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dnet-hadoop
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resolved conflicts

This commit is contained in:
Miriam Baglioni 2021-12-07 10:16:14 +01:00
parent 96a7d46278 5d51b3dd4a
commit b113586207
70 changed files with 457 additions and 805 deletions
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0
dhp-common/src/main/java/eu/dnetlib/dhp/application/SparkScalaApplication.scala → dhp-common/src/main/scala/eu/dnetlib/dhp/application/SparkScalaApplication.scala
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2
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
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@ -107,7 +107,7 @@ class OafMapperUtilsTest {
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("2006-01-02T15:04:05+0000").get());
assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09-07:00").get());
assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09").get());
assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09Z").get());
assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09Z").get());
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.3186369").get());
assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000").get());
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.123").get());

69
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkCreateActionset.scala
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@ -1,69 +0,0 @@
package eu.dnetlib.dhp.actionmanager.scholix
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
import org.apache.spark.SparkConf
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
object SparkCreateActionset {
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/generate_actionset.json")).mkString)
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
val workingDirFolder = parser.get("workingDirFolder")
log.info(s"workingDirFolder -> $workingDirFolder")
implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val resultEncoders: Encoder[Result] = Encoders.kryo[Result]
implicit val relationEncoders: Encoder[Relation] = Encoders.kryo[Relation]
import spark.implicits._
val relation = spark.read.load(s"$sourcePath/relation").as[Relation]
relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
.flatMap(r => List(r.getSource, r.getTarget)).distinct().write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/id_relation")
val idRelation = spark.read.load(s"$workingDirFolder/id_relation").as[String]
log.info("extract source and target Identifier involved in relations")
log.info("save relation filtered")
relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
.write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/actionSetOaf")
log.info("saving entities")
val entities: Dataset[(String, Result)] = spark.read.load(s"$sourcePath/entities/*").as[Result].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING, resultEncoders))
entities
.joinWith(idRelation, entities("_1").equalTo(idRelation("value")))
.map(p => p._1._2)
.write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
}
}

86
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkSaveActionSet.scala
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@ -1,86 +0,0 @@
package eu.dnetlib.dhp.actionmanager.scholix
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{Oaf, Dataset => OafDataset,Publication, Software, OtherResearchProduct, Relation}
import org.apache.hadoop.io.Text
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.hadoop.mapred.SequenceFileOutputFormat
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
object SparkSaveActionSet {
def toActionSet(item: Oaf): (String, String) = {
val mapper = new ObjectMapper()
item match {
case dataset: OafDataset =>
val a: AtomicAction[OafDataset] = new AtomicAction[OafDataset]
a.setClazz(classOf[OafDataset])
a.setPayload(dataset)
(dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
case publication: Publication =>
val a: AtomicAction[Publication] = new AtomicAction[Publication]
a.setClazz(classOf[Publication])
a.setPayload(publication)
(publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
case software: Software =>
val a: AtomicAction[Software] = new AtomicAction[Software]
a.setClazz(classOf[Software])
a.setPayload(software)
(software.getClass.getCanonicalName, mapper.writeValueAsString(a))
case orp: OtherResearchProduct =>
val a: AtomicAction[OtherResearchProduct] = new AtomicAction[OtherResearchProduct]
a.setClazz(classOf[OtherResearchProduct])
a.setPayload(orp)
(orp.getClass.getCanonicalName, mapper.writeValueAsString(a))
case relation: Relation =>
val a: AtomicAction[Relation] = new AtomicAction[Relation]
a.setClazz(classOf[Relation])
a.setPayload(relation)
(relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
case _ =>
null
}
}
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/save_actionset.json")).mkString)
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val tEncoder: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING)
spark.read.load(sourcePath).as[Oaf]
.map(o => toActionSet(o))
.filter(o => o != null)
.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text, Text]], classOf[GzipCodec])
}
}

0
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/CollectionUtils.scala
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0
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/AbstractRestClient.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/AbstractRestClient.scala
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0
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteAPIImporter.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteAPIImporter.scala
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2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteModelConstants.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteModelConstants.scala
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@ -1,8 +1,8 @@
package eu.dnetlib.dhp.datacite
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue}
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue}
import java.io.InputStream
import java.time.format.DateTimeFormatter

35
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala
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@ -6,7 +6,7 @@ import eu.dnetlib.dhp.datacite.DataciteModelConstants._
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils}
import eu.dnetlib.dhp.schema.oaf.{AccessRight, Author, DataInfo, Instance, KeyValue, Oaf, OtherResearchProduct, Publication, Qualifier, Relation, Result, Software, StructuredProperty, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import org.json4s.DefaultFormats
@ -29,6 +29,7 @@ object DataciteToOAFTransformation {
/**
* This method should skip record if json contains invalid text
* defined in gile datacite_filter
*
* @param json
* @return True if the record should be skipped
*/
@ -107,9 +108,9 @@ object DataciteToOAFTransformation {
d
}
def fix_thai_date(input:String, format:String) :String = {
def fix_thai_date(input: String, format: String): String = {
try {
val a_date = LocalDate.parse(input,DateTimeFormatter.ofPattern(format))
val a_date = LocalDate.parse(input, DateTimeFormatter.ofPattern(format))
val d = ThaiBuddhistDate.of(a_date.getYear, a_date.getMonth.getValue, a_date.getDayOfMonth)
LocalDate.from(d).toString
} catch {
@ -236,7 +237,7 @@ object DataciteToOAFTransformation {
val p = match_pattern.get._2
val grantId = m.matcher(awardUri).replaceAll("$2")
val targetId = s"$p${DHPUtils.md5(grantId)}"
List( generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo) )
List(generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo))
}
else
List()
@ -335,15 +336,15 @@ object DataciteToOAFTransformation {
.map(d => d.get)
if (a_date.isDefined) {
if(doi.startsWith("10.14457"))
result.setEmbargoenddate(OafMapperUtils.field(fix_thai_date(a_date.get,"[yyyy-MM-dd]"), null))
if (doi.startsWith("10.14457"))
result.setEmbargoenddate(OafMapperUtils.field(fix_thai_date(a_date.get, "[yyyy-MM-dd]"), null))
else
result.setEmbargoenddate(OafMapperUtils.field(a_date.get, null))
}
if (i_date.isDefined && i_date.get.isDefined) {
if(doi.startsWith("10.14457")) {
result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get,"[yyyy-MM-dd]"), null))
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get,"[yyyy-MM-dd]"), null))
if (doi.startsWith("10.14457")) {
result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get, "[yyyy-MM-dd]"), null))
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get, "[yyyy-MM-dd]"), null))
}
else {
result.setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
@ -351,9 +352,9 @@ object DataciteToOAFTransformation {
}
}
else if (publication_year != null) {
if(doi.startsWith("10.14457")) {
result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year","[dd-MM-yyyy]"), null))
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year","[dd-MM-yyyy]"), null))
if (doi.startsWith("10.14457")) {
result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year", "[dd-MM-yyyy]"), null))
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year", "[dd-MM-yyyy]"), null))
} else {
result.setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
@ -457,7 +458,7 @@ object DataciteToOAFTransformation {
JField("relatedIdentifier", JString(relatedIdentifier)) <- relIdentifier
} yield RelatedIdentifierType(relationType, relatedIdentifier, relatedIdentifierType)
relations = relations ::: generateRelations(rels,result.getId, if (i_date.isDefined && i_date.get.isDefined) i_date.get.get else null)
relations = relations ::: generateRelations(rels, result.getId, if (i_date.isDefined && i_date.get.isDefined) i_date.get.get else null)
}
if (relations != null && relations.nonEmpty) {
List(result) ::: relations
@ -466,7 +467,7 @@ object DataciteToOAFTransformation {
List(result)
}
private def generateRelations(rels: List[RelatedIdentifierType], id:String, date:String):List[Relation] = {
private def generateRelations(rels: List[RelatedIdentifierType], id: String, date: String): List[Relation] = {
rels
.filter(r =>
subRelTypeMapping.contains(r.relationType) && (
@ -484,12 +485,12 @@ object DataciteToOAFTransformation {
rel.setSubRelType(subRelType)
rel.setRelClass(r.relationType)
val dateProps:KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
val dateProps: KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
rel.setProperties(List(dateProps).asJava)
rel.setSource(id)
rel.setTarget(DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier,r.relatedIdentifierType))
rel.setTarget(DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier, r.relatedIdentifierType))
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
rel.getCollectedfrom.asScala.map(c => c.getValue).toList
rel
@ -504,4 +505,4 @@ object DataciteToOAFTransformation {
}
}
}

0
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala
View File

0
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/ImportDatacite.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/ImportDatacite.scala
View File

0
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/SparkDownloadUpdateDatacite.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/SparkDownloadUpdateDatacite.scala
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1
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala
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@ -7,6 +7,7 @@ import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.{compact, parse, render}
import collection.JavaConverters._
object BioDBToOAF {
case class EBILinkItem(id: Long, links: String) {}

12
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala
View File

@ -1,9 +1,9 @@
package eu.dnetlib.dhp.sx.bio
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Oaf
import BioDBToOAF.ScholixResolved
import eu.dnetlib.dhp.collection.CollectionUtils
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
@ -36,13 +36,13 @@ object SparkTransformBioDatabaseToOAF {
import spark.implicits._
database.toUpperCase() match {
case "UNIPROT" =>
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
case "PDB" =>
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
case "SCHOLIX" =>
spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
case "CROSSREF_LINKS" =>
spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
}
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala
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@ -3,7 +3,7 @@ package eu.dnetlib.dhp.sx.bio.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.oaf.Result
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
import eu.dnetlib.dhp.sx.bio.pubmed._
import eu.dnetlib.dhp.utils.ISLookupClientFactory
import org.apache.commons.io.IOUtils
import org.apache.hadoop.conf.Configuration

3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala
View File

@ -1,9 +1,8 @@
package eu.dnetlib.dhp.sx.bio.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
import eu.dnetlib.dhp.sx.bio.pubmed.PMJournal
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
import org.apache.commons.io.IOUtils
import org.apache.http.client.config.RequestConfig
import org.apache.http.client.methods.HttpGet

5
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala
View File

@ -1,11 +1,10 @@
package eu.dnetlib.dhp.sx.bio.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.collection.CollectionUtils
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.sx.bio.BioDBToOAF
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
import BioDBToOAF.EBILinkItem
import eu.dnetlib.dhp.collection.CollectionUtils
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql._
@ -38,7 +37,7 @@ object SparkEBILinksToOaf {
ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
.filter(p => BioDBToOAF.EBITargetLinksFilter(p))
.flatMap(p => BioDBToOAF.convertEBILinksToOaf(p))
.flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null)
.flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null)
.write.mode(SaveMode.Overwrite).save(targetPath)
}
}

0
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala
View File

19
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala → dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
View File

@ -4,7 +4,7 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType}
import eu.dnetlib.dhp.schema.oaf._
import scala.collection.JavaConverters._
import collection.JavaConverters._
import java.util.regex.Pattern
@ -22,10 +22,10 @@ object PubMedToOaf {
val collectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
/**
* Cleaning the DOI Applying regex in order to
* remove doi starting with URL
*
* @param doi input DOI
* @return cleaned DOI
*/
@ -49,7 +49,7 @@ object PubMedToOaf {
* starting from OAF instanceType value
*
* @param cobjQualifier OAF instance type
* @param vocabularies All dnet vocabularies
* @param vocabularies All dnet vocabularies
* @return the correct instance
*/
def createResult(cobjQualifier: Qualifier, vocabularies: VocabularyGroup): Result = {
@ -65,7 +65,7 @@ object PubMedToOaf {
}
/**
* Mapping the Pubmedjournal info into the OAF Journale
* Mapping the Pubmedjournal info into the OAF Journale
*
* @param j the pubmedJournal
* @return the OAF Journal
@ -91,9 +91,8 @@ object PubMedToOaf {
* Find vocabulary term into synonyms and term in the vocabulary
*
* @param vocabularyName the input vocabulary name
* @param vocabularies all the vocabularies
* @param term the term to find
*
* @param vocabularies all the vocabularies
* @param term the term to find
* @return the cleaned term value
*/
def getVocabularyTerm(vocabularyName: String, vocabularies: VocabularyGroup, term: String): Qualifier = {
@ -104,10 +103,9 @@ object PubMedToOaf {
/**
* Map the Pubmed Article into the OAF instance
* Map the Pubmed Article into the OAF instance
*
*
* @param article the pubmed articles
* @param article the pubmed articles
* @param vocabularies the vocabularies
* @return The OAF instance if the mapping did not fail
*/
@ -185,7 +183,6 @@ object PubMedToOaf {
//--------------------------------------------------------------------------------------
// RESULT MAPPING
//--------------------------------------------------------------------------------------
result.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo))

28
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java
View File

@ -89,13 +89,13 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet1"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
@ -121,13 +121,13 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet2"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet2", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
@ -153,13 +153,13 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet3"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet3", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
@ -186,13 +186,13 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet4"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet4", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
@ -226,13 +226,13 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet5"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet5", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
@ -261,13 +261,13 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet6"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet6", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
@ -306,13 +306,13 @@ public class CreateOpenCitationsASTest {
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
workingDir.toString() + "/actionSet7"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.sequenceFile(workingDir.toString() + "/actionSet7", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));

2
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala → dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala
View File

