forked from D-Net/dnet-hadoop
code refactor
This commit is contained in:
parent
79c26382da
commit
7d29b61c62
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@ -244,20 +244,20 @@ public class Result extends OafEntity implements Serializable {
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subject = mergeLists(subject, r.getSubject());
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//merge title lists: main title with higher trust and distinct between the others
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// merge title lists: main title with higher trust and distinct between the others
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StructuredProperty baseMainTitle = null;
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if(title != null) {
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if (title != null) {
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baseMainTitle = getMainTitle(title);
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title.remove(baseMainTitle);
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}
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StructuredProperty newMainTitle = null;
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if(r.getTitle() != null) {
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if (r.getTitle() != null) {
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newMainTitle = getMainTitle(r.getTitle());
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r.getTitle().remove(newMainTitle);
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}
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if (newMainTitle != null && compareTrust(this, r) < 0 )
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if (newMainTitle != null && compareTrust(this, r) < 0)
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baseMainTitle = newMainTitle;
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title = mergeLists(title, r.getTitle());
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@ -314,8 +314,9 @@ public class Result extends OafEntity implements Serializable {
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}
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private StructuredProperty getMainTitle(List<StructuredProperty> titles) {
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//need to check if the list of titles contains more than 1 main title? (in that case, we should chose which main title select in the list)
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for (StructuredProperty title: titles) {
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// need to check if the list of titles contains more than 1 main title? (in that case, we should chose which
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// main title select in the list)
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for (StructuredProperty title : titles) {
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if (title.getQualifier() != null && title.getQualifier().getClassid() != null)
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if (title.getQualifier().getClassid().equals("main title"))
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return title;
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@ -91,9 +91,9 @@ public class EntityMergerTest implements Serializable {
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assertEquals(pub_merged.getAuthor().size(), 9);
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assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4);
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//verify title
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// verify title
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int count = 0;
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for (StructuredProperty title: pub_merged.getTitle()){
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for (StructuredProperty title : pub_merged.getTitle()) {
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if (title.getQualifier().getClassid().equals("main title"))
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count++;
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}
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@ -4,7 +4,7 @@
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<parent>
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<artifactId>dhp-workflows</artifactId>
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<groupId>eu.dnetlib.dhp</groupId>
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<version>1.2.1-SNAPSHOT</version>
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<version>1.2.2-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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@ -41,6 +41,9 @@
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</build>
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<dependencies>
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<dependency>
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<groupId>org.apache.hadoop</groupId>
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@ -3,12 +3,9 @@ package eu.dnetlib.doiboost
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.action.AtomicAction
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import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset}
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import org.apache.hadoop.io.Text
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import org.apache.commons.io.IOUtils
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import org.apache.hadoop.io.compress.GzipCodec
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import org.apache.hadoop.mapred.{SequenceFileOutputFormat, TextOutputFormat}
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import org.apache.spark.SparkConf
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.apache.spark.sql.{ Encoder, Encoders, SaveMode, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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object SparkGenerateDOIBoostActionSet {
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@ -25,45 +22,43 @@ object SparkGenerateDOIBoostActionSet {
