[Dump] resolved conflicts with beta and merging

This commit is contained in:
Miriam Baglioni 2021-12-14 15:03:45 +01:00
commit 56409d1281
85 changed files with 3818 additions and 894 deletions

2
.gitignore vendored
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@ -3,8 +3,6 @@
*.iws *.iws
*.ipr *.ipr
*.iml *.iml
*.ipr
*.iws
*~ *~
.vscode .vscode
.metals .metals

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@ -57,9 +57,17 @@ public class VocabularyGroup implements Serializable {
final String syn = arr[2].trim(); final String syn = arr[2].trim();
vocs.addSynonyms(vocId, termId, syn); vocs.addSynonyms(vocId, termId, syn);
} }
} }
// add the term names as synonyms
vocs.vocs.values().forEach(voc -> {
voc.getTerms().values().forEach(term -> {
voc.addSynonym(term.getName().toLowerCase(), term.getId());
});
});
return vocs; return vocs;
} }

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@ -16,6 +16,8 @@ import com.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.collect.Lists; import com.google.common.collect.Lists;
import com.google.common.collect.Sets; import com.google.common.collect.Sets;
import eu.dnetlib.dhp.common.vocabulary.Vocabulary;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
@ -86,6 +88,22 @@ public class GraphCleaningFunctions extends CleaningFunctions {
} }
public static <T extends Oaf> boolean filter(T value) { public static <T extends Oaf> boolean filter(T value) {
if (Boolean.TRUE
.equals(
Optional
.ofNullable(value)
.map(
o -> Optional
.ofNullable(o.getDataInfo())
.map(
d -> Optional
.ofNullable(d.getInvisible())
.orElse(true))
.orElse(true))
.orElse(true))) {
return false;
}
if (value instanceof Datasource) { if (value instanceof Datasource) {
// nothing to evaluate here // nothing to evaluate here
} else if (value instanceof Project) { } else if (value instanceof Project) {
@ -115,7 +133,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
return true; return true;
} }
public static <T extends Oaf> T cleanup(T value) { public static <T extends Oaf> T cleanup(T value, VocabularyGroup vocs) {
if (value instanceof Datasource) { if (value instanceof Datasource) {
// nothing to clean here // nothing to clean here
} else if (value instanceof Project) { } else if (value instanceof Project) {
@ -212,6 +230,15 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.map(GraphCleaningFunctions::cleanValue) .map(GraphCleaningFunctions::cleanValue)
.collect(Collectors.toList())); .collect(Collectors.toList()));
} }
if (Objects.nonNull(r.getFormat())) {
r
.setFormat(
r
.getFormat()
.stream()
.map(GraphCleaningFunctions::cleanValue)
.collect(Collectors.toList()));
}
if (Objects.nonNull(r.getDescription())) { if (Objects.nonNull(r.getDescription())) {
r r
.setDescription( .setDescription(
@ -234,6 +261,38 @@ public class GraphCleaningFunctions extends CleaningFunctions {
if (Objects.nonNull(r.getInstance())) { if (Objects.nonNull(r.getInstance())) {
for (Instance i : r.getInstance()) { for (Instance i : r.getInstance()) {
if (!vocs.termExists(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getClassid())) {
if (r instanceof Publication) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0038", "Other literature type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
} else if (r instanceof Dataset) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0039", "Other dataset type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
} else if (r instanceof Software) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0040", "Other software type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
} else if (r instanceof OtherResearchProduct) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0020", "Other ORP type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
}
}
if (Objects.nonNull(i.getPid())) { if (Objects.nonNull(i.getPid())) {
i.setPid(processPidCleaning(i.getPid())); i.setPid(processPidCleaning(i.getPid()));
} }

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@ -107,7 +107,7 @@ class OafMapperUtilsTest {
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("2006-01-02T15:04:05+0000").get()); 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("2009-08-13", 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("2009-08-12T22:15:09").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("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("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()); assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.123").get());

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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")
}
}

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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])
}
}

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@ -1,8 +1,8 @@
package eu.dnetlib.dhp.datacite package eu.dnetlib.dhp.datacite
import eu.dnetlib.dhp.schema.common.ModelConstants 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.utils.OafMapperUtils
import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue}
import java.io.InputStream import java.io.InputStream
import java.time.format.DateTimeFormatter import java.time.format.DateTimeFormatter

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

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@ -7,6 +7,7 @@ import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.{compact, parse, render} import org.json4s.jackson.JsonMethods.{compact, parse, render}
import collection.JavaConverters._ import collection.JavaConverters._
object BioDBToOAF { object BioDBToOAF {
case class EBILinkItem(id: Long, links: String) {} case class EBILinkItem(id: Long, links: String) {}

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@ -1,9 +1,9 @@
package eu.dnetlib.dhp.sx.bio package eu.dnetlib.dhp.sx.bio
import eu.dnetlib.dhp.application.ArgumentApplicationParser 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.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.commons.io.IOUtils
import org.apache.spark.SparkConf import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
@ -36,13 +36,13 @@ object SparkTransformBioDatabaseToOAF {
import spark.implicits._ import spark.implicits._
database.toUpperCase() match { database.toUpperCase() match {
case "UNIPROT" => 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" => 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" => 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" => 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)
} }
} }

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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.application.ArgumentApplicationParser
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.oaf.Result 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 eu.dnetlib.dhp.utils.ISLookupClientFactory
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.hadoop.conf.Configuration import org.apache.hadoop.conf.Configuration

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@ -1,9 +1,8 @@
package eu.dnetlib.dhp.sx.bio.ebi package eu.dnetlib.dhp.sx.bio.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser 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.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.commons.io.IOUtils
import org.apache.http.client.config.RequestConfig import org.apache.http.client.config.RequestConfig
import org.apache.http.client.methods.HttpGet import org.apache.http.client.methods.HttpGet

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

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

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

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

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

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@ -1,21 +1,19 @@
package eu.dnetlib.doiboost package eu.dnetlib.doiboost
import java.time.LocalDate import com.fasterxml.jackson.databind.ObjectMapper
import java.time.format.DateTimeFormatter
import eu.dnetlib.dhp.schema.action.AtomicAction 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 eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils 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
import org.json4s.DefaultFormats import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory} import org.slf4j.{Logger, LoggerFactory}
import java.time.LocalDate
import java.time.format.DateTimeFormatter
import scala.collection.JavaConverters._ import scala.collection.JavaConverters._