@ -8,6 +8,7 @@ import org.apache.commons.io.FileUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.functions.{col, count}
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.extension.ExtendWith
import org.junit.jupiter.api.{AfterEach, BeforeEach, Test}
import org.mockito.junit.jupiter.MockitoExtension
@ -17,7 +18,6 @@ import java.nio.file.{Files, Path}
import java.text.SimpleDateFormat
import java.util.Locale
import scala.io.Source
import org.junit.jupiter.api.Assertions._
@ExtendWith(Array(classOf[MockitoExtension]))
class DataciteToOAFTest extends AbstractVocabularyTest{

0
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala → dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
View File

2
dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java
View File

@ -90,7 +90,7 @@ public class ReadBlacklistFromDB implements Closeable {
inverse.setSource(target_direct);
String encoding = rs.getString("relationship");
RelationInverse ri = ModelSupport.relationInverseMap.get(encoding);
RelationInverse ri = ModelSupport.findInverse(encoding);
direct.setRelClass(ri.getRelClass());
inverse.setRelClass(ri.getInverseRelClass());
direct.setRelType(ri.getRelType());

14
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala
View File

@ -1,21 +1,19 @@
package eu.dnetlib.doiboost
import java.time.LocalDate
import java.time.format.DateTimeFormatter
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{AccessRight, DataInfo, Dataset, Field, Instance, KeyValue, Oaf, OpenAccessRoute, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf._
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{getClosedAccessQualifier, getEmbargoedAccessQualifier, getUnknownQualifier}
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
import java.time.LocalDate
import java.time.format.DateTimeFormatter
import scala.collection.JavaConverters._

45
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala
View File

@ -8,11 +8,12 @@ import org.apache.hadoop.io.Text
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.hadoop.mapred.SequenceFileOutputFormat
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkGenerateDOIBoostActionSet {
val logger: Logger = LoggerFactory.getLogger(getClass)
def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf()
@ -33,53 +34,41 @@ object SparkGenerateDOIBoostActionSet {
implicit val mapEncoderAtomiAction: Encoder[AtomicAction[OafDataset]] = Encoders.kryo[AtomicAction[OafDataset]]
val dbPublicationPath = parser.get("dbPublicationPath")
val dbDatasetPath = parser.get("dbDatasetPath")
val crossRefRelation = parser.get("crossRefRelation")
val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath")
val dbOrganizationPath = parser.get("dbOrganizationPath")
val sequenceFilePath = parser.get("sFilePath")
val dbPublicationPath = parser.get("dbPublicationPath")
val dbDatasetPath = parser.get("dbDatasetPath")
val crossRefRelation = parser.get("crossRefRelation")
val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath")
val dbOrganizationPath = parser.get("dbOrganizationPath")
val sequenceFilePath = parser.get("sFilePath")
val asDataset = spark.read.load(dbDatasetPath).as[OafDataset]
.filter(p => p != null || p.getId != null)
.map(d =>DoiBoostMappingUtil.fixResult(d))
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.map(d => DoiBoostMappingUtil.fixResult(d))
.map(d => DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
val asPublication =spark.read.load(dbPublicationPath).as[Publication]
val asPublication = spark.read.load(dbPublicationPath).as[Publication]
.filter(p => p != null || p.getId != null)
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.map(d => DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
val asOrganization = spark.read.load(dbOrganizationPath).as[Organization]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.map(d => DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
val asCRelation = spark.read.load(crossRefRelation).as[Relation]
.filter(r => r!= null && r.getSource != null && r.getTarget != null)
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.filter(r => r != null && r.getSource != null && r.getTarget != null)
.map(d => DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
val asRelAffiliation = spark.read.load(dbaffiliationRelationPath).as[Relation]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.map(d => DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
val d: Dataset[(String, String)] = asDataset.union(asPublication).union(asOrganization).union(asCRelation).union(asRelAffiliation)
d.rdd.repartition(6000).map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$sequenceFilePath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
d.rdd.repartition(6000).map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$sequenceFilePath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text, Text]], classOf[GzipCodec])
}

80
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala
View File

@ -9,28 +9,26 @@ import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql.functions.col
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import org.apache.spark.sql._
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString,JArray}
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
object SparkGenerateDoiBoost {
def extractIdGRID(input:String):List[(String,String)] = {
def extractIdGRID(input: String): List[(String, String)] = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(input)
val id:String = (json \ "id").extract[String]
val id: String = (json \ "id").extract[String]
val grids:List[String] = for {
val grids: List[String] = for {
JObject(pid) <- json \ "pid"
JField("qualifier", JObject(qualifier)) <- pid
JField("classid", JString(classid)) <-qualifier
JField("classid", JString(classid)) <- qualifier
JField("value", JString(vl)) <- pid
if classid == "GRID"
} yield vl
@ -38,7 +36,6 @@ object SparkGenerateDoiBoost {
}
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(getClass)
@ -73,7 +70,7 @@ object SparkGenerateDoiBoost {
if (a != null && a._2 != null) {
b.mergeFrom(a._2)
b.setId(a._1)
val authors =AuthorMerger.mergeAuthor(b.getAuthor, a._2.getAuthor)
val authors = AuthorMerger.mergeAuthor(b.getAuthor, a._2.getAuthor)
b.setAuthor(authors)
return b
}
@ -87,11 +84,11 @@ object SparkGenerateDoiBoost {
return b2
}
else {
if (b2 != null ) {
if (b2 != null) {
b1.mergeFrom(b2)
val authors =AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor)
val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor)
b1.setAuthor(authors)
if (b2.getId!= null && b2.getId.nonEmpty)
if (b2.getId != null && b2.getId.nonEmpty)
b1.setId(b2.getId)
return b1
}
@ -118,10 +115,9 @@ object SparkGenerateDoiBoost {
val crossrefPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/crossrefPublication").as[Publication].map(p => (p.getId, p))
val uwPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/uwPublication").as[Publication].map(p => (p.getId, p))
def applyMerge(item:((String, Publication), (String, Publication))) : Publication =
{
def applyMerge(item: ((String, Publication), (String, Publication))): Publication = {
val crossrefPub = item._1._2
if (item._2!= null) {
if (item._2 != null) {
val otherPub = item._2._2
if (otherPub != null) {
crossrefPub.mergeFrom(otherPub)
@ -130,6 +126,7 @@ object SparkGenerateDoiBoost {
}
crossrefPub
}
crossrefPublication.joinWith(uwPublication, crossrefPublication("_1").equalTo(uwPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/firstJoin")
logger.info("Phase 3) Join Result with ORCID")
val fj: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/firstJoin").as[Publication].map(p => (p.getId, p))
@ -143,9 +140,9 @@ object SparkGenerateDoiBoost {
sj.joinWith(magPublication, sj("_1").equalTo(magPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublication")
val doiBoostPublication: Dataset[(String,Publication)] = spark.read.load(s"$workingDirPath/doiBoostPublication").as[Publication].filter(p=>DoiBoostMappingUtil.filterPublication(p)).map(DoiBoostMappingUtil.toISSNPair)(tupleForJoinEncoder)
val doiBoostPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/doiBoostPublication").as[Publication].filter(p => DoiBoostMappingUtil.filterPublication(p)).map(DoiBoostMappingUtil.toISSNPair)(tupleForJoinEncoder)
val hostedByDataset : Dataset[(String, HostedByItemType)] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath).map(DoiBoostMappingUtil.toHostedByItem))
val hostedByDataset: Dataset[(String, HostedByItemType)] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath).map(DoiBoostMappingUtil.toHostedByItem))
doiBoostPublication.joinWith(hostedByDataset, doiBoostPublication("_1").equalTo(hostedByDataset("_1")), "left")
@ -164,21 +161,20 @@ object SparkGenerateDoiBoost {
val paperAffiliation = spark.read.load(paperAffiliationPath).select(col("AffiliationId").alias("affId"), col("PaperId"))
val a:Dataset[DoiBoostAffiliation] = paperAffiliation
val a: Dataset[DoiBoostAffiliation] = paperAffiliation
.joinWith(affiliation, paperAffiliation("affId").equalTo(affiliation("AffiliationId")))
.select(col("_1.PaperId"), col("_2.AffiliationId"), col("_2.GridId"), col("_2.OfficialPage"), col("_2.DisplayName")).as[DoiBoostAffiliation]
val magPubs:Dataset[(String,Publication)]= spark.read.load(s"$workingDirPath/doiBoostPublicationFiltered").as[Publication]
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p))(tupleForJoinEncoder).filter(s =>s._1!= null )
val magPubs: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/doiBoostPublicationFiltered").as[Publication]
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p))(tupleForJoinEncoder).filter(s => s._1 != null)
magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).flatMap(item => {
val pub:Publication = item._1._2
magPubs.joinWith(a, magPubs("_1").equalTo(a("PaperId"))).flatMap(item => {
val pub: Publication = item._1._2
val affiliation = item._2
val affId:String = if (affiliation.GridId.isDefined) s"unresolved::grid::${affiliation.GridId.get.toLowerCase}" else DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString)
val r:Relation = new Relation
val affId: String = if (affiliation.GridId.isDefined) s"unresolved::grid::${affiliation.GridId.get.toLowerCase}" else DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString)
val r: Relation = new Relation
r.setSource(pub.getId)
r.setTarget(affId)
r.setRelType(ModelConstants.RESULT_ORGANIZATION)
@ -186,7 +182,7 @@ object SparkGenerateDoiBoost {
r.setSubRelType(ModelConstants.AFFILIATION)
r.setDataInfo(pub.getDataInfo)
r.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava)
val r1:Relation = new Relation
val r1: Relation = new Relation
r1.setTarget(pub.getId)
r1.setSource(affId)
r1.setRelType(ModelConstants.RESULT_ORGANIZATION)
@ -198,33 +194,31 @@ object SparkGenerateDoiBoost {
})(mapEncoderRel).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation_unresolved")
val unresolvedRels:Dataset[(String, Relation)] = spark.read.load(s"$workingDirPath/doiBoostPublicationAffiliation_unresolved").as[Relation].map(r => {
val unresolvedRels: Dataset[(String, Relation)] = spark.read.load(s"$workingDirPath/doiBoostPublicationAffiliation_unresolved").as[Relation].map(r => {
if (r.getSource.startsWith("unresolved"))
(r.getSource, r)
else if (r.getTarget.startsWith("unresolved"))
(r.getTarget,r)
else
(r.getTarget, r)
else
("resolved", r)
})(Encoders.tuple(Encoders.STRING, mapEncoderRel))
val openaireOrganization:Dataset[(String,String)] = spark.read.text(openaireOrganizationPath).as[String].flatMap(s => extractIdGRID(s)).groupByKey(_._2).reduceGroups((x,y) => if (x != null) x else y ).map(_._2)
val openaireOrganization: Dataset[(String, String)] = spark.read.text(openaireOrganizationPath).as[String].flatMap(s => extractIdGRID(s)).groupByKey(_._2).reduceGroups((x, y) => if (x != null) x else y).map(_._2)
unresolvedRels.joinWith(openaireOrganization,unresolvedRels("_1").equalTo(openaireOrganization("_2")))
unresolvedRels.joinWith(openaireOrganization, unresolvedRels("_1").equalTo(openaireOrganization("_2")))
.map { x =>
val currentRels = x._1._2
val currentOrgs = x._2
if (currentOrgs!= null)
if(currentRels.getSource.startsWith("unresolved"))
if (currentOrgs != null)
if (currentRels.getSource.startsWith("unresolved"))
currentRels.setSource(currentOrgs._1)
else
currentRels.setTarget(currentOrgs._1)
currentRels
}.filter(r=> !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved")).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation")
currentRels
}.filter(r => !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved")).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation")
magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).map( item => {
magPubs.joinWith(a, magPubs("_1").equalTo(a("PaperId"))).map(item => {
val affiliation = item._2
if (affiliation.GridId.isEmpty) {
val o = new Organization
@ -241,7 +235,7 @@ object SparkGenerateDoiBoost {
}
else
null
}).filter(o=> o!=null).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostOrganization")
}
}).filter(o => o != null).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostOrganization")
}
}

9
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
View File

@ -4,20 +4,19 @@ import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf._
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils}
import eu.dnetlib.dhp.utils.DHPUtils
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{decideAccessRight, _}
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
import org.apache.commons.lang.StringUtils
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JValue, _}
import org.json4s.JsonAST._
import org.json4s.jackson.JsonMethods._
import org.slf4j.{Logger, LoggerFactory}
import java.util
import scala.collection.JavaConverters._
import scala.collection.mutable
import scala.util.matching.Regex
import java.util
import eu.dnetlib.doiboost.DoiBoostMappingUtil
case class CrossrefDT(doi: String, json:String, timestamp: Long) {}

25
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefDataset.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/CrossrefDataset.scala
View File