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.appName(getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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// implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
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// implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
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// implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation]
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//
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// implicit val mapEncoderAtomiAction: Encoder[AtomicAction[OafDataset]] = Encoders.kryo[AtomicAction[OafDataset]]
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//
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//
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//
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// val dbPublicationPath = parser.get("dbPublicationPath")
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// val dbDatasetPath = parser.get("dbDatasetPath")
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// val crossRefRelation = parser.get("crossRefRelation")
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// val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath")
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val workingDirPath = parser.get("targetPath")
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//
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// spark.read.load(dbDatasetPath).as[OafDataset]
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// .map(d =>DoiBoostMappingUtil.fixResult(d))
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// .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
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//
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// spark.read.load(dbPublicationPath).as[Publication]
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// .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
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//
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// spark.read.load(crossRefRelation).as[Relation]
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// .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
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//
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// spark.read.load(dbaffiliationRelationPath).as[Relation]
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// .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
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implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
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implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
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implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation]
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implicit val mapEncoderAtomiAction: Encoder[AtomicAction[OafDataset]] = Encoders.kryo[AtomicAction[OafDataset]]
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val dbPublicationPath = parser.get("dbPublicationPath")
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val dbDatasetPath = parser.get("dbDatasetPath")
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val crossRefRelation = parser.get("crossRefRelation")
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val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath")
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val workingDirPath = parser.get("targetPath")
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spark.read.load(dbDatasetPath).as[OafDataset]
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.map(d =>DoiBoostMappingUtil.fixResult(d))
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.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
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spark.read.load(dbPublicationPath).as[Publication]
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.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
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spark.read.load(crossRefRelation).as[Relation]
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.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
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spark.read.load(dbaffiliationRelationPath).as[Relation]
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.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
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.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
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implicit val mapEncoderPub: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING)
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val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)]
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SequenceFileOutputFormat
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d.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingDirPath/rawset_a8c2f90b-a3ae-4d6e-8187-47a437156e18_1590223414", classOf[Text], classOf[Text], classOf[TextOutputFormat[Text,Text]], classOf[GzipCodec])
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// implicit val mapEncoderPub: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING)
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//
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// val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)]
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//
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//
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//
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// d.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingDirPath/rawset_a8c2f90b-a3ae-4d6e-8187-47a437156e18_1590223414", classOf[Text], classOf[Text], classOf[TextOutputFormat[Text,Text]], classOf[GzipCodec])
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@ -1,9 +1,8 @@
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package eu.dnetlib.doiboost.crossref
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import java.util
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import eu.dnetlib.dhp.schema.oaf._
