forked from D-Net/dnet-hadoop
Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop
This commit is contained in:
commit
5e8509bef7
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@ -6,7 +6,7 @@
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp</artifactId>
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<version>1.2.4-SNAPSHOT</version>
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<relativePath>../</relativePath>
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<relativePath>../pom.xml</relativePath>
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</parent>
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<artifactId>dhp-schemas</artifactId>
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@ -0,0 +1,24 @@
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package eu.dnetlib.dhp.schema.orcid;
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import java.util.List;
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public class OrcidDOI {
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private String doi;
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private List<AuthorData> authors;
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public String getDoi() {
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return doi;
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}
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public void setDoi(String doi) {
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this.doi = doi;
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}
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public List<AuthorData> getAuthors() {
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return authors;
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}
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public void setAuthors(List<AuthorData> authors) {
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this.authors = authors;
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}
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}
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@ -200,7 +200,7 @@ case object Crossref2Oaf {
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a.setSurname(family)
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a.setFullname(s"$given $family")
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if (StringUtils.isNotBlank(orcid))
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a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava)
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a.setPid(List(createSP(orcid, ORCID, PID_TYPES, generateDataInfo())).asJava)
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a
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}
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@ -248,7 +248,7 @@ case object Crossref2Oaf {
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def snsfRule(award:String): String = {
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var tmp1 = StringUtils.substringAfter(award,"_")
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val tmp1 = StringUtils.substringAfter(award,"_")
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val tmp2 = StringUtils.substringBefore(tmp1,"/")
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logger.debug(s"From $award to $tmp2")
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tmp2
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@ -294,7 +294,7 @@ case object Crossref2Oaf {
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}
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def getProjectId (nsPrefix:String, targetId:String):String = {
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"40|$nsPrefix::$targetId"
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s"40|$nsPrefix::$targetId"
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}
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@ -2,6 +2,7 @@ package eu.dnetlib.doiboost.crossref
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import org.apache.commons.io.IOUtils
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import org.apache.hadoop.io.{IntWritable, Text}
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import org.apache.spark.SparkConf
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import org.apache.spark.sql.expressions.Aggregator
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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@ -12,21 +13,23 @@ import org.slf4j.{Logger, LoggerFactory}
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object CrossrefDataset {
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val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
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def extractTimestamp(input:String): Long = {
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def to_item(input:String):CrossrefDT = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: json4s.JValue = parse(input)
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(json\"indexed"\"timestamp").extractOrElse[Long](0)
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val ts:Long = (json \ "indexed" \ "timestamp").extract[Long]
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val doi:String = (json \ "DOI").extract[String]
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CrossrefDT(doi, input, ts)
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}
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def main(args: Array[String]): Unit = {
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val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(IOUtils.toString(CrossrefDataset.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json")))
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parser.parseArgument(args)
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@ -49,9 +52,8 @@ object CrossrefDataset {
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if (a == null)
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return b
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val tb = extractTimestamp(b.json)
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val ta = extractTimestamp(a.json)
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if(ta >tb) {
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if(a.timestamp >b.timestamp) {
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return a
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}
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b
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@ -63,9 +65,7 @@ object CrossrefDataset {
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if (a == null)
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return b
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val tb = extractTimestamp(b.json)
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val ta = extractTimestamp(a.json)
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if(ta >tb) {
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if(a.timestamp >b.timestamp) {
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return a
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}
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b
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@ -78,15 +78,21 @@ object CrossrefDataset {
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override def finish(reduction: CrossrefDT): CrossrefDT = reduction
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}
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val sourcePath:String = parser.get("sourcePath")
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val targetPath:String = parser.get("targetPath")
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val workingPath:String = parser.get("workingPath")
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val ds:Dataset[CrossrefDT] = spark.read.load(sourcePath).as[CrossrefDT]
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ds.groupByKey(_.doi)
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val main_ds:Dataset[CrossrefDT] = spark.read.load(s"$workingPath/crossref_ds").as[CrossrefDT]
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val update =
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spark.createDataset(spark.sparkContext.sequenceFile(s"$workingPath/index_update", classOf[IntWritable], classOf[Text])
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.map(i =>CrossrefImporter.decompressBlob(i._2.toString))
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.map(i =>to_item(i)))
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main_ds.union(update).groupByKey(_.doi)
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.agg(crossrefAggregator.toColumn)
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.map(s=>s._2)
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.write.mode(SaveMode.Overwrite).save(targetPath)
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.write.mode(SaveMode.Overwrite).save(s"$workingPath/crossref_ds_updated")
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}
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@ -34,85 +34,21 @@ object SparkMapDumpIntoOAF {
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implicit val mapEncoderRelatons: Encoder[Relation] = Encoders.kryo[Relation]
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implicit val mapEncoderDatasets: Encoder[oaf.Dataset] = Encoders.kryo[OafDataset]
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val sc = spark.sparkContext
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val targetPath = parser.get("targetPath")
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import spark.implicits._
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spark.read.load(parser.get("sourcePath")).as[CrossrefDT]
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.flatMap(k => Crossref2Oaf.convert(k.json))
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.filter(o => o != null)
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.write.mode(SaveMode.Overwrite).save(s"$targetPath/mixObject")
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val ds:Dataset[Oaf] = spark.read.load(s"$targetPath/mixObject").as[Oaf]
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ds.filter(o => o.isInstanceOf[Publication]).map(o => o.asInstanceOf[Publication]).write.save(s"$targetPath/publication")
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ds.filter(o => o.isInstanceOf[Publication]).map(o => o.asInstanceOf[Publication]).write.mode(SaveMode.Overwrite).save(s"$targetPath/crossrefPublication")