@ -6,7 +6,7 @@ import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.{IntWritable, Text}
import org.apache.spark.SparkConf
import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql.{Dataset, Encoder, SaveMode, SparkSession}
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
@ -17,12 +17,12 @@ object CrossrefDataset {
val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
def to_item(input:String):CrossrefDT = {
def to_item(input: String): CrossrefDT = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
val ts:Long = (json \ "indexed" \ "timestamp").extract[Long]
val doi:String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String])
val ts: Long = (json \ "indexed" \ "timestamp").extract[Long]
val doi: String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String])
CrossrefDT(doi, input, ts)
}
@ -30,7 +30,6 @@ object CrossrefDataset {
def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(CrossrefDataset.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json")))
parser.parseArgument(args)
@ -54,7 +53,7 @@ object CrossrefDataset {
return b
if(a.timestamp >b.timestamp) {
if (a.timestamp > b.timestamp) {
return a
}
b
@ -66,7 +65,7 @@ object CrossrefDataset {
if (a == null)
return b
if(a.timestamp >b.timestamp) {
if (a.timestamp > b.timestamp) {
return a
}
b
@ -79,20 +78,20 @@ object CrossrefDataset {
override def finish(reduction: CrossrefDT): CrossrefDT = reduction
}
val workingPath:String = parser.get("workingPath")
val workingPath: String = parser.get("workingPath")
val main_ds:Dataset[CrossrefDT] = spark.read.load(s"$workingPath/crossref_ds").as[CrossrefDT]
val main_ds: Dataset[CrossrefDT] = spark.read.load(s"$workingPath/crossref_ds").as[CrossrefDT]
val update =
spark.createDataset(spark.sparkContext.sequenceFile(s"$workingPath/index_update", classOf[IntWritable], classOf[Text])
.map(i =>CrossrefImporter.decompressBlob(i._2.toString))
.map(i =>to_item(i)))
spark.createDataset(spark.sparkContext.sequenceFile(s"$workingPath/index_update", classOf[IntWritable], classOf[Text])
.map(i => CrossrefImporter.decompressBlob(i._2.toString))
.map(i => to_item(i)))
main_ds.union(update).groupByKey(_.doi)
.agg(crossrefAggregator.toColumn)
.map(s=>s._2)
.map(s => s._2)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/crossref_ds_updated")
}

20
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/GenerateCrossrefDataset.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/GenerateCrossrefDataset.scala
View File

@ -2,17 +2,12 @@ package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.crossref.CrossrefDataset.to_item
import eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries.getClass
import org.apache.hadoop.io.{IntWritable, Text}
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.spark.rdd.RDD
import org.apache.spark.{SparkConf, SparkContext}
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.{SparkConf, SparkContext}
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.JsonAST.JArray
import org.json4s.jackson.JsonMethods.{compact, parse, render}
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
@ -24,11 +19,10 @@ object GenerateCrossrefDataset {
implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT]
def crossrefElement(meta: String): CrossrefDT = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(meta)
val doi:String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String])
val doi: String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String])
val timestamp: Long = (json \ "indexed" \ "timestamp").extract[Long]
CrossrefDT(doi, meta, timestamp)
@ -51,14 +45,14 @@ object GenerateCrossrefDataset {
import spark.implicits._
val tmp : RDD[String] = sc.textFile(sourcePath,6000)
val tmp: RDD[String] = sc.textFile(sourcePath, 6000)
spark.createDataset(tmp)
.map(entry => crossrefElement(entry))
.write.mode(SaveMode.Overwrite).save(targetPath)
// .map(meta => crossrefElement(meta))
// .toDS.as[CrossrefDT]
// .write.mode(SaveMode.Overwrite).save(targetPath)
// .map(meta => crossrefElement(meta))
// .toDS.as[CrossrefDT]
// .write.mode(SaveMode.Overwrite).save(targetPath)
}

4
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala
View File

@ -4,10 +4,8 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf
import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset}
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}

9
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/UnpackCrtossrefEntries.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/UnpackCrtossrefEntries.scala
View File

@ -2,8 +2,8 @@ package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.spark.sql.SparkSession
import org.apache.spark.{SparkConf, SparkContext}
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.JsonAST.JArray
@ -17,9 +17,7 @@ object UnpackCrtossrefEntries {
val log: Logger = LoggerFactory.getLogger(UnpackCrtossrefEntries.getClass)
def extractDump(input:String):List[String] = {
def extractDump(input: String): List[String] = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
@ -30,7 +28,6 @@ object UnpackCrtossrefEntries {
}
def main(args: Array[String]): Unit = {
val conf = new SparkConf
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json")).mkString)
@ -45,7 +42,7 @@ object UnpackCrtossrefEntries {
.getOrCreate()
val sc: SparkContext = spark.sparkContext
sc.wholeTextFiles(sourcePath,6000).flatMap(d =>extractDump(d._2))
sc.wholeTextFiles(sourcePath, 6000).flatMap(d => extractDump(d._2))
.saveAsTextFile(targetPath, classOf[GzipCodec])

2
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala
View File

@ -5,10 +5,10 @@ import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty}
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
import scala.collection.JavaConverters._
import scala.collection.mutable

7
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala
View File

@ -3,8 +3,8 @@ package eu.dnetlib.doiboost.mag
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{SaveMode, SparkSession}
import org.apache.spark.sql.types._
import org.apache.spark.sql.{SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkImportMagIntoDataset {
@ -24,13 +24,13 @@ object SparkImportMagIntoDataset {
"Affiliations" -> Tuple2("mag/Affiliations.txt", Seq("AffiliationId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "GridId:string", "OfficialPage:string", "WikiPage:string", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "Iso3166Code:string", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")),
"AuthorExtendedAttributes" -> Tuple2("mag/AuthorExtendedAttributes.txt", Seq("AuthorId:long", "AttributeType:int", "AttributeValue:string")),
"Authors" -> Tuple2("mag/Authors.txt", Seq("AuthorId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "LastKnownAffiliationId:long?", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
"ConferenceInstances" -> Tuple2("mag/ConferenceInstances.txt", Seq("ConferenceInstanceId:long", "NormalizedName:string", "DisplayName:string", "ConferenceSeriesId:long", "Location:string", "OfficialUrl:string", "StartDate:DateTime?", "EndDate:DateTime?", "AbstractRegistrationDate:DateTime?", "SubmissionDeadlineDate:DateTime?", "NotificationDueDate:DateTime?", "FinalVersionDueDate:DateTime?", "PaperCount:long", "PaperFamilyCount:long" ,"CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")),
"ConferenceInstances" -> Tuple2("mag/ConferenceInstances.txt", Seq("ConferenceInstanceId:long", "NormalizedName:string", "DisplayName:string", "ConferenceSeriesId:long", "Location:string", "OfficialUrl:string", "StartDate:DateTime?", "EndDate:DateTime?", "AbstractRegistrationDate:DateTime?", "SubmissionDeadlineDate:DateTime?", "NotificationDueDate:DateTime?", "FinalVersionDueDate:DateTime?", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")),
"ConferenceSeries" -> Tuple2("mag/ConferenceSeries.txt", Seq("ConferenceSeriesId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
"EntityRelatedEntities" -> Tuple2("advanced/EntityRelatedEntities.txt", Seq("EntityId:long", "EntityType:string", "RelatedEntityId:long", "RelatedEntityType:string", "RelatedType:int", "Score:float")),
"FieldOfStudyChildren" -> Tuple2("advanced/FieldOfStudyChildren.txt", Seq("FieldOfStudyId:long", "ChildFieldOfStudyId:long")),
"FieldOfStudyExtendedAttributes" -> Tuple2("advanced/FieldOfStudyExtendedAttributes.txt", Seq("FieldOfStudyId:long", "AttributeType:int", "AttributeValue:string")),
"FieldsOfStudy" -> Tuple2("advanced/FieldsOfStudy.txt", Seq("FieldOfStudyId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "MainType:string", "Level:int", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
"Journals" -> Tuple2("mag/Journals.txt", Seq("JournalId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "Issn:string", "Publisher:string", "Webpage:string", "PaperCount:long", "PaperFamilyCount:long" ,"CitationCount:long", "CreatedDate:DateTime")),
"Journals" -> Tuple2("mag/Journals.txt", Seq("JournalId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "Issn:string", "Publisher:string", "Webpage:string", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
"PaperAbstractsInvertedIndex" -> Tuple2("nlp/PaperAbstractsInvertedIndex.txt.*", Seq("PaperId:long", "IndexedAbstract:string")),
"PaperAuthorAffiliations" -> Tuple2("mag/PaperAuthorAffiliations.txt", Seq("PaperId:long", "AuthorId:long", "AffiliationId:long?", "AuthorSequenceNumber:uint", "OriginalAuthor:string", "OriginalAffiliation:string")),
"PaperCitationContexts" -> Tuple2("nlp/PaperCitationContexts.txt", Seq("PaperId:long", "PaperReferenceId:long", "CitationContext:string")),
@ -75,7 +75,6 @@ object SparkImportMagIntoDataset {
.master(parser.get("master")).getOrCreate()
stream.foreach { case (k, v) =>
val s: StructType = getSchema(k)
val df = spark.read

22
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala
View File

@ -5,22 +5,19 @@ import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.functions._
import org.apache.spark.sql.functions.{col, collect_list, struct}
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
object SparkProcessMAG {
def getDistinctResults (d:Dataset[MagPapers]):Dataset[MagPapers]={
def getDistinctResults(d: Dataset[MagPapers]): Dataset[MagPapers] = {
d.where(col("Doi").isNotNull)
.groupByKey(mp => DoiBoostMappingUtil.normalizeDoi(mp.Doi))(Encoders.STRING)
.reduceGroups((p1:MagPapers,p2:MagPapers) => ConversionUtil.choiceLatestMagArtitcle(p1,p2))
.reduceGroups((p1: MagPapers, p2: MagPapers) => ConversionUtil.choiceLatestMagArtitcle(p1, p2))
.map(_._2)(Encoders.product[MagPapers])
.map(mp => {
new MagPapers(mp.PaperId, mp.Rank, DoiBoostMappingUtil.normalizeDoi(mp.Doi),
MagPapers(mp.PaperId, mp.Rank, DoiBoostMappingUtil.normalizeDoi(mp.Doi),
mp.DocType, mp.PaperTitle, mp.OriginalTitle,
mp.BookTitle, mp.Year, mp.Date, mp.Publisher: String,
mp.JournalId, mp.ConferenceSeriesId, mp.ConferenceInstanceId,
@ -98,13 +95,13 @@ object SparkProcessMAG {
var magPubs: Dataset[(String, Publication)] =
spark.read.load(s"$workingPath/merge_step_2").as[Publication]
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
val conference = spark.read.load(s"$sourcePath/ConferenceInstances")
.select($"ConferenceInstanceId".as("ci"), $"DisplayName", $"Location", $"StartDate",$"EndDate" )
.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", $"_2.PaperId").as[MagConferenceInstance]
.select($"_1.ci", $"_1.DisplayName", $"_1.Location", $"_1.StartDate", $"_1.EndDate", $"_2.PaperId").as[MagConferenceInstance]
magPubs.joinWith(conferenceInstance, col("_1").equalTo(conferenceInstance("PaperId")), "left")
@ -122,7 +119,7 @@ object SparkProcessMAG {
magPubs.joinWith(paperAbstract, col("_1").equalTo(paperAbstract("PaperId")), "left")
.map(item => ConversionUtil.updatePubsWithDescription(item)
).write.mode(SaveMode.Overwrite).save(s"$workingPath/merge_step_4")
).write.mode(SaveMode.Overwrite).save(s"$workingPath/merge_step_4")
logger.info("Phase 7) Enrich Publication with FieldOfStudy")
@ -148,11 +145,10 @@ object SparkProcessMAG {
spark.read.load(s"$workingPath/mag_publication").as[Publication]
.filter(p => p.getId != null)
.groupByKey(p => p.getId)
.reduceGroups((a:Publication, b:Publication) => ConversionUtil.mergePublication(a,b))
.reduceGroups((a: Publication, b: Publication) => ConversionUtil.mergePublication(a, b))
.map(_._2)
.write.mode(SaveMode.Overwrite).save(s"$targetPath/magPublication")
}
}

7
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala
View File

@ -4,17 +4,16 @@ import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication}
import eu.dnetlib.dhp.schema.orcid.{AuthorData, OrcidDOI}
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{createSP, generateDataInfo}
import org.apache.commons.lang.StringUtils
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.JsonAST._
import org.json4s.jackson.JsonMethods._
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
case class ORCIDItem(doi:String, authors:List[OrcidAuthor]){}

8
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala
View File

@ -11,10 +11,10 @@ object SparkConvertORCIDToOAF {
val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)
def run(spark:SparkSession, workingPath:String, targetPath:String) :Unit = {
def run(spark: SparkSession, workingPath: String, targetPath: String): Unit = {
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
import spark.implicits._
val dataset: Dataset[ORCIDItem] =spark.read.load(s"$workingPath/orcidworksWithAuthor").as[ORCIDItem]
val dataset: Dataset[ORCIDItem] = spark.read.load(s"$workingPath/orcidworksWithAuthor").as[ORCIDItem]
logger.info("Converting ORCID to OAF")
dataset.map(o => ORCIDToOAF.convertTOOAF(o)).write.mode(SaveMode.Overwrite).save(targetPath)
@ -35,8 +35,8 @@ object SparkConvertORCIDToOAF {
val workingPath = parser.get("workingPath")
val targetPath = parser.get("targetPath")
run(spark,workingPath, targetPath)
run(spark, workingPath, targetPath)
}
}
}