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import eu.dnetlib.dhp.utils.DHPUtils
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import eu.dnetlib.doiboost.DoiBoostMappingUtil._
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import org.apache.commons.lang.StringUtils
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import org.json4s
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import org.json4s.DefaultFormats
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@ -14,7 +13,6 @@ import org.slf4j.{Logger, LoggerFactory}
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import scala.collection.JavaConverters._
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import scala.collection.mutable
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import scala.util.matching.Regex
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import eu.dnetlib.doiboost.DoiBoostMappingUtil._
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case class mappingAffiliation(name: String) {}
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@ -26,8 +24,6 @@ case class mappingFunder(name: String, DOI: Option[String], award: Option[List[S
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case object Crossref2Oaf {
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val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
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val mappingCrossrefType = Map(
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"book-section" -> "publication",
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"book" -> "publication",
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@ -113,17 +109,18 @@ case object Crossref2Oaf {
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result.setPublisher(asField(publisher))
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// TITLE
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val mainTitles = for {JString(title) <- json \ "title"} yield createSP(title, "main title", "dnet:dataCite_title")
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val originalTitles = for {JString(title) <- json \ "original-title"} yield createSP(title, "alternative title", "dnet:dataCite_title")
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val shortTitles = for {JString(title) <- json \ "short-title"} yield createSP(title, "alternative title", "dnet:dataCite_title")
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val subtitles = for {JString(title) <- json \ "subtitle"} yield createSP(title, "subtitle", "dnet:dataCite_title")
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val mainTitles = for {JString(title) <- json \ "title" if title.nonEmpty} yield createSP(title, "main title", "dnet:dataCite_title")
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val originalTitles = for {JString(title) <- json \ "original-title" if title.nonEmpty} yield createSP(title, "alternative title", "dnet:dataCite_title")
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val shortTitles = for {JString(title) <- json \ "short-title" if title.nonEmpty} yield createSP(title, "alternative title", "dnet:dataCite_title")
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val subtitles = for {JString(title) <- json \ "subtitle" if title.nonEmpty} yield createSP(title, "subtitle", "dnet:dataCite_title")
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result.setTitle((mainTitles ::: originalTitles ::: shortTitles ::: subtitles).asJava)
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// DESCRIPTION
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val descriptionList = for {JString(description) <- json \ "abstract"} yield asField(description)
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result.setDescription(descriptionList.asJava)
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// Source
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val sourceList = for {JString(source) <- json \ "source"} yield asField(source)
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val sourceList = for {JString(source) <- json \ "source" if source.nonEmpty} yield asField(source)
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result.setSource(sourceList.asJava)
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//RELEVANT DATE Mapping
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@ -142,7 +139,6 @@ case object Crossref2Oaf {
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}
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result.setRelevantdate(List(createdDate, postedDate, acceptedDate, publishedOnlineDate, publishedPrintDate).filter(p => p != null).asJava)
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//Mapping Subject
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val subjectList:List[String] = (json \ "subject").extractOrElse[List[String]](List())
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@ -152,7 +148,7 @@ case object Crossref2Oaf {
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//Mapping AUthor
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//Mapping Author
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val authorList: List[mappingAuthor] = (json \ "author").extractOrElse[List[mappingAuthor]](List())
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result.setAuthor(authorList.map(a => generateAuhtor(a.given.orNull, a.family, a.ORCID.orNull)).asJava)
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@ -173,7 +169,6 @@ case object Crossref2Oaf {
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instance.setAccessright(createQualifier("Restricted", "dnet:access_modes"))
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result.setInstance(List(instance).asJava)
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instance.setInstancetype(createQualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), "dnet:publication_resource", "dnet:publication_resource"))
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@ -405,11 +400,8 @@ case object Crossref2Oaf {
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publication.setJournal(journal)
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}
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}
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}
