObjectMap.asScala.foreach(s => logger.info(s"${s._1} -> ${s._2}"))
logger.info("Converting sequential file into Dataset")
val sc:SparkContext = spark.sparkContext
val workingPath:String = parser.get("workingPath")
implicit val pangaeaEncoders: Encoder[PangaeaDataModel] = Encoders.kryo[PangaeaDataModel]
val inputRDD:RDD[PangaeaDataModel] = sc.textFile(s"$workingPath/update").map(s => PangaeaUtils.toDataset(s))
spark.createDataset(inputRDD).as[PangaeaDataModel]
.map(s => (s.identifier,s))(Encoders.tuple(Encoders.STRING, pangaeaEncoders))
.groupByKey(_._1)(Encoders.STRING)
.agg(PangaeaUtils.getDatasetAggregator().toColumn)
.map(s => s._2)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/dataset_updated")
}
}

19
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pangaea/oozie_app/config-default.xml Normal file
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@ -0,0 +1,19 @@
<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>
</configuration>

40
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pangaea/oozie_app/workflow.xml Normal file
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@ -0,0 +1,40 @@
<workflow-app name="Transform_Pangaea_Workflow" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>pangaeaWorkingPath</name>
<description>the Pangaea Working Path</description>
</property>
</parameters>
<start to="ConvertDataset"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ConvertDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Convert Pangaea to Dataset</name>
<class>eu.dnetlib.sx.pangaea.SparkGeneratePanagaeaDataset</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--workingPath</arg><arg>${pangaeaWorkingPath}</arg>
<arg>--master</arg><arg>yarn</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

4
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pangaea/pangaea_to_dataset.json Normal file
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@ -0,0 +1,4 @@
[
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}
]

25
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/pangaea/PangaeaTransformTest.scala Normal file
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@ -0,0 +1,25 @@
package eu.dnetlib.dhp.sx.pangaea
import org.junit.jupiter.api.Test
import java.util.TimeZone
import java.text.SimpleDateFormat
import java.util.Date
class PangaeaTransformTest {
@Test
def test_dateStamp() :Unit ={
val d = new Date()
val s:String = s"${new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSS")format(d)}Z"
println(s)
}
}