29
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala
View File

@ -1,48 +1,45 @@
package eu.dnetlib.doiboost.orcid
import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper}
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.oa.merge.AuthorMerger
import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.dhp.schema.orcid.OrcidDOI
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.functions._
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql.functions.{col, collect_list}
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}
object SparkPreprocessORCID {
val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)
def fixORCIDItem(item :ORCIDItem):ORCIDItem = {
ORCIDItem(item.doi, item.authors.groupBy(_.oid).map(_._2.head).toList)
def fixORCIDItem(item: ORCIDItem): ORCIDItem = {
ORCIDItem(item.doi, item.authors.groupBy(_.oid).map(_._2.head).toList)
}
def run(spark:SparkSession,sourcePath:String,workingPath:String):Unit = {
def run(spark: SparkSession, sourcePath: String, workingPath: String): Unit = {
import spark.implicits._
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
val inputRDD:RDD[OrcidAuthor] = spark.sparkContext.textFile(s"$sourcePath/authors").map(s => ORCIDToOAF.convertORCIDAuthor(s)).filter(s => s!= null).filter(s => ORCIDToOAF.authorValid(s))
val inputRDD: RDD[OrcidAuthor] = spark.sparkContext.textFile(s"$sourcePath/authors").map(s => ORCIDToOAF.convertORCIDAuthor(s)).filter(s => s != null).filter(s => ORCIDToOAF.authorValid(s))
spark.createDataset(inputRDD).as[OrcidAuthor].write.mode(SaveMode.Overwrite).save(s"$workingPath/author")
val res = spark.sparkContext.textFile(s"$sourcePath/works").flatMap(s => ORCIDToOAF.extractDOIWorks(s)).filter(s => s!= null)
val res = spark.sparkContext.textFile(s"$sourcePath/works").flatMap(s => ORCIDToOAF.extractDOIWorks(s)).filter(s => s != null)
spark.createDataset(res).as[OrcidWork].write.mode(SaveMode.Overwrite).save(s"$workingPath/works")
val authors :Dataset[OrcidAuthor] = spark.read.load(s"$workingPath/author").as[OrcidAuthor]
val authors: Dataset[OrcidAuthor] = spark.read.load(s"$workingPath/author").as[OrcidAuthor]
val works :Dataset[OrcidWork] = spark.read.load(s"$workingPath/works").as[OrcidWork]
val works: Dataset[OrcidWork] = spark.read.load(s"$workingPath/works").as[OrcidWork]
works.joinWith(authors, authors("oid").equalTo(works("oid")))
.map(i =>{
.map(i => {
val doi = i._1.doi
val author = i._2
(doi, author)
}).groupBy(col("_1").alias("doi"))
(doi, author)
}).groupBy(col("_1").alias("doi"))
.agg(collect_list(col("_2")).alias("authors")).as[ORCIDItem]
.map(s => fixORCIDItem(s))
.write.mode(SaveMode.Overwrite).save(s"$workingPath/orcidworksWithAuthor")
@ -67,4 +64,4 @@ object SparkPreprocessORCID {
}
}
}

8
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala
View File

@ -1,16 +1,14 @@
package eu.dnetlib.doiboost.uw
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF
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.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}
object SparkMapUnpayWallToOAF {
def main(args: Array[String]): Unit = {
@ -32,11 +30,11 @@ object SparkMapUnpayWallToOAF {
val sourcePath = parser.get("sourcePath")
val targetPath = parser.get("targetPath")
val inputRDD:RDD[String] = spark.sparkContext.textFile(s"$sourcePath")
val inputRDD: RDD[String] = spark.sparkContext.textFile(s"$sourcePath")
logger.info("Converting UnpayWall to OAF")
val d:Dataset[Publication] = spark.createDataset(inputRDD.map(UnpayWallToOAF.convertToOAF).filter(p=>p!=null)).as[Publication]
val d: Dataset[Publication] = spark.createDataset(inputRDD.map(UnpayWallToOAF.convertToOAF).filter(p => p != null)).as[Publication]
d.write.mode(SaveMode.Overwrite).save(targetPath)
}

3
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala → dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala
View File

@ -4,14 +4,13 @@ import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
import eu.dnetlib.dhp.schema.oaf.{AccessRight, Instance, OpenAccessRoute, Publication}
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
import eu.dnetlib.doiboost.uw.UnpayWallToOAF.get_unpaywall_color

70
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostHostedByMapTest.scala
View File

@ -1,70 +0,0 @@
package eu.dnetlib.dhp.doiboost
import eu.dnetlib.dhp.schema.oaf.{Publication, Dataset => OafDataset}
import eu.dnetlib.doiboost.{DoiBoostMappingUtil, HostedByItemType}
import eu.dnetlib.doiboost.SparkGenerateDoiBoost.getClass
import eu.dnetlib.doiboost.mag.ConversionUtil
import eu.dnetlib.doiboost.orcid.ORCIDElement
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Test
import scala.io.Source
class DoiBoostHostedByMapTest {
// @Test
// def testMerge():Unit = {
// val conf: SparkConf = new SparkConf()
// val spark: SparkSession =
// SparkSession
// .builder()
// .config(conf)
// .appName(getClass.getSimpleName)
// .master("local[*]").getOrCreate()
//
//
//
// implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
// implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
// implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPub)
//
//
// import spark.implicits._
// val dataset:RDD[String]= spark.sparkContext.textFile("/home/sandro/Downloads/hbMap.gz")
//
//
// val hbMap:Dataset[(String, HostedByItemType)] =spark.createDataset(dataset.map(DoiBoostMappingUtil.toHostedByItem))
//
//
// hbMap.show()
//
//
//
//
//
//
//
//
//
//
// }
@Test
def idDSGeneration():Unit = {
val s ="doajarticles::0066-782X"
println(DoiBoostMappingUtil.generateDSId(s))
}
}

20
dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/DoiBoostHostedByMapTest.scala Normal file
View File

@ -0,0 +1,20 @@
package eu.dnetlib.dhp.doiboost
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import org.junit.jupiter.api.Test
class DoiBoostHostedByMapTest {
@Test
def idDSGeneration():Unit = {
val s ="doajarticles::0066-782X"
println(DoiBoostMappingUtil.generateDSId(s))
}
}

0
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/NormalizeDoiTest.scala → dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/NormalizeDoiTest.scala
View File

86
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala → dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala
View File

@ -1,7 +1,8 @@
package eu.dnetlib.doiboost.crossref
package eu.dnetlib.dhp.doiboost.crossref
import eu.dnetlib.dhp.schema.oaf._
import eu.dnetlib.dhp.utils.DHPUtils
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test
@ -21,9 +22,9 @@ class CrossrefMappingTest {
@Test
def testFunderRelationshipsMapping(): Unit = {
val template = Source.fromInputStream(getClass.getResourceAsStream("article_funder_template.json")).mkString
val funder_doi = Source.fromInputStream(getClass.getResourceAsStream("funder_doi")).mkString
val funder_name = Source.fromInputStream(getClass.getResourceAsStream("funder_doi")).mkString
val template = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article_funder_template.json")).mkString
val funder_doi = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/funder_doi")).mkString
val funder_name = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/funder_doi")).mkString
for (line <- funder_doi.lines) {
@ -72,7 +73,7 @@ class CrossrefMappingTest {
@Test
def testOrcidID() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("orcid_data.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/orcid_data.json")).mkString
assertNotNull(json)
@ -93,7 +94,7 @@ class CrossrefMappingTest {
@Test
def testEmptyTitle() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("empty_title.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/empty_title.json")).mkString
assertNotNull(json)
@ -115,7 +116,7 @@ class CrossrefMappingTest {
@Test
def testPeerReviewed(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("prwTest.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/prwTest.json")).mkString
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
assertNotNull(json)
@ -156,7 +157,7 @@ class CrossrefMappingTest {
@Test
def testJournalRelation(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("awardTest.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/awardTest.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty)
@ -177,7 +178,7 @@ class CrossrefMappingTest {
@Test
def testConvertBookFromCrossRef2Oaf(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("book.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/book.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
@ -233,7 +234,7 @@ class CrossrefMappingTest {
@Test
def testConvertPreprintFromCrossRef2Oaf(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("preprint.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/preprint.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
@ -291,7 +292,7 @@ class CrossrefMappingTest {
@Test
def testConvertDatasetFromCrossRef2Oaf(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("dataset.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/dataset.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
@ -332,7 +333,7 @@ class CrossrefMappingTest {
@Test
def testConvertArticleFromCrossRef2Oaf(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("article.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
@ -400,7 +401,7 @@ class CrossrefMappingTest {
@Test
def testSetDateOfAcceptanceCrossRef2Oaf(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("dump_file.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/dump_file.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
@ -415,55 +416,12 @@ class CrossrefMappingTest {
assert(items.size == 1)
val result: Result = items.head.asInstanceOf[Publication]
assertNotNull(result)
logger.info(mapper.writeValueAsString(result));
// assertNotNull(result.getDataInfo, "Datainfo test not null Failed");
// assertNotNull(
// result.getDataInfo.getProvenanceaction,
// "DataInfo/Provenance test not null Failed");
// assertFalse(
// result.getDataInfo.getProvenanceaction.getClassid.isEmpty,
// "DataInfo/Provenance/classId test not null Failed");
// assertFalse(
// result.getDataInfo.getProvenanceaction.getClassname.isEmpty,
// "DataInfo/Provenance/className test not null Failed");
// assertFalse(
// result.getDataInfo.getProvenanceaction.getSchemeid.isEmpty,
// "DataInfo/Provenance/SchemeId test not null Failed");
// assertFalse(
// result.getDataInfo.getProvenanceaction.getSchemename.isEmpty,
// "DataInfo/Provenance/SchemeName test not null Failed");
//
// assertNotNull(result.getCollectedfrom, "CollectedFrom test not null Failed");
// assertFalse(result.getCollectedfrom.isEmpty);
//
// val collectedFromList = result.getCollectedfrom.asScala
// assert(collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")), "Wrong collected from assertion")
//
// assert(collectedFromList.exists(c => c.getValue.equalsIgnoreCase("crossref")), "Wrong collected from assertion")
//
//
// val relevantDates = result.getRelevantdate.asScala
//
// assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("created")), "Missing relevant date of type created")
//
// val rels = resultList.filter(p => p.isInstanceOf[Relation]).asInstanceOf[List[Relation]]
// assertFalse(rels.isEmpty)
// rels.foreach(relation => {
// assertNotNull(relation)
// assertFalse(relation.getSource.isEmpty)
// assertFalse(relation.getTarget.isEmpty)
// assertFalse(relation.getRelClass.isEmpty)
// assertFalse(relation.getRelType.isEmpty)
// assertFalse(relation.getSubRelType.isEmpty)
//
// })
}
@Test
def testNormalizeDOI(): Unit = {
val template = Source.fromInputStream(getClass.getResourceAsStream("article_funder_template.json")).mkString
val template = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article_funder_template.json")).mkString
val line :String = "\"funder\": [{\"name\": \"Wellcome Trust Masters Fellowship\",\"award\": [\"090633\"]}],"
val json = template.replace("%s", line)
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
@ -479,7 +437,7 @@ class CrossrefMappingTest {
@Test
def testNormalizeDOI2(): Unit = {
val template = Source.fromInputStream(getClass.getResourceAsStream("article.json")).mkString
val template = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article.json")).mkString
val resultList: List[Oaf] = Crossref2Oaf.convert(template)
assertTrue(resultList.nonEmpty)
@ -494,7 +452,7 @@ class CrossrefMappingTest {
@Test
def testLicenseVorClosed() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_vor.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_vor.json")).mkString
assertNotNull(json)
@ -521,7 +479,7 @@ class CrossrefMappingTest {
@Test
def testLicenseOpen() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_open.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_open.json")).mkString
assertNotNull(json)
@ -544,7 +502,7 @@ class CrossrefMappingTest {
@Test
def testLicenseEmbargoOpen() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo_open.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo_open.json")).mkString
assertNotNull(json)
@ -567,7 +525,7 @@ class CrossrefMappingTest {
@Test
def testLicenseEmbargo() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo.json")).mkString
assertNotNull(json)
@ -591,7 +549,7 @@ class CrossrefMappingTest {
@Test
def testLicenseEmbargoDateTime() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo_datetime.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo_datetime.json")).mkString
assertNotNull(json)
@ -614,7 +572,7 @@ class CrossrefMappingTest {
@Test
def testMultipleURLs() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("multiple_urls.json")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/multiple_urls.json")).mkString
assertNotNull(json)

11
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala → dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/mag/MAGMappingTest.scala
View File

@ -1,11 +1,12 @@
package eu.dnetlib.doiboost.mag
package eu.dnetlib.dhp.doiboost.mag
import eu.dnetlib.doiboost.mag.{ConversionUtil, MagPapers, SparkProcessMAG}
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, SparkSession}
import org.codehaus.jackson.map.ObjectMapper
import org.json4s.DefaultFormats
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test
import org.json4s.DefaultFormats
import org.slf4j.{Logger, LoggerFactory}
import java.sql.Timestamp
@ -47,7 +48,7 @@ class MAGMappingTest {
@Test
def buildInvertedIndexTest(): Unit = {
val json_input = Source.fromInputStream(getClass.getResourceAsStream("invertedIndex.json")).mkString
val json_input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/mag/invertedIndex.json")).mkString
val description = ConversionUtil.convertInvertedIndexString(json_input)
assertNotNull(description)
assertTrue(description.nonEmpty)
@ -71,7 +72,7 @@ class MAGMappingTest {
.appName(getClass.getSimpleName)
.config(conf)
.getOrCreate()
val path = getClass.getResource("magPapers.json").getPath
val path = getClass.getResource("/eu/dnetlib/doiboost/mag/magPapers.json").getPath
import org.apache.spark.sql.Encoders
val schema = Encoders.product[MagPapers].schema
@ -101,7 +102,7 @@ class MAGMappingTest {
.appName(getClass.getSimpleName)
.config(conf)
.getOrCreate()
val path = getClass.getResource("duplicatedMagPapers.json").getPath
val path = getClass.getResource("/eu/dnetlib/doiboost/mag/duplicatedMagPapers.json").getPath
import org.apache.spark.sql.Encoders
val schema = Encoders.product[MagPapers].schema

8
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala → dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala
View File