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def extractDate(dt: String, datePart: List[List[Int]]): String = {
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if (StringUtils.isNotBlank(dt))
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return dt
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@ -427,18 +419,12 @@ case object Crossref2Oaf {
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}
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def generateDate(dt: String, datePart: List[List[Int]], classId: String, schemeId: String): StructuredProperty = {
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val dp = extractDate(dt, datePart)
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if (StringUtils.isNotBlank(dp))
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return createSP(dp, classId, schemeId)
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null
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}
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def generateItemFromType(objectType: String, objectSubType: String): Result = {
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if (mappingCrossrefType.contains(objectType)) {
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if (mappingCrossrefType(objectType).equalsIgnoreCase("publication"))
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@ -27,20 +27,20 @@ public class CrossrefImporter {
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CrossrefImporter.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/import_from_es.json")));
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Logger logger = LoggerFactory.getLogger(CrossrefImporter.class);
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parser.parseArgument(args);
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final String hdfsuri = parser.get("namenode");
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logger.info("HDFS URI" + hdfsuri);
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System.out.println("HDFS URI" + hdfsuri);
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Path hdfswritepath = new Path(parser.get("targetPath"));
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logger.info("TargetPath: " + hdfsuri);
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System.out.println("TargetPath: " + hdfsuri);
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final Long timestamp = StringUtils.isNotBlank(parser.get("timestamp"))
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? Long.parseLong(parser.get("timestamp"))
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: -1;
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if (timestamp > 0)
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logger.info("Timestamp added " + timestamp);
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System.out.println("Timestamp added " + timestamp);
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// ====== Init HDFS File System Object
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Configuration conf = new Configuration();
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@ -70,11 +70,11 @@ public class CrossrefImporter {
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key.set(i++);
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value.set(client.next());
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writer.append(key, value);
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if (i % 1000000 == 0) {
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if (i % 100000 == 0) {
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end = System.currentTimeMillis();
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final float time = (end - start) / 1000.0F;
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logger
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.info(
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System.out
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.println(
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String.format("Imported %d records last 100000 imported in %f seconds", i, time));
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start = System.currentTimeMillis();
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}
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@ -2,10 +2,11 @@ package eu.dnetlib.doiboost.crossref
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result}
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset}
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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.rdd.RDD
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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@ -28,9 +29,9 @@ object SparkMapDumpIntoOAF {
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.appName(SparkMapDumpIntoOAF.getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication])
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implicit val mapEncoderRelatons: Encoder[Relation] = Encoders.bean(classOf[Relation])
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implicit val mapEncoderDatasets: Encoder[oaf.Dataset] = Encoders.bean(classOf[eu.dnetlib.dhp.schema.oaf.Dataset])
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implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
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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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@ -40,19 +41,56 @@ object SparkMapDumpIntoOAF {
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.map(k => k._2.toString).map(CrossrefImporter.decompressBlob)
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.flatMap(k => Crossref2Oaf.convert(k)).saveAsObjectFile(s"${targetPath}/mixObject")
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val inputRDD = sc.objectFile[Oaf](s"${targetPath}/mixObject").filter(p=> p!= null)
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val pubs: Dataset[Publication] = spark.createDataset(inputRDD.filter(k => k != null && k.isInstanceOf[Publication])
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.map(k => k.asInstanceOf[Publication]))