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

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

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

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

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

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

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

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

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@ -3,8 +3,8 @@ package eu.dnetlib.doiboost.mag
import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.application.ArgumentApplicationParser
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf import org.apache.spark.SparkConf
import org.apache.spark.sql.{SaveMode, SparkSession}
import org.apache.spark.sql.types._ import org.apache.spark.sql.types._
import org.apache.spark.sql.{SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory} import org.slf4j.{Logger, LoggerFactory}
object SparkImportMagIntoDataset { 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")), "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")), "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")), "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")), "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")), "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")), "FieldOfStudyChildren" -> Tuple2("advanced/FieldOfStudyChildren.txt", Seq("FieldOfStudyId:long", "ChildFieldOfStudyId:long")),
"FieldOfStudyExtendedAttributes" -> Tuple2("advanced/FieldOfStudyExtendedAttributes.txt", Seq("FieldOfStudyId:long", "AttributeType:int", "AttributeValue:string")), "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")), "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")), "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")), "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")), "PaperCitationContexts" -> Tuple2("nlp/PaperCitationContexts.txt", Seq("PaperId:long", "PaperReferenceId:long", "CitationContext:string")),
@ -75,7 +75,6 @@ object SparkImportMagIntoDataset {
.master(parser.get("master")).getOrCreate() .master(parser.get("master")).getOrCreate()
stream.foreach { case (k, v) => stream.foreach { case (k, v) =>
val s: StructType = getSchema(k) val s: StructType = getSchema(k)
val df = spark.read val df = spark.read

View File

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

View File

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

View File

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

View File

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

View File

@ -1,16 +1,14 @@
package eu.dnetlib.doiboost.uw package eu.dnetlib.doiboost.uw
import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Publication import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF import eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD 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} import org.slf4j.{Logger, LoggerFactory}
object SparkMapUnpayWallToOAF { object SparkMapUnpayWallToOAF {
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
@ -32,11 +30,11 @@ object SparkMapUnpayWallToOAF {
val sourcePath = parser.get("sourcePath") val sourcePath = parser.get("sourcePath")
val targetPath = parser.get("targetPath") 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") 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) d.write.mode(SaveMode.Overwrite).save(targetPath)
} }

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

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))
}
}

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))
}
}

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.schema.oaf._
import eu.dnetlib.dhp.utils.DHPUtils import eu.dnetlib.dhp.utils.DHPUtils
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
@ -21,9 +22,9 @@ class CrossrefMappingTest {
@Test @Test
def testFunderRelationshipsMapping(): Unit = { def testFunderRelationshipsMapping(): 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 funder_doi = Source.fromInputStream(getClass.getResourceAsStream("funder_doi")).mkString val funder_doi = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/funder_doi")).mkString
val funder_name = Source.fromInputStream(getClass.getResourceAsStream("funder_doi")).mkString val funder_name = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/funder_doi")).mkString
for (line <- funder_doi.lines) { for (line <- funder_doi.lines) {
@ -72,7 +73,7 @@ class CrossrefMappingTest {
@Test @Test
def testOrcidID() :Unit = { 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) assertNotNull(json)
@ -93,7 +94,7 @@ class CrossrefMappingTest {
@Test @Test
def testEmptyTitle() :Unit = { 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) assertNotNull(json)
@ -115,7 +116,7 @@ class CrossrefMappingTest {
@Test @Test
def testPeerReviewed(): Unit = { 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) mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
assertNotNull(json) assertNotNull(json)
@ -156,7 +157,7 @@ class CrossrefMappingTest {
@Test @Test
def testJournalRelation(): Unit = { 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) assertNotNull(json)
assertFalse(json.isEmpty) assertFalse(json.isEmpty)
@ -177,7 +178,7 @@ class CrossrefMappingTest {
@Test @Test
def testConvertBookFromCrossRef2Oaf(): Unit = { 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) assertNotNull(json)
assertFalse(json.isEmpty); assertFalse(json.isEmpty);
@ -233,7 +234,7 @@ class CrossrefMappingTest {
@Test @Test
def testConvertPreprintFromCrossRef2Oaf(): Unit = { 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) assertNotNull(json)
assertFalse(json.isEmpty); assertFalse(json.isEmpty);
@ -291,7 +292,7 @@ class CrossrefMappingTest {
@Test @Test
def testConvertDatasetFromCrossRef2Oaf(): Unit = { 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) assertNotNull(json)
assertFalse(json.isEmpty); assertFalse(json.isEmpty);
@ -332,7 +333,7 @@ class CrossrefMappingTest {
@Test @Test
def testConvertArticleFromCrossRef2Oaf(): Unit = { 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) assertNotNull(json)
assertFalse(json.isEmpty); assertFalse(json.isEmpty);
@ -400,7 +401,7 @@ class CrossrefMappingTest {
@Test @Test
def testSetDateOfAcceptanceCrossRef2Oaf(): Unit = { 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) assertNotNull(json)
assertFalse(json.isEmpty); assertFalse(json.isEmpty);
@ -415,55 +416,12 @@ class CrossrefMappingTest {
assert(items.size == 1) assert(items.size == 1)
val result: Result = items.head.asInstanceOf[Publication] val result: Result = items.head.asInstanceOf[Publication]
assertNotNull(result) assertNotNull(result)
logger.info(mapper.writeValueAsString(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 @Test
def testNormalizeDOI(): Unit = { 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 line :String = "\"funder\": [{\"name\": \"Wellcome Trust Masters Fellowship\",\"award\": [\"090633\"]}],"
val json = template.replace("%s", line) val json = template.replace("%s", line)
val resultList: List[Oaf] = Crossref2Oaf.convert(json) val resultList: List[Oaf] = Crossref2Oaf.convert(json)
@ -479,7 +437,7 @@ class CrossrefMappingTest {
@Test @Test
def testNormalizeDOI2(): Unit = { 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) val resultList: List[Oaf] = Crossref2Oaf.convert(template)
assertTrue(resultList.nonEmpty) assertTrue(resultList.nonEmpty)
@ -494,7 +452,7 @@ class CrossrefMappingTest {
@Test @Test
def testLicenseVorClosed() :Unit = { 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) assertNotNull(json)
@ -521,7 +479,7 @@ class CrossrefMappingTest {
@Test @Test
def testLicenseOpen() :Unit = { 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) assertNotNull(json)
@ -544,7 +502,7 @@ class CrossrefMappingTest {
@Test @Test
def testLicenseEmbargoOpen() :Unit = { 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) assertNotNull(json)
@ -567,7 +525,7 @@ class CrossrefMappingTest {
@Test @Test
def testLicenseEmbargo() :Unit = { 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) assertNotNull(json)
@ -591,7 +549,7 @@ class CrossrefMappingTest {
@Test @Test
def testLicenseEmbargoDateTime() :Unit = { 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) assertNotNull(json)
@ -614,7 +572,7 @@ class CrossrefMappingTest {
@Test @Test
def testMultipleURLs() :Unit = { 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) assertNotNull(json)