@ -1,7 +1,8 @@
package eu.dnetlib.doiboost.orcid
package eu.dnetlib.dhp.doiboost.orcid
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.orcid._
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
import org.junit.jupiter.api.Assertions._
@ -10,9 +11,8 @@ import org.junit.jupiter.api.io.TempDir
import org.slf4j.{Logger, LoggerFactory}
import java.nio.file.Path
import scala.io.Source
import scala.collection.JavaConversions._
import scala.io.Source
class MappingORCIDToOAFTest {
val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass)
@ -20,7 +20,7 @@ class MappingORCIDToOAFTest {
@Test
def testExtractData():Unit ={
val json = Source.fromInputStream(getClass.getResourceAsStream("dataOutput")).mkString
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/orcid/dataOutput")).mkString
assertNotNull(json)
assertFalse(json.isEmpty)
json.lines.foreach(s => {

10
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala → dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala
View File

@ -1,13 +1,13 @@
package eu.dnetlib.doiboost.uw
package eu.dnetlib.dhp.doiboost.uw
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.oaf.OpenAccessRoute
import eu.dnetlib.doiboost.uw.UnpayWallToOAF
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
import org.junit.jupiter.api.Assertions._
import org.slf4j.{Logger, LoggerFactory}
class UnpayWallMappingTest {
@ -18,7 +18,7 @@ class UnpayWallMappingTest {
@Test
def testMappingToOAF():Unit ={
val Ilist = Source.fromInputStream(getClass.getResourceAsStream("input.json")).mkString
val Ilist = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/uw/input.json")).mkString
var i:Int = 0
for (line <-Ilist.lines) {

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala
View File

@ -1,8 +1,8 @@
package eu.dnetlib.dhp.oa.graph.hostedbymap
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
import org.apache.spark.sql.{Dataset, Encoder, Encoders, TypedColumn}
import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql.{Dataset, Encoder, Encoders, TypedColumn}
case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {}

13
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala
View File

@ -2,13 +2,12 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.oa.graph.hostedbymap.SparkApplyHostedByMapToResult.{applyHBtoPubs, getClass}
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{Datasource, Publication}
import eu.dnetlib.dhp.schema.oaf.Datasource
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql._
import org.json4s.DefaultFormats
import org.slf4j.{Logger, LoggerFactory}
@ -52,18 +51,18 @@ object SparkApplyHostedByMapToDatasource {
val mapper = new ObjectMapper()
val dats : Dataset[Datasource] = spark.read.textFile(graphPath + "/datasource")
val dats: Dataset[Datasource] = spark.read.textFile(graphPath + "/datasource")
.map(r => mapper.readValue(r, classOf[Datasource]))
val pinfo : Dataset[EntityInfo] = Aggregators.datasourceToSingleId( spark.read.textFile(preparedInfoPath)
val pinfo: Dataset[EntityInfo] = Aggregators.datasourceToSingleId(spark.read.textFile(preparedInfoPath)
.map(ei => mapper.readValue(ei, classOf[EntityInfo])))
applyHBtoDats(pinfo, dats).write.mode(SaveMode.Overwrite).option("compression","gzip").json(outputPath)
applyHBtoDats(pinfo, dats).write.mode(SaveMode.Overwrite).option("compression", "gzip").json(outputPath)
spark.read.textFile(outputPath)
.write
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.option("compression", "gzip")
.text(graphPath + "/datasource")
}

19
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala
View File

@ -5,16 +5,14 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
import eu.dnetlib.dhp.schema.oaf.{Datasource, Instance, OpenAccessRoute, Publication}
import eu.dnetlib.dhp.schema.oaf.{Instance, OpenAccessRoute, Publication}
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql._
import org.json4s.DefaultFormats
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
object SparkApplyHostedByMapToResult {
def applyHBtoPubs(join: Dataset[EntityInfo], pubs: Dataset[Publication]) = {
@ -25,7 +23,7 @@ object SparkApplyHostedByMapToResult {
val ei: EntityInfo = t2._2
val i = p.getInstance().asScala
if (i.size == 1) {
val inst: Instance = i(0)
val inst: Instance = i.head
inst.getHostedby.setKey(ei.getHostedById)
inst.getHostedby.setValue(ei.getName)
if (ei.getOpenAccess) {
@ -39,6 +37,7 @@ object SparkApplyHostedByMapToResult {
p
})(Encoders.bean(classOf[Publication]))
}
def main(args: Array[String]): Unit = {
@ -67,18 +66,18 @@ object SparkApplyHostedByMapToResult {
implicit val mapEncoderEinfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo])
val mapper = new ObjectMapper()
val pubs : Dataset[Publication] = spark.read.textFile(graphPath + "/publication")
val pubs: Dataset[Publication] = spark.read.textFile(graphPath + "/publication")
.map(r => mapper.readValue(r, classOf[Publication]))
val pinfo : Dataset[EntityInfo] = spark.read.textFile(preparedInfoPath)
.map(ei => mapper.readValue(ei, classOf[EntityInfo]))
val pinfo: Dataset[EntityInfo] = spark.read.textFile(preparedInfoPath)
.map(ei => mapper.readValue(ei, classOf[EntityInfo]))
applyHBtoPubs(pinfo, pubs).write.mode(SaveMode.Overwrite).option("compression","gzip").json(outputPath)
applyHBtoPubs(pinfo, pubs).write.mode(SaveMode.Overwrite).option("compression", "gzip").json(outputPath)
spark.read.textFile(outputPath)
.write
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.option("compression", "gzip")
.text(graphPath + "/publication")
}

35
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala
View File

@ -3,61 +3,58 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
import eu.dnetlib.dhp.schema.oaf.{Journal, Publication}
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql._
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
object SparkPrepareHostedByInfoToApply {
implicit val mapEncoderPInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo])
def getList(id: String, j: Journal, name: String ) : List[EntityInfo] = {
var lst:List[EntityInfo] = List()
def getList(id: String, j: Journal, name: String): List[EntityInfo] = {
var lst: List[EntityInfo] = List()
if (j.getIssnLinking != null && !j.getIssnLinking.equals("")){
if (j.getIssnLinking != null && !j.getIssnLinking.equals("")) {
lst = EntityInfo.newInstance(id, j.getIssnLinking, name) :: lst
}
if (j.getIssnOnline != null && !j.getIssnOnline.equals("")){
if (j.getIssnOnline != null && !j.getIssnOnline.equals("")) {
lst = EntityInfo.newInstance(id, j.getIssnOnline, name) :: lst
}
if (j.getIssnPrinted != null && !j.getIssnPrinted.equals("")){
if (j.getIssnPrinted != null && !j.getIssnPrinted.equals("")) {
lst = EntityInfo.newInstance(id, j.getIssnPrinted, name) :: lst
}
lst
}
def prepareResultInfo(spark:SparkSession, publicationPath:String) : Dataset[EntityInfo] = {
def prepareResultInfo(spark: SparkSession, publicationPath: String): Dataset[EntityInfo] = {
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication])
val mapper = new ObjectMapper()
val dd : Dataset[Publication] = spark.read.textFile(publicationPath)
val dd: Dataset[Publication] = spark.read.textFile(publicationPath)
.map(r => mapper.readValue(r, classOf[Publication]))
dd.filter(p => p.getJournal != null ).flatMap(p => getList(p.getId, p.getJournal, ""))
dd.filter(p => p.getJournal != null).flatMap(p => getList(p.getId, p.getJournal, ""))
}
def toEntityInfo(input:String): EntityInfo = {
def toEntityInfo(input: String): EntityInfo = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
val c :Map[String,HostedByItemType] = json.extract[Map[String, HostedByItemType]]
val c: Map[String, HostedByItemType] = json.extract[Map[String, HostedByItemType]]
toEntityItem(c.keys.head, c.values.head)
}
def toEntityItem(journal_id: String , hbi: HostedByItemType): EntityInfo = {
def toEntityItem(journal_id: String, hbi: HostedByItemType): EntityInfo = {
EntityInfo.newInstance(hbi.id, journal_id, hbi.officialname, hbi.openAccess)
@ -67,7 +64,7 @@ object SparkPrepareHostedByInfoToApply {
Aggregators.resultToSingleId(res.joinWith(hbm, res.col("journalId").equalTo(hbm.col("journalId")), "left")
.map(t2 => {
val res: EntityInfo = t2._1
if(t2._2 != null ){
if (t2._2 != null) {
val ds = t2._2
res.setHostedById(ds.getId)
res.setOpenAccess(ds.getOpenAccess)
@ -107,10 +104,10 @@ object SparkPrepareHostedByInfoToApply {
//STEP1: read the hostedbymap and transform it in EntityInfo
val hostedByInfo:Dataset[EntityInfo] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath)).map(toEntityInfo)
val hostedByInfo: Dataset[EntityInfo] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath)).map(toEntityInfo)
//STEP2: create association (publication, issn), (publication, eissn), (publication, lissn)
val resultInfoDataset:Dataset[EntityInfo] = prepareResultInfo(spark, graphPath + "/publication")
//STEP2: create association (publication, issn), (publication, eissn), (publication, lissn)
val resultInfoDataset: Dataset[EntityInfo] = prepareResultInfo(spark, graphPath + "/publication")
//STEP3: left join resultInfo with hostedByInfo on journal_id. Reduction of all the results with the same id in just
//one entry (one result could be associated to issn and eissn and so possivly matching more than once against the map)