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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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val pubs:Dataset[Publication] = spark.createDataset(distinctPubs)
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pubs.write.mode(SaveMode.Overwrite).save(s"${targetPath}/publication")
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|
||||
val ds: Dataset[eu.dnetlib.dhp.schema.oaf.Dataset] = spark.createDataset(inputRDD.filter(k => k != null && k.isInstanceOf[eu.dnetlib.dhp.schema.oaf.Dataset])
|
||||
.map(k => k.asInstanceOf[eu.dnetlib.dhp.schema.oaf.Dataset]))
|
||||
ds.write.mode(SaveMode.Overwrite).save(s"${targetPath}/dataset")
|
||||
|
||||
val rels: Dataset[Relation] = spark.createDataset(inputRDD.filter(k => k != null && k.isInstanceOf[Relation])
|
||||
.map(k => k.asInstanceOf[Relation]))
|
||||
val distincDatasets:RDD[OafDataset] = inputRDD.filter(k => k != null && k.isInstanceOf[OafDataset])
|
||||
.map(k => k.asInstanceOf[OafDataset]).map(p => Tuple2(p.getId, p)).reduceByKey { case (p1: OafDataset, p2: OafDataset) =>
|
||||
var r = if (p1 == null) p2 else p1
|
||||
if (p1 != null && p2 != null) {
|
||||
if (p1.getLastupdatetimestamp != null && p2.getLastupdatetimestamp != null) {
|
||||
if (p1.getLastupdatetimestamp < p2.getLastupdatetimestamp)
|
||||
r = p2
|
||||
else
|
||||
r = p1
|
||||
} else {
|
||||
r = if (p1.getLastupdatetimestamp == null) p2 else p1
|
||||
}
|
||||
}
|
||||
r
|
||||
}.map(_._2)
|
||||
|
||||
spark.createDataset(distincDatasets).write.mode(SaveMode.Overwrite).save(s"${targetPath}/dataset")
|
||||
|
||||
|
||||
|
||||
val distinctRels =inputRDD.filter(k => k != null && k.isInstanceOf[Relation])
|
||||
.map(k => k.asInstanceOf[Relation]).map(r=> (s"${r.getSource}::${r.getTarget}",r))
|
||||
.reduceByKey { case (p1: Relation, p2: Relation) =>
|
||||
if (p1 == null) p2 else p1
|
||||
}.map(_._2)
|
||||
|
||||
val rels: Dataset[Relation] = spark.createDataset(distinctRels)
|
||||
|
||||
rels.write.mode(SaveMode.Overwrite).save(s"${targetPath}/relations")
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,7 +1,8 @@
|
|||
package eu.dnetlib.doiboost.mag
|
||||
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication}
|
||||
import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty}
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
|
|
@ -63,12 +64,98 @@ case object ConversionUtil {
|
|||
}
|
||||
|
||||
|
||||
def mergePublication(a: Publication, b:Publication) : Publication = {
|
||||
if ((a != null) && (b != null)) {
|
||||
a.mergeFrom(b)
|
||||
a
|
||||
} else {
|
||||
if (a == null) b else a
|
||||
}
|
||||
}
|
||||
|
||||
def choiceLatestMagArtitcle(p1: MagPapers, p2:MagPapers) :MagPapers = {
|
||||
var r = if (p1 == null) p2 else p1
|
||||
if (p1 != null && p2 != null) {
|
||||
if (p1.CreatedDate != null && p2.CreatedDate != null) {
|
||||
if (p1.CreatedDate.before(p2.CreatedDate))
|
||||
r = p2
|
||||
else
|
||||
r = p1
|
||||
} else {
|
||||
r = if (p1.CreatedDate == null) p2 else p1
|
||||
}
|
||||
}
|
||||
r
|
||||
|
||||
}
|
||||
|
||||
|
||||
def updatePubsWithDescription(inputItem:((String, Publication), MagPaperAbstract)) : Publication = {
|
||||
val pub = inputItem._1._2
|
||||
val abst = inputItem._2
|
||||
if (abst != null) {
|
||||
pub.setDescription(List(asField(abst.IndexedAbstract)).asJava)
|
||||
}
|
||||
pub
|
||||
|
||||
}
|
||||
|
||||
|
||||
def updatePubsWithConferenceInfo(inputItem:((String, Publication), MagConferenceInstance)) : Publication = {
|
||||
val publication:Publication= inputItem._1._2
|
||||
val ci:MagConferenceInstance = inputItem._2
|
||||
|
||||
if (ci!= null){
|
||||
|
||||
val j:Journal = new Journal
|
||||
if (ci.Location.isDefined)
|
||||
j.setConferenceplace(ci.Location.get)
|
||||
j.setName(ci.DisplayName.get)
|
||||
if (ci.StartDate.isDefined && ci.EndDate.isDefined)
|
||||
{
|
||||
j.setConferencedate(s"${ci.StartDate.get.toString} - ${ci.EndDate.get.toString}")
|
||||
}
|
||||
|
||||
publication.setJournal(j)
|
||||
}
|
||||
publication
|
||||
}
|
||||
|
||||
def updatePubsWithSubject(item:((String, Publication), MagFieldOfStudy)) : Publication = {
|
||||
|
||||
val publication = item._1._2
|
||||
val fieldOfStudy = item._2
|
||||
if (fieldOfStudy != null && fieldOfStudy.subjects != null && fieldOfStudy.subjects.nonEmpty) {
|
||||
val p: List[StructuredProperty] = fieldOfStudy.subjects.flatMap(s => {
|
||||
val s1 = createSP(s.DisplayName, "keywords", "dnet:subject_classification_typologies")
|
||||
val di = DoiBoostMappingUtil.generateDataInfo(s.Score.toString)
|
||||
var resList: List[StructuredProperty] = List(s1)
|
||||
if (s.MainType.isDefined) {
|
||||
val maintp = s.MainType.get
|
||||
val s2 = createSP(s.MainType.get, "keywords", "dnet:subject_classification_typologies")
|
||||
s2.setDataInfo(di)
|
||||
resList = resList ::: List(s2)
|
||||
if (maintp.contains(".")) {
|
||||
val s3 = createSP(maintp.split("\\.").head, "keywords", "dnet:subject_classification_typologies")
|
||||
s3.setDataInfo(di)
|
||||
resList = resList ::: List(s3)
|
||||
}
|
||||
}
|
||||
resList
|
||||
})
|
||||
publication.setSubject(p.asJava)
|
||||
}
|
||||
publication
|
||||
}
|
||||
|
||||
|
||||
|
||||
def addInstances(a: (Publication, MagUrl)): Publication = {
|
||||
val pub = a._1
|
||||
val urls = a._2
|
||||
|
||||
|
||||
|
||||
val i = new Instance
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -1,15 +1,13 @@
|
|||
package eu.dnetlib.doiboost.mag
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.{Journal, Publication, StructuredProperty}
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{asField, createSP}
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
import org.apache.spark.sql.functions._
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
|
||||
|
|
@ -36,25 +34,15 @@ object SparkPreProcessMAG {
|
|||
val d: Dataset[MagPapers] = spark.read.load(s"${parser.get("sourcePath")}/Papers").as[MagPapers]
|
||||
|
||||
// Filtering Papers with DOI, and since for the same DOI we have multiple version of item with different PapersId we get the last one
|
||||
val result: RDD[MagPapers] = d.where(col("Doi").isNotNull).rdd.map { p: MagPapers => Tuple2(p.Doi, p) }.reduceByKey { case (p1: MagPapers, p2: MagPapers) =>
|
||||
var r = if (p1 == null) p2 else p1
|