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.SparkConf
import org.apache.spark.sql.{Dataset, SparkSession} import org.apache.spark.sql.{Dataset, SparkSession}
import org.codehaus.jackson.map.ObjectMapper import org.codehaus.jackson.map.ObjectMapper
import org.json4s.DefaultFormats
import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
import org.json4s.DefaultFormats
import org.slf4j.{Logger, LoggerFactory} import org.slf4j.{Logger, LoggerFactory}
import java.sql.Timestamp import java.sql.Timestamp
@ -47,7 +48,7 @@ class MAGMappingTest {
@Test @Test
def buildInvertedIndexTest(): Unit = { 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) val description = ConversionUtil.convertInvertedIndexString(json_input)
assertNotNull(description) assertNotNull(description)
assertTrue(description.nonEmpty) assertTrue(description.nonEmpty)
@ -71,7 +72,7 @@ class MAGMappingTest {
.appName(getClass.getSimpleName) .appName(getClass.getSimpleName)
.config(conf) .config(conf)
.getOrCreate() .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 import org.apache.spark.sql.Encoders
val schema = Encoders.product[MagPapers].schema val schema = Encoders.product[MagPapers].schema
@ -101,7 +102,7 @@ class MAGMappingTest {
.appName(getClass.getSimpleName) .appName(getClass.getSimpleName)
.config(conf) .config(conf)
.getOrCreate() .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 import org.apache.spark.sql.Encoders
val schema = Encoders.product[MagPapers].schema val schema = Encoders.product[MagPapers].schema

View File

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

View File

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

View File

@ -88,7 +88,7 @@ public class CleanGraphSparkJob {
readTableFromPath(spark, inputPath, clazz) readTableFromPath(spark, inputPath, clazz)
.map((MapFunction<T, T>) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz)) .map((MapFunction<T, T>) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz))
.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz)) .map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
.map((MapFunction<T, T>) GraphCleaningFunctions::cleanup, Encoders.bean(clazz)) .map((MapFunction<T, T>) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz))
.filter((FilterFunction<T>) GraphCleaningFunctions::filter) .filter((FilterFunction<T>) GraphCleaningFunctions::filter)
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)

View File

@ -1,8 +1,8 @@
package eu.dnetlib.dhp.oa.graph.hostedbymap package eu.dnetlib.dhp.oa.graph.hostedbymap
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo 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.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) {} case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {}

View File

@ -2,13 +2,12 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser 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.oa.graph.hostedbymap.model.EntityInfo
import eu.dnetlib.dhp.schema.common.ModelConstants 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.commons.io.IOUtils
import org.apache.spark.SparkConf 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.json4s.DefaultFormats
import org.slf4j.{Logger, LoggerFactory} import org.slf4j.{Logger, LoggerFactory}
@ -52,18 +51,18 @@ object SparkApplyHostedByMapToDatasource {
val mapper = new ObjectMapper() 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])) .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]))) .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) spark.read.textFile(outputPath)
.write .write
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression","gzip") .option("compression", "gzip")
.text(graphPath + "/datasource") .text(graphPath + "/datasource")
} }

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

View File

@ -3,61 +3,58 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo
import eu.dnetlib.dhp.schema.oaf.{Journal, Publication} import eu.dnetlib.dhp.schema.oaf.{Journal, Publication}
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf 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
import org.json4s.DefaultFormats import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory} import org.slf4j.{Logger, LoggerFactory}
object SparkPrepareHostedByInfoToApply { object SparkPrepareHostedByInfoToApply {
implicit val mapEncoderPInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) implicit val mapEncoderPInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo])
def getList(id: String, j: Journal, name: String ) : List[EntityInfo] = { def getList(id: String, j: Journal, name: String): List[EntityInfo] = {
var lst:List[EntityInfo] = List() 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 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 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 = EntityInfo.newInstance(id, j.getIssnPrinted, name) :: lst
} }
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]) implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication])
val mapper = new ObjectMapper() 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])) .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 implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input) 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) 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) 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") Aggregators.resultToSingleId(res.joinWith(hbm, res.col("journalId").equalTo(hbm.col("journalId")), "left")
.map(t2 => { .map(t2 => {
val res: EntityInfo = t2._1 val res: EntityInfo = t2._1
if(t2._2 != null ){ if (t2._2 != null) {
val ds = t2._2 val ds = t2._2
res.setHostedById(ds.getId) res.setHostedById(ds.getId)
res.setOpenAccess(ds.getOpenAccess) res.setOpenAccess(ds.getOpenAccess)
@ -107,10 +104,10 @@ object SparkPrepareHostedByInfoToApply {
//STEP1: read the hostedbymap and transform it in EntityInfo //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) //STEP2: create association (publication, issn), (publication, eissn), (publication, lissn)
val resultInfoDataset:Dataset[EntityInfo] = prepareResultInfo(spark, graphPath + "/publication") 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 //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) //one entry (one result could be associated to issn and eissn and so possivly matching more than once against the map)