109
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala
View File

@ -1,41 +1,39 @@
package eu.dnetlib.dhp.oa.graph.hostedbymap
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.{DOAJModel, UnibiGoldModel}
import eu.dnetlib.dhp.schema.oaf.Datasource
import org.apache.commons.io.IOUtils
import org.apache.hadoop.conf.Configuration
import org.apache.hadoop.fs.{FileSystem, Path}
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
import org.json4s.DefaultFormats
import org.slf4j.{Logger, LoggerFactory}
import com.fasterxml.jackson.databind.ObjectMapper
import org.apache.hadoop.conf.Configuration
import org.apache.hadoop.fs.FileSystem
import org.apache.hadoop.fs.Path
import java.io.PrintWriter
import org.apache.hadoop.io.compress.GzipCodec
object SparkProduceHostedByMap {
implicit val tupleForJoinEncoder: Encoder[(String, HostedByItemType)] = Encoders.tuple(Encoders.STRING, Encoders.product[HostedByItemType])
def toHostedByItemType(input: ((HostedByInfo, HostedByInfo), HostedByInfo)) : HostedByItemType = {
def toHostedByItemType(input: ((HostedByInfo, HostedByInfo), HostedByInfo)): HostedByItemType = {
val openaire: HostedByInfo = input._1._1
val doaj: HostedByInfo = input._1._2
val gold: HostedByInfo = input._2
val isOpenAccess: Boolean = doaj == null && gold == null
openaire.journal_id match {
case Constants.ISSN => HostedByItemType(openaire.id, openaire.officialname, openaire.journal_id, "", "", isOpenAccess)
case Constants.EISSN => HostedByItemType(openaire.id, openaire.officialname, "", openaire.journal_id, "", isOpenAccess)
case Constants.ISSNL => HostedByItemType(openaire.id, openaire.officialname, "", "", openaire.journal_id, isOpenAccess)
case Constants.ISSN => HostedByItemType(openaire.id, openaire.officialname, openaire.journal_id, "", "", isOpenAccess)
case Constants.EISSN => HostedByItemType(openaire.id, openaire.officialname, "", openaire.journal_id, "", isOpenAccess)
case Constants.ISSNL => HostedByItemType(openaire.id, openaire.officialname, "", "", openaire.journal_id, isOpenAccess)
// catch the default with a variable so you can print it
case whoa => null
case whoa => null
}
}
@ -44,7 +42,7 @@ object SparkProduceHostedByMap {
implicit val formats = org.json4s.DefaultFormats
val map: Map [String, HostedByItemType] = Map (input._1 -> input._2 )
val map: Map[String, HostedByItemType] = Map(input._1 -> input._2)
Serialization.write(map)
@ -52,34 +50,33 @@ object SparkProduceHostedByMap {
}
def getHostedByItemType(id:String, officialname: String, issn:String, eissn:String, issnl:String, oa:Boolean): HostedByItemType = {
if(issn != null){
if(eissn != null){
if(issnl != null){
HostedByItemType(id, officialname, issn, eissn, issnl , oa)
}else{
HostedByItemType(id, officialname, issn, eissn, "" , oa)
def getHostedByItemType(id: String, officialname: String, issn: String, eissn: String, issnl: String, oa: Boolean): HostedByItemType = {
if (issn != null) {
if (eissn != null) {
if (issnl != null) {
HostedByItemType(id, officialname, issn, eissn, issnl, oa)
} else {
HostedByItemType(id, officialname, issn, eissn, "", oa)
}
}else{
if(issnl != null){
HostedByItemType(id, officialname, issn, "", issnl , oa)
}else{
HostedByItemType(id, officialname, issn, "", "" , oa)
} else {
if (issnl != null) {
HostedByItemType(id, officialname, issn, "", issnl, oa)
} else {
HostedByItemType(id, officialname, issn, "", "", oa)
}
}
}else{
if(eissn != null){
if(issnl != null){
HostedByItemType(id, officialname, "", eissn, issnl , oa)
}else{
HostedByItemType(id, officialname, "", eissn, "" , oa)
} else {
if (eissn != null) {
if (issnl != null) {
HostedByItemType(id, officialname, "", eissn, issnl, oa)
} else {
HostedByItemType(id, officialname, "", eissn, "", oa)
}
}else{
if(issnl != null){
HostedByItemType(id, officialname, "", "", issnl , oa)
}else{
HostedByItemType("", "", "", "", "" , oa)
} else {
if (issnl != null) {
HostedByItemType(id, officialname, "", "", issnl, oa)
} else {
HostedByItemType("", "", "", "", "", oa)
}
}
}
@ -90,10 +87,10 @@ object SparkProduceHostedByMap {
return getHostedByItemType(dats.getId, dats.getOfficialname.getValue, dats.getJournal.getIssnPrinted, dats.getJournal.getIssnOnline, dats.getJournal.getIssnLinking, false)
}
HostedByItemType("","","","","",false)
HostedByItemType("", "", "", "", "", false)
}
def oaHostedByDataset(spark:SparkSession, datasourcePath : String) : Dataset[HostedByItemType] = {
def oaHostedByDataset(spark: SparkSession, datasourcePath: String): Dataset[HostedByItemType] = {
import spark.implicits._
@ -102,10 +99,10 @@ object SparkProduceHostedByMap {
implicit var encoderD = Encoders.kryo[Datasource]
val dd : Dataset[Datasource] = spark.read.textFile(datasourcePath)
val dd: Dataset[Datasource] = spark.read.textFile(datasourcePath)
.map(r => mapper.readValue(r, classOf[Datasource]))
dd.map{ddt => oaToHostedbyItemType(ddt)}.filter(hb => !(hb.id.equals("")))
dd.map { ddt => oaToHostedbyItemType(ddt) }.filter(hb => !(hb.id.equals("")))
}
@ -115,17 +112,17 @@ object SparkProduceHostedByMap {
}
def goldHostedByDataset(spark:SparkSession, datasourcePath:String) : Dataset[HostedByItemType] = {
def goldHostedByDataset(spark: SparkSession, datasourcePath: String): Dataset[HostedByItemType] = {
import spark.implicits._
implicit val mapEncoderUnibi: Encoder[UnibiGoldModel] = Encoders.kryo[UnibiGoldModel]
val mapper = new ObjectMapper()
val dd : Dataset[UnibiGoldModel] = spark.read.textFile(datasourcePath)
val dd: Dataset[UnibiGoldModel] = spark.read.textFile(datasourcePath)
.map(r => mapper.readValue(r, classOf[UnibiGoldModel]))
dd.map{ddt => goldToHostedbyItemType(ddt)}.filter(hb => !(hb.id.equals("")))
dd.map { ddt => goldToHostedbyItemType(ddt) }.filter(hb => !(hb.id.equals("")))
}
@ -134,41 +131,40 @@ object SparkProduceHostedByMap {
return getHostedByItemType(Constants.DOAJ, doaj.getJournalTitle, doaj.getIssn, doaj.getEissn, "", true)
}
def doajHostedByDataset(spark:SparkSession, datasourcePath:String) : Dataset[HostedByItemType] = {
def doajHostedByDataset(spark: SparkSession, datasourcePath: String): Dataset[HostedByItemType] = {
import spark.implicits._
implicit val mapEncoderDOAJ: Encoder[DOAJModel] = Encoders.kryo[DOAJModel]
val mapper = new ObjectMapper()
val dd : Dataset[DOAJModel] = spark.read.textFile(datasourcePath)
val dd: Dataset[DOAJModel] = spark.read.textFile(datasourcePath)
.map(r => mapper.readValue(r, classOf[DOAJModel]))
dd.map{ddt => doajToHostedbyItemType(ddt)}.filter(hb => !(hb.id.equals("")))
dd.map { ddt => doajToHostedbyItemType(ddt) }.filter(hb => !(hb.id.equals("")))
}
def toList(input: HostedByItemType): List[(String, HostedByItemType)] = {
var lst : List[(String, HostedByItemType)] = List()
if(!input.issn.equals("")){
var lst: List[(String, HostedByItemType)] = List()
if (!input.issn.equals("")) {
lst = (input.issn, input) :: lst
}
if(!input.eissn.equals("")){
if (!input.eissn.equals("")) {
lst = (input.eissn, input) :: lst
}
if(!input.lissn.equals("")){
if (!input.lissn.equals("")) {
lst = (input.lissn, input) :: lst
}
lst
}
def writeToHDFS(input: Array[String], outputPath: String, hdfsNameNode : String):Unit = {
def writeToHDFS(input: Array[String], outputPath: String, hdfsNameNode: String): Unit = {
val conf = new Configuration()
conf.set("fs.defaultFS", hdfsNameNode)
val fs= FileSystem.get(conf)
val fs = FileSystem.get(conf)
val output = fs.create(new Path(outputPath))
val writer = new PrintWriter(output)
try {
@ -182,7 +178,6 @@ object SparkProduceHostedByMap {
}
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(getClass)
@ -213,7 +208,7 @@ object SparkProduceHostedByMap {
.union(doajHostedByDataset(spark, workingDirPath + "/doaj.json"))
.flatMap(hbi => toList(hbi))).filter(hbi => hbi._2.id.startsWith("10|"))
.map(hbi => toHostedByMap(hbi))(Encoders.STRING)
.rdd.saveAsTextFile(outputPath , classOf[GzipCodec])
.rdd.saveAsTextFile(outputPath, classOf[GzipCodec])
}

8
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala
View File

@ -4,17 +4,11 @@ import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.common.HdfsSupport
import eu.dnetlib.dhp.schema.common.ModelSupport
import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.io.IOUtils
import org.apache.commons.lang3.StringUtils
import org.apache.http.client.methods.HttpGet
import org.apache.http.impl.client.HttpClients
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.{SparkConf, SparkContext}
import org.slf4j.LoggerFactory
import scala.collection.JavaConverters._
import scala.io.Source
@ -59,7 +53,7 @@ object CopyHdfsOafSparkApplication {
if (validPaths.nonEmpty) {
val oaf = spark.read.load(validPaths: _*).as[Oaf]
val mapper = new ObjectMapper()
val l =ModelSupport.oafTypes.entrySet.asScala.map(e => e.getKey).toList
val l = ModelSupport.oafTypes.entrySet.asScala.map(e => e.getKey).toList
l.foreach(
e =>
oaf.filter(o => o.getClass.getSimpleName.equalsIgnoreCase(e))

5
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala
View File

@ -2,9 +2,8 @@ package eu.dnetlib.dhp.oa.graph.resolution
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.common.HdfsSupport
import eu.dnetlib.dhp.schema.common.EntityType
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Result, Software, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset,_}
import org.apache.commons.io.IOUtils
import org.apache.hadoop.fs.{FileSystem, Path}
import org.apache.spark.SparkConf
@ -75,7 +74,7 @@ object SparkResolveEntities {
}
}
def generateResolvedEntities(spark: SparkSession, workingPath: String, graphBasePath: String, targetPath:String) = {
def generateResolvedEntities(spark: SparkSession, workingPath: String, graphBasePath: String, targetPath: String) = {
implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
import spark.implicits._

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala
View File

@ -3,7 +3,7 @@ package eu.dnetlib.dhp.oa.graph.resolution
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.common.HdfsSupport
import eu.dnetlib.dhp.schema.oaf.{Relation, Result}
import eu.dnetlib.dhp.schema.oaf.Relation
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.io.IOUtils
import org.apache.hadoop.fs.{FileSystem, Path}

1
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/sx/graphimport/SparkDataciteToOAF.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/sx/graphimport/SparkDataciteToOAF.scala
View File

@ -18,7 +18,6 @@ object SparkDataciteToOAF {
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
import spark.implicits._
val sc = spark.sparkContext

10
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertDatasetToJsonRDD.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertDatasetToJsonRDD.scala
View File

@ -2,7 +2,7 @@ package eu.dnetlib.dhp.sx.graph
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, OtherResearchProduct, Publication, Result, Software, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.oaf.Result
import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.spark.SparkConf
@ -29,13 +29,13 @@ object SparkConvertDatasetToJsonRDD {
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
val resultObject = List("publication","dataset","software", "otherResearchProduct")
val resultObject = List("publication", "dataset", "software", "otherResearchProduct")
val mapper = new ObjectMapper()
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
resultObject.foreach{item =>
spark.read.load(s"$sourcePath/$item").as[Result].map(r=> mapper.writeValueAsString(r))(Encoders.STRING).rdd.saveAsTextFile(s"$targetPath/${item.toLowerCase}", classOf[GzipCodec])
resultObject.foreach { item =>
spark.read.load(s"$sourcePath/$item").as[Result].map(r => mapper.writeValueAsString(r))(Encoders.STRING).rdd.saveAsTextFile(s"$targetPath/${item.toLowerCase}", classOf[GzipCodec])
}
}

10
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala
View File

@ -5,10 +5,10 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.sx.scholix.Scholix
import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import org.apache.hadoop.io.compress._
object SparkConvertObjectToJson {
@ -32,8 +32,8 @@ object SparkConvertObjectToJson {
log.info(s"objectType -> $objectType")
implicit val scholixEncoder :Encoder[Scholix]= Encoders.kryo[Scholix]
implicit val summaryEncoder :Encoder[ScholixSummary]= Encoders.kryo[ScholixSummary]
implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
val mapper = new ObjectMapper
@ -42,11 +42,11 @@ object SparkConvertObjectToJson {
case "scholix" =>
log.info("Serialize Scholix")
val d: Dataset[Scholix] = spark.read.load(sourcePath).as[Scholix]
d.map(s => mapper.writeValueAsString(s))(Encoders.STRING).rdd.repartition(6000).saveAsTextFile(targetPath, classOf[GzipCodec])
d.map(s => mapper.writeValueAsString(s))(Encoders.STRING).rdd.repartition(6000).saveAsTextFile(targetPath, classOf[GzipCodec])
case "summary" =>
log.info("Serialize Summary")
val d: Dataset[ScholixSummary] = spark.read.load(sourcePath).as[ScholixSummary]
d.map(s => mapper.writeValueAsString(s))(Encoders.STRING).rdd.repartition(1000).saveAsTextFile(targetPath, classOf[GzipCodec])
d.map(s => mapper.writeValueAsString(s))(Encoders.STRING).rdd.repartition(1000).saveAsTextFile(targetPath, classOf[GzipCodec])
}
}

27
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala
View File

@ -2,11 +2,12 @@ package eu.dnetlib.dhp.sx.graph
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Software,Dataset => OafDataset}
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkConvertRDDtoDataset {
def main(args: Array[String]): Unit = {
@ -31,39 +32,39 @@ object SparkConvertRDDtoDataset {
val entityPath = s"$t/entities"
val relPath = s"$t/relation"
val mapper = new ObjectMapper()
implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset])
implicit val publicationEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication])
implicit val relationEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
implicit val orpEncoder: Encoder[OtherResearchProduct] = Encoders.kryo(classOf[OtherResearchProduct])
implicit val softwareEncoder: Encoder[Software] = Encoders.kryo(classOf[Software])
implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset])
implicit val publicationEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication])
implicit val relationEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
implicit val orpEncoder: Encoder[OtherResearchProduct] = Encoders.kryo(classOf[OtherResearchProduct])
implicit val softwareEncoder: Encoder[Software] = Encoders.kryo(classOf[Software])
log.info("Converting dataset")
val rddDataset =spark.sparkContext.textFile(s"$sourcePath/dataset").map(s => mapper.readValue(s, classOf[OafDataset]))
val rddDataset = spark.sparkContext.textFile(s"$sourcePath/dataset").map(s => mapper.readValue(s, classOf[OafDataset]))
spark.createDataset(rddDataset).as[OafDataset].write.mode(SaveMode.Overwrite).save(s"$entityPath/dataset")
log.info("Converting publication")
val rddPublication =spark.sparkContext.textFile(s"$sourcePath/publication").map(s => mapper.readValue(s, classOf[Publication]))
val rddPublication = spark.sparkContext.textFile(s"$sourcePath/publication").map(s => mapper.readValue(s, classOf[Publication]))
spark.createDataset(rddPublication).as[Publication].write.mode(SaveMode.Overwrite).save(s"$entityPath/publication")
log.info("Converting software")
val rddSoftware =spark.sparkContext.textFile(s"$sourcePath/software").map(s => mapper.readValue(s, classOf[Software]))
val rddSoftware = spark.sparkContext.textFile(s"$sourcePath/software").map(s => mapper.readValue(s, classOf[Software]))
spark.createDataset(rddSoftware).as[Software].write.mode(SaveMode.Overwrite).save(s"$entityPath/software")
log.info("Converting otherresearchproduct")
val rddOtherResearchProduct =spark.sparkContext.textFile(s"$sourcePath/otherresearchproduct").map(s => mapper.readValue(s, classOf[OtherResearchProduct]))
val rddOtherResearchProduct = spark.sparkContext.textFile(s"$sourcePath/otherresearchproduct").map(s => mapper.readValue(s, classOf[OtherResearchProduct]))
spark.createDataset(rddOtherResearchProduct).as[OtherResearchProduct].write.mode(SaveMode.Overwrite).save(s"$entityPath/otherresearchproduct")
log.info("Converting Relation")
val relationSemanticFilter = List("cites", "iscitedby","merges", "ismergedin")
val relationSemanticFilter = List("cites", "iscitedby", "merges", "ismergedin")
val rddRelation =spark.sparkContext.textFile(s"$sourcePath/relation")
val rddRelation = spark.sparkContext.textFile(s"$sourcePath/relation")
.map(s => mapper.readValue(s, classOf[Relation]))
.filter(r=> r.getSource.startsWith("50") && r.getTarget.startsWith("50"))
.filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50"))
.filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass)))
spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath")