||||
if (p1 != null && p2 != null) {
|
||||
if (p1.CreatedDate != null && p2.CreatedDate != null) {
|
||||
if (p1.CreatedDate.before(p2.CreatedDate))
|
||||
r = p1
|
||||
else
|
||||
r = p2
|
||||
} else {
|
||||
r = if (p1.CreatedDate == null) p2 else p1
|
||||
}
|
||||
}
|
||||
r
|
||||
}.map(_._2)
|
||||
|
||||
val result: RDD[MagPapers] = d.where(col("Doi").isNotNull)
|
||||
.rdd
|
||||
.map{ p: MagPapers => Tuple2(p.Doi, p) }
|
||||
.reduceByKey((p1:MagPapers,p2:MagPapers) => ConversionUtil.choiceLatestMagArtitcle(p1,p2))
|
||||
.map(_._2)
|
||||
|
||||
val distinctPaper: Dataset[MagPapers] = spark.createDataset(result)
|
||||
distinctPaper.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/Papers_distinct")
|
||||
logger.info(s"Total number of element: ${result.count()}")
|
||||
|
||||
|
||||
logger.info("Phase 3) Group Author by PaperId")
|
||||
val authors = spark.read.load(s"$sourcePath/Authors").as[MagAuthor]
|
||||
|
|
@ -85,46 +73,35 @@ object SparkPreProcessMAG {
|
|||
|
||||
val firstJoin = papers.joinWith(journals, papers("JournalId").equalTo(journals("JournalId")), "left")
|
||||
firstJoin.joinWith(paperWithAuthors, firstJoin("_1.PaperId").equalTo(paperWithAuthors("PaperId")), "left")
|
||||
.map { a: ((MagPapers, MagJournal), MagPaperWithAuthorList) => ConversionUtil.createOAFFromJournalAuthorPaper(a) }.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_2")
|
||||
.map { a => ConversionUtil.createOAFFromJournalAuthorPaper(a) }
|
||||
.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_2")
|
||||
|
||||
|
||||
var magPubs: Dataset[(String, Publication)] = spark.read.load(s"${parser.get("targetPath")}/merge_step_2").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
|
||||
var magPubs: Dataset[(String, Publication)] =
|
||||
spark.read.load(s"${parser.get("targetPath")}/merge_step_2").as[Publication]
|
||||
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
|
||||
|
||||
|
||||
val conference = spark.read.load(s"$sourcePath/ConferenceInstances").select($"ConferenceInstanceId".as("ci"), $"DisplayName", $"Location", $"StartDate",$"EndDate" )
|
||||
val conferenceInstance = conference.joinWith(papers, papers("ConferenceInstanceId").equalTo(conference("ci"))).select($"_1.ci", $"_1.DisplayName", $"_1.Location", $"_1.StartDate",$"_1.EndDate", $"_2.PaperId").as[MagConferenceInstance]
|
||||
val conference = spark.read.load(s"$sourcePath/ConferenceInstances")
|
||||
.select($"ConferenceInstanceId".as("ci"), $"DisplayName", $"Location", $"StartDate",$"EndDate" )
|
||||
val conferenceInstance = conference.joinWith(papers, papers("ConferenceInstanceId").equalTo(conference("ci")))
|
||||
.select($"_1.ci", $"_1.DisplayName", $"_1.Location", $"_1.StartDate",$"_1.EndDate", $"_2.PaperId").as[MagConferenceInstance]
|
||||
|
||||
|
||||
magPubs.joinWith(conferenceInstance, col("_1").equalTo(conferenceInstance("PaperId")), "left")
|
||||
.map(p => {
|
||||
val publication:Publication= p._1._2
|
||||
val ci:MagConferenceInstance = p._2
|
||||
|
||||
if (ci!= null){
|
||||
|
||||
val j:Journal = new Journal
|
||||
if (ci.Location.isDefined)
|
||||
j.setConferenceplace(ci.Location.get)
|
||||
j.setName(ci.DisplayName.get)
|
||||
if (ci.StartDate.isDefined && ci.EndDate.isDefined)
|
||||
{
|
||||
j.setConferencedate(s"${ci.StartDate.get.toString} - ${ci.EndDate.get.toString}")
|
||||
}
|
||||
|
||||
publication.setJournal(j)
|
||||
}
|
||||
publication
|
||||
|
||||
}).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_2_conference")
|
||||
.map(item => ConversionUtil.updatePubsWithConferenceInfo(item))
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"${parser.get("targetPath")}/merge_step_2_conference")
|
||||
|
||||
|
||||
magPubs= spark.read.load(s"${parser.get("targetPath")}/merge_step_2_conference").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
|
||||
magPubs= spark.read.load(s"${parser.get("targetPath")}/merge_step_2_conference").as[Publication]
|
||||
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
|
||||
|
||||
val paperUrlDataset = spark.read.load(s"$sourcePath/PaperUrls").as[MagPaperUrl].groupBy("PaperId").agg(collect_list(struct("sourceUrl")).as("instances")).as[MagUrl]
|
||||
|
||||
|
||||
logger.info("Phase 5) enrich publication with URL and Instances")
|
||||
|
||||
magPubs.joinWith(paperUrlDataset, col("_1").equalTo(paperUrlDataset("PaperId")), "left")
|
||||
.map { a: ((String, Publication), MagUrl) => ConversionUtil.addInstances((a._1._2, a._2)) }
|
||||
.write.mode(SaveMode.Overwrite)
|
||||
|
|
@ -138,22 +115,18 @@ object SparkPreProcessMAG {
|
|||
val paperAbstract = spark.read.load((s"${parser.get("targetPath")}/PaperAbstract")).as[MagPaperAbstract]
|
||||
|
||||
|
||||
magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_3").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
|
||||
magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_3").as[Publication]
|
||||
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
|
||||
|
||||
magPubs.joinWith(paperAbstract, col("_1").equalTo(paperAbstract("PaperId")), "left").map(p => {
|
||||
val pub = p._1._2
|
||||
val abst = p._2
|
||||
if (abst != null) {
|
||||
pub.setDescription(List(asField(abst.IndexedAbstract)).asJava)
|
||||
}
|
||||
pub
|
||||
}
|
||||
magPubs.joinWith(paperAbstract, col("_1").equalTo(paperAbstract("PaperId")), "left")
|
||||
.map(item => ConversionUtil.updatePubsWithDescription(item)
|
||||
).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_4")
|
||||
|
||||
|
||||
logger.info("Phase 7) Enrich Publication with FieldOfStudy")
|
||||
|
||||
magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_4").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
|
||||
magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_4").as[Publication]
|
||||
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
|
||||
|
||||
val fos = spark.read.load(s"$sourcePath/FieldsOfStudy").select($"FieldOfStudyId".alias("fos"), $"DisplayName", $"MainType")
|
||||
|
||||
|
|
@ -164,31 +137,18 @@ object SparkPreProcessMAG {
|
|||
.groupBy($"PaperId").agg(collect_list(struct($"FieldOfStudyId", $"DisplayName", $"MainType", $"Score")).as("subjects"))
|
||||
.as[MagFieldOfStudy]
|
||||
|
||||
magPubs.joinWith(paperField, col("_1").equalTo(paperField("PaperId")), "left").