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ds.filter(o => o.isInstanceOf[Relation]).map(o => o.asInstanceOf[Relation]).write.save(s"$targetPath/relation")
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ds.filter(o => o.isInstanceOf[Relation]).map(o => o.asInstanceOf[Relation]).write.mode(SaveMode.Overwrite).save(s"$targetPath/crossrefRelation")
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ds.filter(o => o.isInstanceOf[OafDataset]).map(o => o.asInstanceOf[OafDataset]).write.save(s"$targetPath/dataset")
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//
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//
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//
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// sc.sequenceFile(parser.get("sourcePath"), classOf[IntWritable], classOf[Text])
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// .map(k => k._2.toString).map(CrossrefImporter.decompressBlob)
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// .flatMap(k => Crossref2Oaf.convert(k)).saveAsObjectFile(s"${targetPath}/mixObject")
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//
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// val inputRDD = sc.objectFile[Oaf](s"${targetPath}/mixObject").filter(p=> p!= null)
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//
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// val distinctPubs:RDD[Publication] = inputRDD.filter(k => k != null && k.isInstanceOf[Publication])
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// .map(k => k.asInstanceOf[Publication]).map { p: Publication => Tuple2(p.getId, p) }.reduceByKey { case (p1: Publication, p2: Publication) =>
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// var r = if (p1 == null) p2 else p1
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// if (p1 != null && p2 != null) {
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// if (p1.getLastupdatetimestamp != null && p2.getLastupdatetimestamp != null) {
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// if (p1.getLastupdatetimestamp < p2.getLastupdatetimestamp)
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// r = p2
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// else
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// r = p1
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// } else {
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// r = if (p1.getLastupdatetimestamp == null) p2 else p1
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// }
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// }
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// r
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// }.map(_._2)
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//
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// val pubs:Dataset[Publication] = spark.createDataset(distinctPubs)
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// pubs.write.mode(SaveMode.Overwrite).save(s"${targetPath}/publication")
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//
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//
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// val distincDatasets:RDD[OafDataset] = inputRDD.filter(k => k != null && k.isInstanceOf[OafDataset])
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// .map(k => k.asInstanceOf[OafDataset]).map(p => Tuple2(p.getId, p)).reduceByKey { case (p1: OafDataset, p2: OafDataset) =>
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// var r = if (p1 == null) p2 else p1
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// if (p1 != null && p2 != null) {
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// if (p1.getLastupdatetimestamp != null && p2.getLastupdatetimestamp != null) {
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// if (p1.getLastupdatetimestamp < p2.getLastupdatetimestamp)
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// r = p2
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// else
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// r = p1
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// } else {
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// r = if (p1.getLastupdatetimestamp == null) p2 else p1
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// }
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// }
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// r
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// }.map(_._2)
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//
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// spark.createDataset(distincDatasets).write.mode(SaveMode.Overwrite).save(s"${targetPath}/dataset")
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//
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//
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//
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// val distinctRels =inputRDD.filter(k => k != null && k.isInstanceOf[Relation])
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// .map(k => k.asInstanceOf[Relation]).map(r=> (s"${r.getSource}::${r.getTarget}",r))
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// .reduceByKey { case (p1: Relation, p2: Relation) =>
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// if (p1 == null) p2 else p1
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// }.map(_._2)
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//
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// val rels: Dataset[Relation] = spark.createDataset(distinctRels)
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//
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// rels.write.mode(SaveMode.Overwrite).save(s"${targetPath}/relations")
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ds.filter(o => o.isInstanceOf[OafDataset]).map(o => o.asInstanceOf[OafDataset]).write.mode(SaveMode.Overwrite).save(s"$targetPath/crossrefDataset")
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}
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@ -16,88 +16,86 @@
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<!-- <property>-->
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<!-- <name>timestamp</name>-->
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<!-- <description>Timestamp for incremental Harvesting</description>-->
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<!-- </property>-->
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<property>
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<name>timestamp</name>
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<description>Timestamp for incremental Harvesting</description>
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</property>
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</parameters>
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<start to="ExtractCrossrefToOAF"/>
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<start to="ImportCrossRef"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<!-- <action name="ResetWorkingPath">-->
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<!-- <fs>-->
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<!-- <delete path='${workingPath}/input/crossref/index_dump'/>-->
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<!--<!– <mkdir path='${workingPath}/input/crossref'/>–>-->
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<!-- </fs>-->
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<!-- <ok to="ImportCrossRef"/>-->
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<!-- <error to="Kill"/>-->
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<!-- </action>-->
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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="${workingPath}/input/crossref/crossref_ds"/>
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</fs>
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<ok to="ConvertCrossrefToOAF"/>
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<error to="Kill"/>
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</action>
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<!-- <action name="ImportCrossRef">-->
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<!-- <java>-->
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<!-- <job-tracker>${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_dump_1</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="End"/>-->
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<!-- <error to="Kill"/>-->
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<!-- </action>-->
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<action name="ExtractCrossrefToOAF">
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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>ExtractCrossrefToOAF</name>
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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>${workingPath}/input/crossref</arg>
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<arg>--targetPath</arg><arg>${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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<!-- <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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<!-- ${sparkExtraOPT}-->
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<!-- </spark-opts>-->
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<!-- <arg>--sourcePath</arg><arg>/data/doiboost/crossref/cr_dataset</arg>-->
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<!-- <arg>--targetPath</arg><arg>/data/doiboost/crossref/crossrefDataset</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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@ -1,6 +1,5 @@
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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":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true}
|
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|
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]
|
|
@ -7,7 +7,7 @@
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<groupId>eu.dnetlib.dhp</groupId>
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||||
<artifactId>dhp</artifactId>
|
||||
<version>1.2.4-SNAPSHOT</version>
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||||
<relativePath>../</relativePath>
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||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
<artifactId>dhp-workflows</artifactId>
|
||||
|
|
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