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@ -1,41 +1,39 @@
package eu.dnetlib.dhp.oa.graph.hostedbymap package eu.dnetlib.dhp.oa.graph.hostedbymap
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.oa.graph.hostedbymap.model.{DOAJModel, UnibiGoldModel} import eu.dnetlib.dhp.oa.graph.hostedbymap.model.{DOAJModel, UnibiGoldModel}
import eu.dnetlib.dhp.schema.oaf.Datasource import eu.dnetlib.dhp.schema.oaf.Datasource
import org.apache.commons.io.IOUtils 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.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.json4s.DefaultFormats
import org.slf4j.{Logger, LoggerFactory} 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 java.io.PrintWriter
import org.apache.hadoop.io.compress.GzipCodec
object SparkProduceHostedByMap { object SparkProduceHostedByMap {
implicit val tupleForJoinEncoder: Encoder[(String, HostedByItemType)] = Encoders.tuple(Encoders.STRING, Encoders.product[HostedByItemType]) 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 openaire: HostedByInfo = input._1._1
val doaj: HostedByInfo = input._1._2 val doaj: HostedByInfo = input._1._2
val gold: HostedByInfo = input._2 val gold: HostedByInfo = input._2
val isOpenAccess: Boolean = doaj == null && gold == null val isOpenAccess: Boolean = doaj == null && gold == null
openaire.journal_id match { openaire.journal_id match {
case Constants.ISSN => 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.EISSN => HostedByItemType(openaire.id, openaire.officialname, "", openaire.journal_id, "", isOpenAccess)
case Constants.ISSNL => 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 // 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 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) Serialization.write(map)
@ -52,34 +50,33 @@ object SparkProduceHostedByMap {
} }
def getHostedByItemType(id: String, officialname: String, issn: String, eissn: String, issnl: String, oa: Boolean): HostedByItemType = {
def getHostedByItemType(id:String, officialname: String, issn:String, eissn:String, issnl:String, oa:Boolean): HostedByItemType = { if (issn != null) {
if(issn != null){ if (eissn != null) {
if(eissn != null){ if (issnl != null) {
if(issnl != null){ HostedByItemType(id, officialname, issn, eissn, issnl, oa)
HostedByItemType(id, officialname, issn, eissn, issnl , oa) } else {
}else{ HostedByItemType(id, officialname, issn, eissn, "", oa)
HostedByItemType(id, officialname, issn, eissn, "" , oa)
} }
}else{ } else {
if(issnl != null){ if (issnl != null) {
HostedByItemType(id, officialname, issn, "", issnl , oa) HostedByItemType(id, officialname, issn, "", issnl, oa)
}else{ } else {
HostedByItemType(id, officialname, issn, "", "" , oa) HostedByItemType(id, officialname, issn, "", "", oa)
} }
} }
}else{ } else {
if(eissn != null){ if (eissn != null) {
if(issnl != null){ if (issnl != null) {
HostedByItemType(id, officialname, "", eissn, issnl , oa) HostedByItemType(id, officialname, "", eissn, issnl, oa)
}else{ } else {
HostedByItemType(id, officialname, "", eissn, "" , oa) HostedByItemType(id, officialname, "", eissn, "", oa)
} }
}else{ } else {
if(issnl != null){ if (issnl != null) {
HostedByItemType(id, officialname, "", "", issnl , oa) HostedByItemType(id, officialname, "", "", issnl, oa)
}else{ } else {
HostedByItemType("", "", "", "", "" , oa) 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) 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._ import spark.implicits._
@ -102,10 +99,10 @@ object SparkProduceHostedByMap {
implicit var encoderD = Encoders.kryo[Datasource] 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])) .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._ import spark.implicits._
implicit val mapEncoderUnibi: Encoder[UnibiGoldModel] = Encoders.kryo[UnibiGoldModel] implicit val mapEncoderUnibi: Encoder[UnibiGoldModel] = Encoders.kryo[UnibiGoldModel]
val mapper = new ObjectMapper() 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])) .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) 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._ import spark.implicits._
implicit val mapEncoderDOAJ: Encoder[DOAJModel] = Encoders.kryo[DOAJModel] implicit val mapEncoderDOAJ: Encoder[DOAJModel] = Encoders.kryo[DOAJModel]
val mapper = new ObjectMapper() 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])) .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)] = { def toList(input: HostedByItemType): List[(String, HostedByItemType)] = {
var lst : List[(String, HostedByItemType)] = List() var lst: List[(String, HostedByItemType)] = List()
if(!input.issn.equals("")){ if (!input.issn.equals("")) {
lst = (input.issn, input) :: lst lst = (input.issn, input) :: lst
} }
if(!input.eissn.equals("")){ if (!input.eissn.equals("")) {
lst = (input.eissn, input) :: lst lst = (input.eissn, input) :: lst
} }
if(!input.lissn.equals("")){ if (!input.lissn.equals("")) {
lst = (input.lissn, input) :: lst lst = (input.lissn, input) :: lst
} }
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() val conf = new Configuration()
conf.set("fs.defaultFS", hdfsNameNode) conf.set("fs.defaultFS", hdfsNameNode)
val fs= FileSystem.get(conf) val fs = FileSystem.get(conf)
val output = fs.create(new Path(outputPath)) val output = fs.create(new Path(outputPath))
val writer = new PrintWriter(output) val writer = new PrintWriter(output)
try { try {
@ -182,7 +178,6 @@ object SparkProduceHostedByMap {
} }
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(getClass) val logger: Logger = LoggerFactory.getLogger(getClass)
@ -213,7 +208,7 @@ object SparkProduceHostedByMap {
.union(doajHostedByDataset(spark, workingDirPath + "/doaj.json")) .union(doajHostedByDataset(spark, workingDirPath + "/doaj.json"))
.flatMap(hbi => toList(hbi))).filter(hbi => hbi._2.id.startsWith("10|")) .flatMap(hbi => toList(hbi))).filter(hbi => hbi._2.id.startsWith("10|"))
.map(hbi => toHostedByMap(hbi))(Encoders.STRING) .map(hbi => toHostedByMap(hbi))(Encoders.STRING)
.rdd.saveAsTextFile(outputPath , classOf[GzipCodec]) .rdd.saveAsTextFile(outputPath, classOf[GzipCodec])
} }

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

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@ -2,9 +2,8 @@ package eu.dnetlib.dhp.oa.graph.resolution
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.common.HdfsSupport
import eu.dnetlib.dhp.schema.common.EntityType 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.commons.io.IOUtils
import org.apache.hadoop.fs.{FileSystem, Path} import org.apache.hadoop.fs.{FileSystem, Path}
import org.apache.spark.SparkConf 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]) implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
import spark.implicits._ import spark.implicits._

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

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

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

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

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

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@ -1,14 +1,12 @@
package eu.dnetlib.dhp.sx.graph package eu.dnetlib.dhp.sx.graph
import eu.dnetlib.dhp.application.ArgumentApplicationParser 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.commons.io.IOUtils
import org.apache.spark.SparkConf 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} import org.slf4j.{Logger, LoggerFactory}
object SparkCreateInputGraph { object SparkCreateInputGraph {
def main(args: Array[String]): Unit = { 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 publicationEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication])
implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset]) implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset])
implicit val softwareEncoder: Encoder[Software] = Encoders.kryo(classOf[Software]) implicit val softwareEncoder: Encoder[Software] = Encoders.kryo(classOf[Software])
@ -41,16 +39,13 @@ object SparkCreateInputGraph {
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation]) implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
val sourcePath = parser.get("sourcePath") val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath") log.info(s"sourcePath -> $sourcePath")
val targetPath = parser.get("targetPath") val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $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") log.info("Extract Publication")
@ -70,27 +65,27 @@ object SparkCreateInputGraph {
resultObject.foreach { r => resultObject.foreach { r =>
log.info(s"Make ${r._1} unique") 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}") log.info(s"Extract ${clazz.getSimpleName}")
oafDs.filter(o => o.isInstanceOf[T]).map(p => p.asInstanceOf[T]).write.mode(SaveMode.Overwrite).save(targetPath) 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._ 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.mergeFrom(y)
x x
}.map(_._2).write.mode(SaveMode.Overwrite).save(targetPath) }.map(_._2).write.mode(SaveMode.Overwrite).save(targetPath)