27
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala
View File

@ -1,14 +1,12 @@
package eu.dnetlib.dhp.sx.graph
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset,_}
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}
object SparkCreateInputGraph {
def main(args: Array[String]): Unit = {
@ -33,7 +31,7 @@ object SparkCreateInputGraph {
)
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
implicit val publicationEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication])
implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset])
implicit val softwareEncoder: Encoder[Software] = Encoders.kryo(classOf[Software])
@ -41,16 +39,13 @@ object SparkCreateInputGraph {
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
val oafDs:Dataset[Oaf] = spark.read.load(s"$sourcePath/*").as[Oaf]
val oafDs: Dataset[Oaf] = spark.read.load(s"$sourcePath/*").as[Oaf]
log.info("Extract Publication")
@ -70,27 +65,27 @@ object SparkCreateInputGraph {
resultObject.foreach { r =>
log.info(s"Make ${r._1} unique")
makeDatasetUnique(s"$targetPath/extracted/${r._1}",s"$targetPath/preprocess/${r._1}",spark, r._2)
makeDatasetUnique(s"$targetPath/extracted/${r._1}", s"$targetPath/preprocess/${r._1}", spark, r._2)
}
}
def extractEntities[T <: Oaf ](oafDs:Dataset[Oaf], targetPath:String, clazz:Class[T], log:Logger) :Unit = {
def extractEntities[T <: Oaf](oafDs: Dataset[Oaf], targetPath: String, clazz: Class[T], log: Logger): Unit = {
implicit val resEncoder: Encoder[T] = Encoders.kryo(clazz)
implicit val resEncoder: Encoder[T] = Encoders.kryo(clazz)
log.info(s"Extract ${clazz.getSimpleName}")
oafDs.filter(o => o.isInstanceOf[T]).map(p => p.asInstanceOf[T]).write.mode(SaveMode.Overwrite).save(targetPath)
}
def makeDatasetUnique[T <: Result ](sourcePath:String, targetPath:String, spark:SparkSession, clazz:Class[T]) :Unit = {
def makeDatasetUnique[T <: Result](sourcePath: String, targetPath: String, spark: SparkSession, clazz: Class[T]): Unit = {
import spark.implicits._
implicit val resEncoder: Encoder[T] = Encoders.kryo(clazz)
implicit val resEncoder: Encoder[T] = Encoders.kryo(clazz)
val ds:Dataset[T] = spark.read.load(sourcePath).as[T]
val ds: Dataset[T] = spark.read.load(sourcePath).as[T]
ds.groupByKey(_.getId).reduceGroups{(x,y) =>
ds.groupByKey(_.getId).reduceGroups { (x, y) =>
x.mergeFrom(y)
x
}.map(_._2).write.mode(SaveMode.Overwrite).save(targetPath)

28
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala
View File

@ -9,7 +9,7 @@ import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils.RelatedEntities
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.functions.count
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}
object SparkCreateScholix {
@ -42,7 +42,7 @@ object SparkCreateScholix {
val relationDS: Dataset[(String, Relation)] = spark.read.load(relationPath).as[Relation]
.filter(r => (r.getDataInfo== null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
.map(r => (r.getSource, r))(Encoders.tuple(Encoders.STRING, relEncoder))
val summaryDS: Dataset[(String, ScholixSummary)] = spark.read.load(summaryPath).as[ScholixSummary]
@ -51,54 +51,54 @@ object SparkCreateScholix {
relationDS.joinWith(summaryDS, relationDS("_1").equalTo(summaryDS("_1")), "left")
.map { input: ((String, Relation), (String, ScholixSummary)) =>
if (input._1!= null && input._2!= null) {
if (input._1 != null && input._2 != null) {
val rel: Relation = input._1._2
val source: ScholixSummary = input._2._2
(rel.getTarget, ScholixUtils.scholixFromSource(rel, source))
}
else null
else null
}(Encoders.tuple(Encoders.STRING, scholixEncoder))
.filter(r => r!= null)
.filter(r => r != null)
.write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_from_source")
val scholixSource: Dataset[(String, Scholix)] = spark.read.load(s"$targetPath/scholix_from_source").as[(String, Scholix)](Encoders.tuple(Encoders.STRING, scholixEncoder))
scholixSource.joinWith(summaryDS, scholixSource("_1").equalTo(summaryDS("_1")), "left")
.map { input: ((String, Scholix), (String, ScholixSummary)) =>
if (input._2== null) {
if (input._2 == null) {
null
} else {
val s: Scholix = input._1._2
val target: ScholixSummary = input._2._2
ScholixUtils.generateCompleteScholix(s, target)
}
}.filter(s => s!= null).write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_one_verse")
}.filter(s => s != null).write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_one_verse")
val scholix_o_v: Dataset[Scholix] = spark.read.load(s"$targetPath/scholix_one_verse").as[Scholix]
scholix_o_v.flatMap(s => List(s, ScholixUtils.createInverseScholixRelation(s))).as[Scholix]
.map(s=> (s.getIdentifier,s))(Encoders.tuple(Encoders.STRING, scholixEncoder))
.map(s => (s.getIdentifier, s))(Encoders.tuple(Encoders.STRING, scholixEncoder))
.groupByKey(_._1)
.agg(ScholixUtils.scholixAggregator.toColumn)
.map(s => s._2)
.write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix")
val scholix_final:Dataset[Scholix] = spark.read.load(s"$targetPath/scholix").as[Scholix]
val scholix_final: Dataset[Scholix] = spark.read.load(s"$targetPath/scholix").as[Scholix]
val stats:Dataset[(String,String,Long)]= scholix_final.map(s => (s.getSource.getDnetIdentifier, s.getTarget.getObjectType)).groupBy("_1", "_2").agg(count("_1")).as[(String,String,Long)]
val stats: Dataset[(String, String, Long)] = scholix_final.map(s => (s.getSource.getDnetIdentifier, s.getTarget.getObjectType)).groupBy("_1", "_2").agg(count("_1")).as[(String, String, Long)]
stats
.map(s => RelatedEntities(s._1, if ("dataset".equalsIgnoreCase(s._2)) s._3 else 0, if ("publication".equalsIgnoreCase(s._2)) s._3 else 0 ))
.map(s => RelatedEntities(s._1, if ("dataset".equalsIgnoreCase(s._2)) s._3 else 0, if ("publication".equalsIgnoreCase(s._2)) s._3 else 0))
.groupByKey(_.id)
.reduceGroups((a, b) => RelatedEntities(a.id, a.relatedDataset+b.relatedDataset, a.relatedPublication+b.relatedPublication))
.reduceGroups((a, b) => RelatedEntities(a.id, a.relatedDataset + b.relatedDataset, a.relatedPublication + b.relatedPublication))
.map(_._2)
.write.mode(SaveMode.Overwrite).save(s"$targetPath/related_entities")
val relatedEntitiesDS:Dataset[RelatedEntities] = spark.read.load(s"$targetPath/related_entities").as[RelatedEntities].filter(r => r.relatedPublication>0 || r.relatedDataset > 0)
val relatedEntitiesDS: Dataset[RelatedEntities] = spark.read.load(s"$targetPath/related_entities").as[RelatedEntities].filter(r => r.relatedPublication > 0 || r.relatedDataset > 0)
relatedEntitiesDS.joinWith(summaryDS, relatedEntitiesDS("id").equalTo(summaryDS("_1")), "inner").map{i =>
relatedEntitiesDS.joinWith(summaryDS, relatedEntitiesDS("id").equalTo(summaryDS("_1")), "inner").map { i =>
val re = i._1
val sum = i._2._2

12
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateSummaryObject.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateSummaryObject.scala
View File

@ -6,7 +6,7 @@ import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}
object SparkCreateSummaryObject {
@ -28,15 +28,15 @@ object SparkCreateSummaryObject {
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val resultEncoder: Encoder[Result] = Encoders.kryo[Result]
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val summaryEncoder:Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
val ds:Dataset[Result] = spark.read.load(s"$sourcePath/*").as[Result].filter(r=>r.getDataInfo== null || r.getDataInfo.getDeletedbyinference== false)
val ds: Dataset[Result] = spark.read.load(s"$sourcePath/*").as[Result].filter(r => r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false)
ds.repartition(6000).map(r => ScholixUtils.resultToSummary(r)).filter(s => s!= null).write.mode(SaveMode.Overwrite).save(targetPath)
ds.repartition(6000).map(r => ScholixUtils.resultToSummary(r)).filter(s => s != null).write.mode(SaveMode.Overwrite).save(targetPath)
}

1
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/pangaea/PangaeaUtils.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/PangaeaUtils.scala
View File

@ -5,6 +5,7 @@ import org.apache.spark.sql.{Encoder, Encoders}
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import java.util.regex.Pattern
import scala.language.postfixOps
import scala.xml.{Elem, Node, XML}

17
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala
View File

@ -2,11 +2,11 @@ package eu.dnetlib.dhp.sx.graph.pangaea
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import org.apache.spark.rdd.RDD
import org.apache.spark.{SparkConf, SparkContext}
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.{SparkConf, SparkContext}
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import scala.io.Source
object SparkGeneratePanagaeaDataset {
@ -28,17 +28,17 @@ object SparkGeneratePanagaeaDataset {
parser.getObjectMap.asScala.foreach(s => logger.info(s"${s._1} -> ${s._2}"))
logger.info("Converting sequential file into Dataset")
val sc:SparkContext = spark.sparkContext
val sc: SparkContext = spark.sparkContext
val workingPath:String = parser.get("workingPath")
val workingPath: String = parser.get("workingPath")
implicit val pangaeaEncoders: Encoder[PangaeaDataModel] = Encoders.kryo[PangaeaDataModel]
val inputRDD:RDD[PangaeaDataModel] = sc.textFile(s"$workingPath/update").map(s => PangaeaUtils.toDataset(s))
val inputRDD: RDD[PangaeaDataModel] = sc.textFile(s"$workingPath/update").map(s => PangaeaUtils.toDataset(s))
spark.createDataset(inputRDD).as[PangaeaDataModel]
.map(s => (s.identifier,s))(Encoders.tuple(Encoders.STRING, pangaeaEncoders))
.groupByKey(_._1)(Encoders.STRING)
.map(s => (s.identifier, s))(Encoders.tuple(Encoders.STRING, pangaeaEncoders))
.groupByKey(_._1)(Encoders.STRING)
.agg(PangaeaUtils.getDatasetAggregator().toColumn)
.map(s => s._2)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/dataset")
@ -46,7 +46,4 @@ object SparkGeneratePanagaeaDataset {
}
}

141
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala → dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala
View File