|
||||
map(item => {
|
||||
val publication = item._1._2
|
||||
val fieldOfStudy = item._2
|
||||
if (fieldOfStudy != null && fieldOfStudy.subjects != null && fieldOfStudy.subjects.nonEmpty) {
|
||||
val p: List[StructuredProperty] = fieldOfStudy.subjects.flatMap(s => {
|
||||
val s1 = createSP(s.DisplayName, "keywords", "dnet:subject_classification_typologies")
|
||||
val di = DoiBoostMappingUtil.generateDataInfo(s.Score.toString)
|
||||
var resList: List[StructuredProperty] = List(s1)
|
||||
if (s.MainType.isDefined) {
|
||||
val maintp = s.MainType.get
|
||||
val s2 = createSP(s.MainType.get, "keywords", "dnet:subject_classification_typologies")
|
||||
s2.setDataInfo(di)
|
||||
resList = resList ::: List(s2)
|
||||
if (maintp.contains(".")) {
|
||||
val s3 = createSP(maintp.split("\\.").head, "keywords", "dnet:subject_classification_typologies")
|
||||
s3.setDataInfo(di)
|
||||
resList = resList ::: List(s3)
|
||||
}
|
||||
}
|
||||
resList
|
||||
})
|
||||
publication.setSubject(p.asJava)
|
||||
}
|
||||
publication
|
||||
}).map { s: Publication => s }(Encoders.bean(classOf[Publication])).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/mag_publication")
|
||||
magPubs.joinWith(paperField, col("_1")
|
||||
.equalTo(paperField("PaperId")), "left")
|
||||
.map(item => ConversionUtil.updatePubsWithSubject(item))
|
||||
.write.mode(SaveMode.Overwrite)
|
||||
.save(s"${parser.get("targetPath")}/mag_publication")
|
||||
|
||||
|
||||
val s:RDD[Publication] = spark.read.load(s"${parser.get("targetPath")}/mag_publication").as[Publication]
|
||||
.map(p=>Tuple2(p.getId, p)).rdd.reduceByKey((a:Publication, b:Publication) => ConversionUtil.mergePublication(a,b))
|
||||
.map(_._2)
|
||||
|
||||
spark.createDataset(s).as[Publication].write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/mag_publication_u")
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -15,6 +15,10 @@
|
|||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
|
|
|
|||
|
|
@ -16,6 +16,11 @@
|
|||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>timestamp</name>
|
||||
<description>Timestamp for incremental Harvesting</description>
|
||||
</property>
|
||||
|
||||
</parameters>
|
||||
|
||||
<start to="ExtractCrossrefToOAF"/>
|
||||
|
|
@ -27,8 +32,8 @@
|
|||
|
||||
<action name="ResetWorkingPath">
|
||||
<fs>
|
||||
<delete path='${workingPath}'/>
|
||||
<mkdir path='${workingPath}/input/crossref'/>
|
||||
<delete path='${workingPath}/input/crossref/index_dump'/>
|
||||
<!-- <mkdir path='${workingPath}/input/crossref'/>-->
|
||||
</fs>
|
||||
<ok to="ImportCrossRef"/>
|
||||
<error to="Kill"/>
|
||||
|
|
@ -43,13 +48,13 @@
|
|||
<main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>
|
||||
<arg>-t</arg><arg>${workingPath}/input/crossref/index_dump</arg>
|
||||
<arg>-n</arg><arg>${nameNode}</arg>
|
||||
<arg>-ts</arg><arg>${timestamp}</arg>
|
||||
</java>
|
||||
<ok to="End"/>
|
||||
<ok to="ExtractCrossrefToOAF"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
|
||||
<action name="ExtractCrossrefToOAF">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
|
|
@ -63,7 +68,7 @@
|
|||
--driver-memory=${sparkDriverMemory}
|
||||
${sparkExtraOPT}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${workingPath}/crossref/index_dump</arg>
|
||||
<arg>--sourcePath</arg><arg>${workingPath}/input/crossref/index_dump,${workingPath}/crossref/index_dump</arg>
|
||||
<arg>--targetPath</arg><arg>${workingPath}/input/crossref</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
|
|
|
|||
|
|
@ -22,7 +22,7 @@
|
|||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="ResetWorkingPath"/>
|
||||
<start to="PreprocessMag"/>
|
||||
|
||||
|
||||