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@ -9,7 +9,7 @@ import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils.RelatedEntities
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf import org.apache.spark.SparkConf
import org.apache.spark.sql.functions.count 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} import org.slf4j.{Logger, LoggerFactory}
object SparkCreateScholix { object SparkCreateScholix {
@ -42,7 +42,7 @@ object SparkCreateScholix {
val relationDS: Dataset[(String, Relation)] = spark.read.load(relationPath).as[Relation] 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)) .map(r => (r.getSource, r))(Encoders.tuple(Encoders.STRING, relEncoder))
val summaryDS: Dataset[(String, ScholixSummary)] = spark.read.load(summaryPath).as[ScholixSummary] 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") relationDS.joinWith(summaryDS, relationDS("_1").equalTo(summaryDS("_1")), "left")
.map { input: ((String, Relation), (String, ScholixSummary)) => .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 rel: Relation = input._1._2
val source: ScholixSummary = input._2._2 val source: ScholixSummary = input._2._2
(rel.getTarget, ScholixUtils.scholixFromSource(rel, source)) (rel.getTarget, ScholixUtils.scholixFromSource(rel, source))
} }
else null else null
}(Encoders.tuple(Encoders.STRING, scholixEncoder)) }(Encoders.tuple(Encoders.STRING, scholixEncoder))
.filter(r => r!= null) .filter(r => r != null)
.write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_from_source") .write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_from_source")
val scholixSource: Dataset[(String, Scholix)] = spark.read.load(s"$targetPath/scholix_from_source").as[(String, Scholix)](Encoders.tuple(Encoders.STRING, scholixEncoder)) val scholixSource: Dataset[(String, Scholix)] = spark.read.load(s"$targetPath/scholix_from_source").as[(String, Scholix)](Encoders.tuple(Encoders.STRING, scholixEncoder))
scholixSource.joinWith(summaryDS, scholixSource("_1").equalTo(summaryDS("_1")), "left") scholixSource.joinWith(summaryDS, scholixSource("_1").equalTo(summaryDS("_1")), "left")
.map { input: ((String, Scholix), (String, ScholixSummary)) => .map { input: ((String, Scholix), (String, ScholixSummary)) =>
if (input._2== null) { if (input._2 == null) {
null null
} else { } else {
val s: Scholix = input._1._2 val s: Scholix = input._1._2
val target: ScholixSummary = input._2._2 val target: ScholixSummary = input._2._2
ScholixUtils.generateCompleteScholix(s, target) 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"$targetPath/scholix_one_verse").as[Scholix] val scholix_o_v: Dataset[Scholix] = spark.read.load(s"$targetPath/scholix_one_verse").as[Scholix]
scholix_o_v.flatMap(s => List(s, ScholixUtils.createInverseScholixRelation(s))).as[Scholix] 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) .groupByKey(_._1)
.agg(ScholixUtils.scholixAggregator.toColumn) .agg(ScholixUtils.scholixAggregator.toColumn)
.map(s => s._2) .map(s => s._2)
.write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix") .write.mode(SaveMode.Overwrite).save(s"$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 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) .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) .map(_._2)
.write.mode(SaveMode.Overwrite).save(s"$targetPath/related_entities") .write.mode(SaveMode.Overwrite).save(s"$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 re = i._1
val sum = i._2._2 val sum = i._2._2

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@ -6,7 +6,7 @@ import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf 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} import org.slf4j.{Logger, LoggerFactory}
object SparkCreateSummaryObject { object SparkCreateSummaryObject {
@ -28,15 +28,15 @@ object SparkCreateSummaryObject {
val targetPath = parser.get("targetPath") val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath") log.info(s"targetPath -> $targetPath")
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result] implicit val resultEncoder: Encoder[Result] = Encoders.kryo[Result]
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf] implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val summaryEncoder:Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary] implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
val ds:Dataset[Result] = spark.read.load(s"$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)
} }

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

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

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

View File

@ -74,6 +74,53 @@ public class GraphCleaningFunctionsTest {
} }
} }
@Test
void testFilter_false() throws Exception {
assertNotNull(vocabularies);
assertNotNull(mapping);
String json = IOUtils
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json"));
Publication p_in = MAPPER.readValue(json, Publication.class);
assertTrue(p_in instanceof Result);
assertTrue(p_in instanceof Publication);
assertEquals(false, GraphCleaningFunctions.filter(p_in));
}
@Test
void testFilter_true() throws Exception {
assertNotNull(vocabularies);
assertNotNull(mapping);
String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json"));
Publication p_in = MAPPER.readValue(json, Publication.class);
assertTrue(p_in instanceof Result);
assertTrue(p_in instanceof Publication);
assertEquals(true, GraphCleaningFunctions.filter(p_in));
}
@Test
void testFilter_missing_invisible() throws Exception {
assertNotNull(vocabularies);
assertNotNull(mapping);
String json = IOUtils
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json"));
Publication p_in = MAPPER.readValue(json, Publication.class);
assertTrue(p_in instanceof Result);
assertTrue(p_in instanceof Publication);
assertEquals(true, GraphCleaningFunctions.filter(p_in));
}
@Test @Test
void testCleaning() throws Exception { void testCleaning() throws Exception {
@ -104,6 +151,12 @@ public class GraphCleaningFunctionsTest {
assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid()); assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid());
assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname()); assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname());
assertEquals("0027", p_out.getInstance().get(1).getInstancetype().getClassid());
assertEquals("Model", p_out.getInstance().get(1).getInstancetype().getClassname());
assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassid());
assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassname());
assertEquals("CLOSED", p_out.getInstance().get(0).getAccessright().getClassid()); assertEquals("CLOSED", p_out.getInstance().get(0).getAccessright().getClassid());
assertEquals("Closed Access", p_out.getInstance().get(0).getAccessright().getClassname()); assertEquals("Closed Access", p_out.getInstance().get(0).getAccessright().getClassname());
@ -117,7 +170,7 @@ public class GraphCleaningFunctionsTest {
List<Instance> poi = p_out.getInstance(); List<Instance> poi = p_out.getInstance();
assertNotNull(poi); assertNotNull(poi);
assertEquals(1, poi.size()); assertEquals(3, poi.size());
final Instance poii = poi.get(0); final Instance poii = poi.get(0);
assertNotNull(poii); assertNotNull(poii);
@ -145,7 +198,7 @@ public class GraphCleaningFunctionsTest {
assertEquals(5, p_out.getTitle().size()); assertEquals(5, p_out.getTitle().size());
Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out); Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
assertEquals(3, p_cleaned.getTitle().size()); assertEquals(3, p_cleaned.getTitle().size());
@ -164,9 +217,12 @@ public class GraphCleaningFunctionsTest {
assertEquals("1970-10-07", p_cleaned.getDateofacceptance().getValue()); assertEquals("1970-10-07", p_cleaned.getDateofacceptance().getValue());
assertEquals("0038", p_cleaned.getInstance().get(2).getInstancetype().getClassid());
assertEquals("Other literature type", p_cleaned.getInstance().get(2).getInstancetype().getClassname());
final List<Instance> pci = p_cleaned.getInstance(); final List<Instance> pci = p_cleaned.getInstance();
assertNotNull(pci); assertNotNull(pci);
assertEquals(1, pci.size()); assertEquals(3, pci.size());
final Instance pcii = pci.get(0); final Instance pcii = pci.get(0);
assertNotNull(pcii); assertNotNull(pcii);
@ -234,7 +290,7 @@ public class GraphCleaningFunctionsTest {
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub.json")); .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub.json"));
Publication p_in = MAPPER.readValue(json, Publication.class); Publication p_in = MAPPER.readValue(json, Publication.class);
Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping); Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
Publication cleaned = GraphCleaningFunctions.cleanup(p_out); Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned)); Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));
} }
@ -245,7 +301,7 @@ public class GraphCleaningFunctionsTest {
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub2.json")); .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub2.json"));
Publication p_in = MAPPER.readValue(json, Publication.class); Publication p_in = MAPPER.readValue(json, Publication.class);
Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping); Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
Publication cleaned = GraphCleaningFunctions.cleanup(p_out); Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned)); Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));