@ -1,6 +1,5 @@
package eu.dnetlib.dhp.sx.graph.scholix
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.schema.sx.scholix._
import eu.dnetlib.dhp.schema.sx.summary.{CollectedFromType, SchemeValue, ScholixSummary, Typology}
@ -10,23 +9,22 @@ import org.apache.spark.sql.{Encoder, Encoders}
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import scala.collection.JavaConverters._
import scala.io.Source
import scala.language.postfixOps
object ScholixUtils {
val DNET_IDENTIFIER_SCHEMA: String = "DNET Identifier"
val DATE_RELATION_KEY:String = "RelationDate"
case class RelationVocabulary(original:String, inverse:String){}
val DATE_RELATION_KEY: String = "RelationDate"
case class RelatedEntities(id:String, relatedDataset:Long, relatedPublication:Long){}
case class RelationVocabulary(original: String, inverse: String) {}
val relations:Map[String, RelationVocabulary] = {
val input =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/relations.json")).mkString
case class RelatedEntities(id: String, relatedDataset: Long, relatedPublication: Long) {}
val relations: Map[String, RelationVocabulary] = {
val input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/relations.json")).mkString
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
@ -35,12 +33,12 @@ object ScholixUtils {
}
def extractRelationDate(relation: Relation):String = {
def extractRelationDate(relation: Relation): String = {
if (relation.getProperties== null || !relation.getProperties.isEmpty)
if (relation.getProperties == null || !relation.getProperties.isEmpty)
null
else {
val date =relation.getProperties.asScala.find(p => DATE_RELATION_KEY.equalsIgnoreCase(p.getKey)).map(p => p.getValue)
val date = relation.getProperties.asScala.find(p => DATE_RELATION_KEY.equalsIgnoreCase(p.getKey)).map(p => p.getValue)
if (date.isDefined)
date.get
else
@ -48,9 +46,9 @@ object ScholixUtils {
}
}
def extractRelationDate(summary: ScholixSummary):String = {
def extractRelationDate(summary: ScholixSummary): String = {
if(summary.getDate== null || summary.getDate.isEmpty)
if (summary.getDate == null || summary.getDate.isEmpty)
null
else {
summary.getDate.get(0)
@ -59,15 +57,14 @@ object ScholixUtils {
}
def inverseRelationShip(rel:ScholixRelationship):ScholixRelationship = {
def inverseRelationShip(rel: ScholixRelationship): ScholixRelationship = {
new ScholixRelationship(rel.getInverse, rel.getSchema, rel.getName)
}
val statsAggregator:Aggregator[(String,String, Long), RelatedEntities, RelatedEntities] = new Aggregator[(String,String, Long), RelatedEntities, RelatedEntities] with Serializable {
val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] = new Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] with Serializable {
override def zero: RelatedEntities = null
override def reduce(b: RelatedEntities, a: (String, String, Long)): RelatedEntities = {
@ -78,17 +75,16 @@ object ScholixUtils {
if (b == null)
RelatedEntities(a._1, relatedDataset, relatedPublication)
else
RelatedEntities(a._1,b.relatedDataset+ relatedDataset, b.relatedPublication+ relatedPublication )
RelatedEntities(a._1, b.relatedDataset + relatedDataset, b.relatedPublication + relatedPublication)
}
override def merge(b1: RelatedEntities, b2: RelatedEntities): RelatedEntities = {
if (b1!= null && b2!= null)
RelatedEntities(b1.id, b1.relatedDataset+ b2.relatedDataset, b1.relatedPublication+ b2.relatedPublication)
if (b1 != null && b2 != null)
RelatedEntities(b1.id, b1.relatedDataset + b2.relatedDataset, b1.relatedPublication + b2.relatedPublication)
else if (b1 != null)
b1
else
if (b1!= null)
b1
else
b2
}
@ -104,12 +100,12 @@ object ScholixUtils {
override def zero: Scholix = null
def scholix_complete(s:Scholix):Boolean ={
if (s== null || s.getIdentifier==null) {
def scholix_complete(s: Scholix): Boolean = {
if (s == null || s.getIdentifier == null) {
false
} else if (s.getSource == null || s.getTarget == null) {
false
}
false
}
else if (s.getLinkprovider == null || s.getLinkprovider.isEmpty)
false
else
@ -121,7 +117,7 @@ object ScholixUtils {
}
override def merge(b1: Scholix, b2: Scholix): Scholix = {
if (scholix_complete(b1)) b1 else b2
if (scholix_complete(b1)) b1 else b2
}
override def finish(reduction: Scholix): Scholix = reduction
@ -132,7 +128,7 @@ object ScholixUtils {
}
def createInverseScholixRelation(scholix: Scholix):Scholix = {
def createInverseScholixRelation(scholix: Scholix): Scholix = {
val s = new Scholix
s.setPublicationDate(scholix.getPublicationDate)
s.setPublisher(scholix.getPublisher)
@ -144,34 +140,33 @@ object ScholixUtils {
s
}
def extractCollectedFrom(summary:ScholixSummary): List[ScholixEntityId] = {
if (summary.getDatasources!= null && !summary.getDatasources.isEmpty) {
val l: List[ScholixEntityId] = summary.getDatasources.asScala.map{
def extractCollectedFrom(summary: ScholixSummary): List[ScholixEntityId] = {
if (summary.getDatasources != null && !summary.getDatasources.isEmpty) {
val l: List[ScholixEntityId] = summary.getDatasources.asScala.map {
d => new ScholixEntityId(d.getDatasourceName, List(new ScholixIdentifier(d.getDatasourceId, "DNET Identifier", null)).asJava)
}(collection.breakOut)
l
l
} else List()
}
def extractCollectedFrom(relation: Relation) : List[ScholixEntityId] = {
def extractCollectedFrom(relation: Relation): List[ScholixEntityId] = {
if (relation.getCollectedfrom != null && !relation.getCollectedfrom.isEmpty) {
val l: List[ScholixEntityId] = relation.getCollectedfrom.asScala.map {
c =>
new ScholixEntityId(c.getValue, List(new ScholixIdentifier(c.getKey, DNET_IDENTIFIER_SCHEMA,null)).asJava)
new ScholixEntityId(c.getValue, List(new ScholixIdentifier(c.getKey, DNET_IDENTIFIER_SCHEMA, null)).asJava)
}(collection breakOut)
l
} else List()
}
def generateCompleteScholix(scholix: Scholix, target:ScholixSummary): Scholix = {
def generateCompleteScholix(scholix: Scholix, target: ScholixSummary): Scholix = {
val s = new Scholix
s.setPublicationDate(scholix.getPublicationDate)
s.setPublisher(scholix.getPublisher)
@ -192,29 +187,28 @@ object ScholixUtils {
r.setObjectType(summaryObject.getTypology.toString)
r.setObjectSubType(summaryObject.getSubType)
if (summaryObject.getTitle!= null && !summaryObject.getTitle.isEmpty)
r.setTitle(summaryObject.getTitle.get(0))
if (summaryObject.getTitle != null && !summaryObject.getTitle.isEmpty)
r.setTitle(summaryObject.getTitle.get(0))
if (summaryObject.getAuthor!= null && !summaryObject.getAuthor.isEmpty){
val l:List[ScholixEntityId] = summaryObject.getAuthor.asScala.map(a => new ScholixEntityId(a,null)).toList
if (summaryObject.getAuthor != null && !summaryObject.getAuthor.isEmpty) {
val l: List[ScholixEntityId] = summaryObject.getAuthor.asScala.map(a => new ScholixEntityId(a, null)).toList
if (l.nonEmpty)
r.setCreator(l.asJava)
}
if (summaryObject.getDate!= null && !summaryObject.getDate.isEmpty)
if (summaryObject.getDate != null && !summaryObject.getDate.isEmpty)
r.setPublicationDate(summaryObject.getDate.get(0))
if (summaryObject.getPublisher!= null && !summaryObject.getPublisher.isEmpty)
{
val plist:List[ScholixEntityId] =summaryObject.getPublisher.asScala.map(p => new ScholixEntityId(p, null)).toList
if (summaryObject.getPublisher != null && !summaryObject.getPublisher.isEmpty) {
val plist: List[ScholixEntityId] = summaryObject.getPublisher.asScala.map(p => new ScholixEntityId(p, null)).toList
if (plist.nonEmpty)
r.setPublisher(plist.asJava)
}
if (summaryObject.getDatasources!= null && !summaryObject.getDatasources.isEmpty) {
if (summaryObject.getDatasources != null && !summaryObject.getDatasources.isEmpty) {
val l:List[ScholixCollectedFrom] = summaryObject.getDatasources.asScala.map(c => new ScholixCollectedFrom(
val l: List[ScholixCollectedFrom] = summaryObject.getDatasources.asScala.map(c => new ScholixCollectedFrom(
new ScholixEntityId(c.getDatasourceName, List(new ScholixIdentifier(c.getDatasourceId, DNET_IDENTIFIER_SCHEMA, null)).asJava)
, "collected", "complete"
@ -228,12 +222,9 @@ object ScholixUtils {
}
def scholixFromSource(relation: Relation, source: ScholixSummary): Scholix = {
def scholixFromSource(relation:Relation, source:ScholixSummary):Scholix = {
if (relation== null || source== null)
if (relation == null || source == null)
return null
val s = new Scholix
@ -253,9 +244,9 @@ object ScholixUtils {
s.setPublicationDate(d)
if (source.getPublisher!= null && !source.getPublisher.isEmpty) {
if (source.getPublisher != null && !source.getPublisher.isEmpty) {
val l: List[ScholixEntityId] = source.getPublisher.asScala
.map{
.map {
p =>
new ScholixEntityId(p, null)
}(collection.breakOut)
@ -265,7 +256,7 @@ object ScholixUtils {
}
val semanticRelation = relations.getOrElse(relation.getRelClass.toLowerCase, null)
if (semanticRelation== null)
if (semanticRelation == null)
return null
s.setRelationship(new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse))
s.setSource(generateScholixResourceFromSummary(source))
@ -274,8 +265,8 @@ object ScholixUtils {
}
def findURLForPID(pidValue:List[StructuredProperty], urls:List[String]):List[(StructuredProperty, String)] = {
pidValue.map{
def findURLForPID(pidValue: List[StructuredProperty], urls: List[String]): List[(StructuredProperty, String)] = {
pidValue.map {
p =>
val pv = p.getValue
@ -285,67 +276,67 @@ object ScholixUtils {
}
def extractTypedIdentifierFromInstance(r:Result):List[ScholixIdentifier] = {
def extractTypedIdentifierFromInstance(r: Result): List[ScholixIdentifier] = {
if (r.getInstance() == null || r.getInstance().isEmpty)
return List()
r.getInstance().asScala.filter(i => i.getUrl!= null && !i.getUrl.isEmpty)
.filter(i => i.getPid!= null && i.getUrl != null)
r.getInstance().asScala.filter(i => i.getUrl != null && !i.getUrl.isEmpty)
.filter(i => i.getPid != null && i.getUrl != null)
.flatMap(i => findURLForPID(i.getPid.asScala.toList, i.getUrl.asScala.toList))
.map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2)).distinct.toList
}
def resultToSummary(r:Result):ScholixSummary = {
def resultToSummary(r: Result): ScholixSummary = {
val s = new ScholixSummary
s.setId(r.getId)
if (r.getPid == null || r.getPid.isEmpty)
return null
val persistentIdentifiers:List[ScholixIdentifier] = extractTypedIdentifierFromInstance(r)
val persistentIdentifiers: List[ScholixIdentifier] = extractTypedIdentifierFromInstance(r)
if (persistentIdentifiers.isEmpty)
return null
s.setLocalIdentifier(persistentIdentifiers.asJava)
if (r.isInstanceOf[Publication] )
if (r.isInstanceOf[Publication])
s.setTypology(Typology.publication)
else
s.setTypology(Typology.dataset)
s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)
if (r.getTitle!= null && r.getTitle.asScala.nonEmpty) {
val titles:List[String] =r.getTitle.asScala.map(t => t.getValue)(collection breakOut)
if (r.getTitle != null && r.getTitle.asScala.nonEmpty) {
val titles: List[String] = r.getTitle.asScala.map(t => t.getValue)(collection breakOut)
if (titles.nonEmpty)
s.setTitle(titles.asJava)
else
return null
return null
}
if(r.getAuthor!= null && !r.getAuthor.isEmpty) {
val authors:List[String] = r.getAuthor.asScala.map(a=> a.getFullname)(collection breakOut)
if (r.getAuthor != null && !r.getAuthor.isEmpty) {
val authors: List[String] = r.getAuthor.asScala.map(a => a.getFullname)(collection breakOut)
if (authors nonEmpty)
s.setAuthor(authors.asJava)
}
if (r.getInstance() != null) {
val dt:List[String] = r.getInstance().asScala.filter(i => i.getDateofacceptance != null).map(i => i.getDateofacceptance.getValue)(collection.breakOut)
val dt: List[String] = r.getInstance().asScala.filter(i => i.getDateofacceptance != null).map(i => i.getDateofacceptance.getValue)(collection.breakOut)
if (dt.nonEmpty)
s.setDate(dt.distinct.asJava)
}
if (r.getDescription!= null && !r.getDescription.isEmpty) {
val d = r.getDescription.asScala.find(f => f!= null && f.getValue!=null)
if (r.getDescription != null && !r.getDescription.isEmpty) {
val d = r.getDescription.asScala.find(f => f != null && f.getValue != null)
if (d.isDefined)
s.setDescription(d.get.getValue)
}
if (r.getSubject!= null && !r.getSubject.isEmpty) {
val subjects:List[SchemeValue] =r.getSubject.asScala.map(s => new SchemeValue(s.getQualifier.getClassname, s.getValue))(collection breakOut)
if (r.getSubject != null && !r.getSubject.isEmpty) {
val subjects: List[SchemeValue] = r.getSubject.asScala.map(s => new SchemeValue(s.getQualifier.getClassname, s.getValue))(collection breakOut)
if (subjects.nonEmpty)
s.setSubject(subjects.asJava)
}
if (r.getPublisher!= null)
if (r.getPublisher != null)
s.setPublisher(List(r.getPublisher.getValue).asJava)
if (r.getCollectedfrom!= null && !r.getCollectedfrom.isEmpty) {
val cf:List[CollectedFromType] = r.getCollectedfrom.asScala.map(c => new CollectedFromType(c.getValue, c.getKey, "complete"))(collection breakOut)
if (r.getCollectedfrom != null && !r.getCollectedfrom.isEmpty) {
val cf: List[CollectedFromType] = r.getCollectedfrom.asScala.map(c => new CollectedFromType(c.getValue, c.getKey, "complete"))(collection breakOut)
if (cf.nonEmpty)
s.setDatasources(cf.distinct.asJava)
}

18
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java
View File

@ -171,24 +171,6 @@ public class DumpJobTest {
GraphResult gr = verificationDataset.first();
// Assertions.assertEquals(2, gr.getMeasures().size());
// Assertions
// .assertTrue(
// gr
// .getMeasures()
// .stream()
// .anyMatch(
// m -> m.getKey().equals("influence")
// && m.getValue().equals("1.62759106106e-08")));
// Assertions
// .assertTrue(
// gr
// .getMeasures()
// .stream()
// .anyMatch(
// m -> m.getKey().equals("popularity")
// && m.getValue().equals("0.22519296")));
Assertions.assertEquals(6, gr.getAuthor().size());
Assertions
.assertTrue(

0
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala → dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala
View File

4
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPrepare.scala → dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPrepare.scala
View File

@ -3,13 +3,9 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.oa.graph.hostedbymap.SparkPrepareHostedByInfoToApply.{joinResHBM, prepareResultInfo, toEntityInfo}
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
import eu.dnetlib.dhp.schema.oaf.{Datasource, OpenAccessRoute, Publication}
import javax.management.openmbean.OpenMBeanAttributeInfo
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
import org.json4s
import org.json4s.DefaultFormats
import eu.dnetlib.dhp.schema.common.ModelConstants
import org.junit.jupiter.api.Assertions.{assertEquals, assertTrue}
import org.junit.jupiter.api.Test

5
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPreprocess.scala → dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPreprocess.scala
View File

@ -4,10 +4,9 @@ import eu.dnetlib.dhp.schema.oaf.Datasource
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
import org.json4s.DefaultFormats
import org.junit.jupiter.api.Assertions.{assertNotNull, assertTrue}
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.Assertions._
import org.json4s.jackson.Serialization.write
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test
class TestPreprocess extends java.io.Serializable{

0
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala → dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala
View File

3
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala → dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala
View File

@ -37,7 +37,8 @@ class ScholixGraphTest extends AbstractVocabularyTest{
val input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/scholix/result.json")).mkString
val res =SparkResolveRelation.extractPidsFromRecord(input)
assertNotNull(res)
assertTrue(res._2.size == 2)
assertEquals(1,res._2.size)
}