<kill name="Kill">
|
||||
|
|
@ -31,8 +31,8 @@
|
|||
|
||||
<action name="ResetWorkingPath">
|
||||
<fs>
|
||||
<delete path='${targetPath}'/>
|
||||
<mkdir path='${targetPath}'/>
|
||||
<delete path='${targetPath}/preprocess'/>
|
||||
<mkdir path='${targetPath}/preprocess'/>
|
||||
</fs>
|
||||
<ok to="PreprocessMag"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
|||
|
|
@ -58,6 +58,28 @@ class CrossrefMappingTest {
|
|||
}
|
||||
|
||||
|
||||
@Test
|
||||
def testEmptyTitle() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("empty_title.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
assertFalse(json.isEmpty);
|
||||
|
||||
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
|
||||
|
||||
assertTrue(resultList.nonEmpty)
|
||||
|
||||
val items = resultList.filter(p => p.isInstanceOf[Result])
|
||||
|
||||
|
||||
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
|
||||
items.foreach(p => println(mapper.writeValueAsString(p)))
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
def testPeerReviewed(): Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("prwTest.json")).mkString
|
||||
|
|
|
|||
|
|
@ -0,0 +1,121 @@
|
|||
{
|
||||
"indexed": {
|
||||
"date-parts": [
|
||||
[
|
||||
2020,
|
||||
4,
|
||||
7
|
||||
]
|
||||
],
|
||||
"date-time": "2020-04-07T15:54:28Z",
|
||||
"timestamp": 1586274868901
|
||||
},
|
||||
"reference-count": 0,
|
||||
"publisher": "Japan Society of Mechanical Engineers",
|
||||
"issue": "432",
|
||||
"content-domain": {
|
||||
"domain": [],
|
||||
"crossmark-restriction": false
|
||||
},
|
||||
"short-container-title": [
|
||||
"JSMET"
|
||||
],
|
||||
"published-print": {
|
||||
"date-parts": [
|
||||
[
|
||||
1982
|
||||
]
|
||||
]
|
||||
},
|
||||
"DOI": "10.1299\/kikaib.48.1474",
|
||||
"type": "journal-article",
|
||||
"created": {
|
||||
"date-parts": [
|
||||
[
|
||||
2011,
|
||||
9,
|
||||
13
|
||||
]
|
||||
],
|
||||
"date-time": "2011-09-13T05:59:01Z",
|
||||
"timestamp": 1315893541000
|
||||
},
|
||||
"page": "1474-1482",
|
||||
"source": "Crossref",
|
||||
"is-referenced-by-count": 0,
|
||||
"title": [
|
||||
""
|
||||
],
|
||||
"prefix": "10.1299",
|
||||
"volume": "48",
|
||||
"author": [
|
||||
{
|
||||
"given": "Hiroshi",
|
||||
"family": "KATO",
|
||||
"sequence": "first",
|
||||
"affiliation": []
|
||||
},
|
||||
{
|
||||
"given": "Yoshichika",
|
||||
"family": "MIZUNO",
|
||||
"sequence": "additional",
|
||||
"affiliation": []
|
||||
}
|
||||
],
|
||||
"member": "124",
|
||||
"container-title": [
|
||||
"Transactions of the Japan Society of Mechanical Engineers Series B"
|
||||
],
|
||||
"original-title": [
|
||||
"\u5e0c\u8584\u9ad8\u5206\u5b50\u6eb6\u6db2\u4e2d\u306e\u6709\u9650\u9577\u5186\u67f1\u306e\u62b5\u6297"
|
||||
],
|
||||
"language": "ja",
|
||||
"deposited": {
|
||||
"date-parts": [
|
||||
[
|
||||
2011,
|
||||
9,
|
||||
13
|
||||
]
|
||||
],
|
||||
"date-time": "2011-09-13T06:01:33Z",
|
||||
"timestamp": 1315893693000
|
||||
},
|
||||
"score": 1.0,
|
||||
"subtitle": [],
|
||||
"short-title": [],
|
||||
"issued": {
|
||||
"date-parts": [
|
||||
[
|
||||
1982
|
||||
]
|
||||
]
|
||||
},
|
||||
"references-count": 0,
|
||||
"journal-issue": {
|
||||
"published-print": {
|
||||
"date-parts": [
|
||||
[
|
||||
1982
|
||||
]
|
||||
]
|
||||
},
|
||||
"issue": "432"
|
||||
},
|
||||
"URL": "http:\/\/dx.doi.org\/10.1299\/kikaib.48.1474",
|
||||
"relation": {},
|
||||
"ISSN": [
|
||||
"0387-5016",
|
||||
"1884-8346"
|
||||
],
|
||||
"issn-type": [
|
||||
{
|
||||
"value": "0387-5016",
|
||||
"type": "print"
|
||||
},
|
||||
{
|
||||
"value": "1884-8346",
|
||||
"type": "electronic"
|
||||
}
|
||||
]
|
||||
}
|
||||
Loading…
Reference in New Issue