View File

@ -171,30 +171,6 @@ public class DumpJobTest {
GraphResult gr = verificationDataset.first(); GraphResult gr = verificationDataset.first();
Assertions.assertEquals(1, gr.getInstance().size());
Assertions.assertEquals(2, gr.getInstance().get(0).getMeasures().size());
Assertions
.assertTrue(
gr
.getInstance()
.get(0)
.getMeasures()
.stream()
.anyMatch(
m -> m.getKey().equals("influence")
&& m.getValue().equals("1.62759106106e-08")));
Assertions
.assertTrue(
gr
.getInstance()
.get(0)
.getMeasures()
.stream()
.anyMatch(
m -> m.getKey().equals("popularity")
&& m.getValue().equals("0.22519296")));
Assertions.assertEquals(6, gr.getAuthor().size()); Assertions.assertEquals(6, gr.getAuthor().size());
Assertions Assertions
.assertTrue( .assertTrue(
@ -363,8 +339,6 @@ public class DumpJobTest {
Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId()); Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId());
System.out.println(gr.getOriginalId().size());
Assertions.assertEquals(1, gr.getOriginalId().size()); Assertions.assertEquals(1, gr.getOriginalId().size());
Assertions Assertions
.assertTrue( .assertTrue(

View File

@ -708,7 +708,7 @@ class MappersTest {
assertEquals(1, p.getTitle().size()); assertEquals(1, p.getTitle().size());
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
final Publication p_cleaned = cleanup(fixVocabularyNames(p)); final Publication p_cleaned = cleanup(fixVocabularyNames(p), vocs);
assertNotNull(p_cleaned.getTitle()); assertNotNull(p_cleaned.getTitle());
assertFalse(p_cleaned.getTitle().isEmpty()); assertFalse(p_cleaned.getTitle().isEmpty());

View File

@ -403,6 +403,178 @@
"http://juuli.fi/Record/0275158616", "http://juuli.fi/Record/0275158616",
"http://dx.doi.org/10.1007/s109090161569x" "http://dx.doi.org/10.1007/s109090161569x"
] ]
},
{
"pid": [
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1002/s21010127267xy"
},
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1008/abcd"
}
],
"alternateIdentifier": [
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1007/s109090161569x"
},
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1009/qwerty"
}
],
"accessright": {
"classid": "CLOSED",
"classname": "CLOSED",
"schemeid": "dnet:access_modes",
"schemename": "dnet:access_modes"
},
"collectedfrom": {
"key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
"value": "VIRTA"
},
"dateofacceptance": {
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"value": "2016-01-01"
},
"distributionlocation": "",
"hostedby": {
"key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
"value": "VIRTA"
},
"instancetype": {
"classid": "Model",
"classname": "Model",
"schemeid": "dnet:publication_resource",
"schemename": "dnet:publication_resource"
},
"url": [
"http://dx.doi.org/10.1002/s21010127267xy"
]
},
{
"pid": [
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1002/s21010127267xy"
},
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1008/abcd"
}
],
"alternateIdentifier": [
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1007/s109090161569x"
},
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1009/qwerty"
}
],
"accessright": {
"classid": "CLOSED",
"classname": "CLOSED",
"schemeid": "dnet:access_modes",
"schemename": "dnet:access_modes"
},
"collectedfrom": {
"key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
"value": "VIRTA"
},
"dateofacceptance": {
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"value": "2016-01-01"
},
"distributionlocation": "",
"hostedby": {
"key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
"value": "VIRTA"
},
"instancetype": {
"classid": "xyz",
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"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "main title",
"classname": "main title",
"schemeid": "dnet:dataCite_title",
"schemename": "dnet:dataCite_title"
},
"value": "「マキャベリ的知性と心の理論の進化論」 リチャード・バーン, アンドリュー・ホワイトゥン 編/藤田和生, 山下博志, 友永雅巳 監訳"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "main title",
"classname": "main title",
"schemeid": "dnet:dataCite_title",
"schemename": "dnet:dataCite_title"
},
"value": "-"
}
]
}

View File

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

View File

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

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 input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/scholix/result.json")).mkString
val res =SparkResolveRelation.extractPidsFromRecord(input) val res =SparkResolveRelation.extractPidsFromRecord(input)
assertNotNull(res) assertNotNull(res)
assertTrue(res._2.size == 2)
assertEquals(1,res._2.size)
} }

View File

@ -0,0 +1,158 @@
package eu.dnetlib.dhp.oa.provision.model;
import java.util.Set;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Serializable;
public class XmlInstance implements Serializable {
public static final AccessRight UNKNOWN_ACCESS_RIGHT;
static {
UNKNOWN_ACCESS_RIGHT = new AccessRight();
UNKNOWN_ACCESS_RIGHT.setClassid(ModelConstants.UNKNOWN);
UNKNOWN_ACCESS_RIGHT.setClassname(ModelConstants.UNKNOWN);
UNKNOWN_ACCESS_RIGHT.setSchemeid(ModelConstants.DNET_ACCESS_MODES);
UNKNOWN_ACCESS_RIGHT.setSchemename(ModelConstants.DNET_ACCESS_MODES);
}
private String url;
private AccessRight accessright;
private Set<KeyValue> collectedfrom = Sets.newHashSet();
private Set<KeyValue> hostedby = Sets.newHashSet();
private Set<Qualifier> instancetype = Sets.newHashSet();
private Set<String> license = Sets.newHashSet();
// other research products specifc
private Set<String> distributionlocation = Sets.newHashSet();
private Set<StructuredProperty> pid = Sets.newHashSet();
private Set<StructuredProperty> alternateIdentifier = Sets.newHashSet();
private Set<String> dateofacceptance = Sets.newHashSet();
// ( article | book ) processing charges. Defined here to cope with possible wrongly typed
// results
private String processingchargeamount;
// currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly
// typed results
private String processingchargecurrency;
private Set<Qualifier> refereed = Sets.newHashSet();; // peer-review status
public String getUrl() {
return url;
}
public void setUrl(String url) {
this.url = url;
}
public AccessRight getAccessright() {
return accessright;
}
public void setAccessright(AccessRight accessright) {
this.accessright = accessright;
}
public Set<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(Set<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public Set<KeyValue> getHostedby() {
return hostedby;
}
public void setHostedby(Set<KeyValue> hostedby) {
this.hostedby = hostedby;
}
public Set<Qualifier> getInstancetype() {
return instancetype;
}
public void setInstancetype(Set<Qualifier> instancetype) {
this.instancetype = instancetype;
}
public Set<String> getLicense() {
return license;
}
public void setLicense(Set<String> license) {
this.license = license;
}
public Set<String> getDistributionlocation() {
return distributionlocation;
}
public void setDistributionlocation(Set<String> distributionlocation) {
this.distributionlocation = distributionlocation;
}
public Set<StructuredProperty> getPid() {
return pid;
}
public void setPid(Set<StructuredProperty> pid) {
this.pid = pid;
}
public Set<StructuredProperty> getAlternateIdentifier() {
return alternateIdentifier;
}
public void setAlternateIdentifier(Set<StructuredProperty> alternateIdentifier) {
this.alternateIdentifier = alternateIdentifier;
}
public Set<String> getDateofacceptance() {
return dateofacceptance;
}
public void setDateofacceptance(Set<String> dateofacceptance) {
this.dateofacceptance = dateofacceptance;
}
public String getProcessingchargeamount() {
return processingchargeamount;
}
public void setProcessingchargeamount(String processingchargeamount) {
this.processingchargeamount = processingchargeamount;
}
public String getProcessingchargecurrency() {
return processingchargecurrency;
}
public void setProcessingchargecurrency(String processingchargecurrency) {
this.processingchargecurrency = processingchargecurrency;
}
public Set<Qualifier> getRefereed() {
return refereed;
}
public void setRefereed(Set<Qualifier> refereed) {
this.refereed = refereed;
}
}

View File

@ -8,11 +8,16 @@ import java.io.IOException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collection; import java.util.Collection;
import java.util.List; import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import javax.swing.text.html.Option;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.stringtemplate.v4.ST; import org.stringtemplate.v4.ST;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.OafEntity;
@ -94,13 +99,15 @@ public class TemplateFactory {
} }
public String getInstance( public String getInstance(
final String resultId, final List<String> instancemetadata, final List<String> webresources) { final List<String> instancemetadata, final String url) {
return getTemplate(resources.getInstance()) return getTemplate(resources.getInstance())
.add("instanceId", escapeXml(removePrefix(resultId)))
.add("metadata", instancemetadata) .add("metadata", instancemetadata)
.add( .add(
"webresources", "webresources",
(webresources != null ? webresources : new ArrayList<String>()) Optional
.ofNullable(url)
.map(u -> Lists.newArrayList(url))
.orElse(Lists.newArrayList())
.stream() .stream()
.filter(StringUtils::isNotBlank) .filter(StringUtils::isNotBlank)
.map(this::getWebResource) .map(this::getWebResource)

View File

@ -10,24 +10,18 @@ import java.io.IOException;
import java.io.Serializable; import java.io.Serializable;
import java.io.StringReader; import java.io.StringReader;
import java.io.StringWriter; import java.io.StringWriter;
import java.util.ArrayList; import java.net.URL;
import java.util.HashSet; import java.util.*;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import java.util.stream.Stream;
import javax.xml.transform.OutputKeys; import javax.xml.transform.*;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource; import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult; import javax.xml.transform.stream.StreamResult;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.spark.util.LongAccumulator; import org.apache.spark.util.LongAccumulator;
import org.dom4j.Document; import org.dom4j.Document;
import org.dom4j.DocumentException; import org.dom4j.DocumentException;
@ -49,25 +43,10 @@ import com.mycila.xmltool.XMLTag;
import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper; import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.oa.provision.model.XmlInstance;
import eu.dnetlib.dhp.schema.common.MainEntityType; import eu.dnetlib.dhp.schema.common.*;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.ExternalReference;
import eu.dnetlib.dhp.schema.oaf.ExtraInfo;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
public class XmlRecordFactory implements Serializable { public class XmlRecordFactory implements Serializable {
@ -1112,37 +1091,64 @@ public class XmlRecordFactory implements Serializable {
if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) { if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) {
final List<Instance> instances = ((Result) entity).getInstance(); final List<Instance> instances = ((Result) entity).getInstance();
if (instances != null) { if (instances != null) {
for (final Instance instance : ((Result) entity).getInstance()) {
groupInstancesByUrl(((Result) entity).getInstance()).forEach(instance -> {
final List<String> fields = Lists.newArrayList(); final List<String> fields = Lists.newArrayList();
if (instance.getAccessright() != null && !instance.getAccessright().isBlank()) { if (instance.getAccessright() != null && !instance.getAccessright().isBlank()) {
fields fields
.add(XmlSerializationUtils.mapQualifier("accessright", instance.getAccessright())); .add(XmlSerializationUtils.mapQualifier("accessright", instance.getAccessright()));
} }
if (instance.getCollectedfrom() != null && kvNotBlank(instance.getCollectedfrom())) { if (instance.getCollectedfrom() != null) {
fields fields
.add(XmlSerializationUtils.mapKeyValue("collectedfrom", instance.getCollectedfrom())); .addAll(
instance
.getCollectedfrom()
.stream()
.filter(cf -> kvNotBlank(cf))
.map(cf -> XmlSerializationUtils.mapKeyValue("collectedfrom", cf))
.collect(Collectors.toList()));
} }
if (instance.getHostedby() != null && kvNotBlank(instance.getHostedby())) {
fields.add(XmlSerializationUtils.mapKeyValue("hostedby", instance.getHostedby())); if (instance.getHostedby() != null) {
}
if (instance.getDateofacceptance() != null
&& isNotBlank(instance.getDateofacceptance().getValue())) {
fields fields
.add( .addAll(
XmlSerializationUtils instance
.asXmlElement("dateofacceptance", instance.getDateofacceptance().getValue())); .getHostedby()
.stream()
.filter(hb -> kvNotBlank(hb))
.map(hb -> XmlSerializationUtils.mapKeyValue("hostedby", hb))
.collect(Collectors.toList()));
} }
if (instance.getInstancetype() != null && !instance.getInstancetype().isBlank()) { if (instance.getDateofacceptance() != null) {
fields fields
.add(XmlSerializationUtils.mapQualifier("instancetype", instance.getInstancetype())); .addAll(
instance
.getDateofacceptance()
.stream()
.filter(d -> isNotBlank(d))
.map(d -> XmlSerializationUtils.asXmlElement("dateofacceptance", d))
.collect(Collectors.toList()));
} }
if (isNotBlank(instance.getDistributionlocation())) { if (instance.getInstancetype() != null) {
fields fields
.add( .addAll(
XmlSerializationUtils instance
.asXmlElement("distributionlocation", instance.getDistributionlocation())); .getInstancetype()
.stream()
.filter(t -> !t.isBlank())
.map(t -> XmlSerializationUtils.mapQualifier("instancetype", t))
.collect(Collectors.toList()));
}
if (instance.getDistributionlocation() != null) {
fields
.addAll(
instance
.getDistributionlocation()
.stream()
.filter(d -> isNotBlank(d))
.map(d -> XmlSerializationUtils.asXmlElement("distributionlocation", d))
.collect(Collectors.toList()));
} }
if (instance.getPid() != null) { if (instance.getPid() != null) {
fields fields
@ -1165,32 +1171,50 @@ public class XmlRecordFactory implements Serializable {
.collect(Collectors.toList())); .collect(Collectors.toList()));
} }
if (instance.getRefereed() != null && !instance.getRefereed().isBlank()) { if (instance.getRefereed() != null) {
fields fields
.add(XmlSerializationUtils.mapQualifier("refereed", instance.getRefereed())); .addAll(
instance
.getRefereed()
.stream()
.filter(Objects::nonNull)
.filter(r -> !r.isBlank())
.map(r -> XmlSerializationUtils.mapQualifier("refereed", r))
.collect(Collectors.toList()));
} }
if (instance.getProcessingchargeamount() != null if (instance.getProcessingchargeamount() != null
&& isNotBlank(instance.getProcessingchargeamount().getValue())) { && isNotBlank(instance.getProcessingchargeamount())) {
fields fields
.add( .add(
XmlSerializationUtils XmlSerializationUtils
.asXmlElement( .asXmlElement(
"processingchargeamount", instance.getProcessingchargeamount().getValue())); "processingchargeamount", instance.getProcessingchargeamount()));
} }
if (instance.getProcessingchargecurrency() != null if (instance.getProcessingchargecurrency() != null
&& isNotBlank(instance.getProcessingchargecurrency().getValue())) { && isNotBlank(instance.getProcessingchargecurrency())) {
fields fields
.add( .add(
XmlSerializationUtils XmlSerializationUtils
.asXmlElement( .asXmlElement(
"processingchargecurrency", instance.getProcessingchargecurrency().getValue())); "processingchargecurrency", instance.getProcessingchargecurrency()));
}
if (instance.getLicense() != null) {
fields
.addAll(
instance
.getLicense()
.stream()
.filter(d -> isNotBlank(d))
.map(d -> XmlSerializationUtils.asXmlElement("license", d))
.collect(Collectors.toList()));
} }
children children
.add( .add(
templateFactory templateFactory
.getInstance(instance.getHostedby().getKey(), fields, instance.getUrl())); .getInstance(fields, instance.getUrl()));
} });
} }
final List<ExternalReference> ext = ((Result) entity).getExternalReference(); final List<ExternalReference> ext = ((Result) entity).getExternalReference();
if (ext != null) { if (ext != null) {
@ -1234,6 +1258,97 @@ public class XmlRecordFactory implements Serializable {
return children; return children;
} }
private Stream<XmlInstance> groupInstancesByUrl(List<Instance> instance) {
return instance
.stream()
.filter(i -> Objects.nonNull(i.getUrl()))
.map(i -> {
i
.setUrl(
i
.getUrl()
.stream()
.filter(this::isValidUrl)
.collect(Collectors.toList()));
return i;
})
.filter(
i -> Optional
.ofNullable(i.getUrl())
.map(u -> !u.isEmpty())
.orElse(false))
.map(this::pickByUrl)
.collect(Collectors.groupingBy(ImmutablePair::getLeft))
.values()
.stream()
.filter(Objects::nonNull)
.map(this::mergeInstances);
}
private boolean isValidUrl(String url) {
try {
new URL(url).toURI();
return true;
} catch (Exception e) {
return false;
}
}
private ImmutablePair<String, Instance> pickByUrl(Instance i) {
return new ImmutablePair<>(i.getUrl().get(0), i);
}
private XmlInstance mergeInstances(List<ImmutablePair<String, Instance>> instances) {
final XmlInstance instance = new XmlInstance();
instance.setUrl(instances.get(0).getLeft());
instance
.setAccessright(
instances
.stream()
.map(Pair::getValue)
.map(Instance::getAccessright)
.min(new AccessRightComparator<AccessRight>())
.orElse(XmlInstance.UNKNOWN_ACCESS_RIGHT));
instances.forEach(p -> {
final Instance i = p.getRight();
instance.getCollectedfrom().add(i.getCollectedfrom());
instance.getHostedby().add(i.getHostedby());
instance.getInstancetype().add(i.getInstancetype());
instance.getRefereed().add(i.getRefereed());
instance
.setProcessingchargeamount(
Optional.ofNullable(i.getProcessingchargeamount()).map(apc -> apc.getValue()).orElse(null));
instance
.setProcessingchargecurrency(
Optional.ofNullable(i.getProcessingchargecurrency()).map(c -> c.getValue()).orElse(null));
Optional
.ofNullable(i.getPid())
.ifPresent(pid -> instance.getPid().addAll(pid));
Optional
.ofNullable(i.getAlternateIdentifier())
.ifPresent(altId -> instance.getAlternateIdentifier().addAll(altId));
Optional
.ofNullable(i.getDateofacceptance())
.ifPresent(d -> instance.getDateofacceptance().add(d.getValue()));
Optional
.ofNullable(i.getLicense())
.ifPresent(license -> instance.getLicense().add(license.getValue()));
Optional
.ofNullable(i.getDistributionlocation())
.ifPresent(dl -> instance.getDistributionlocation().add(dl));
});
if (instance.getHostedby().size() > 1
&& instance.getHostedby().stream().anyMatch(hb -> ModelConstants.UNKNOWN_REPOSITORY.equals(hb))) {
instance.getHostedby().remove(ModelConstants.UNKNOWN_REPOSITORY);
}
return instance;
}
private boolean isDuplicate(final RelatedEntityWrapper link) { private boolean isDuplicate(final RelatedEntityWrapper link) {
return ModelConstants.DEDUP.equalsIgnoreCase(link.getRelation().getSubRelType()); return ModelConstants.DEDUP.equalsIgnoreCase(link.getRelation().getSubRelType());
} }

View File

@ -1,4 +1,4 @@
<instance id="$instanceId$"> <instance>
$metadata:{ it | $it$ }$ $metadata:{ it | $it$ }$
$webresources:{ it | $it$ }$ $webresources:{ it | $it$ }$
</instance> </instance>

View File

@ -12,7 +12,6 @@ import org.apache.commons.io.IOUtils;
import org.dom4j.Document; import org.dom4j.Document;
import org.dom4j.DocumentException; import org.dom4j.DocumentException;
import org.dom4j.io.SAXReader; import org.dom4j.io.SAXReader;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.DeserializationFeature;
@ -54,18 +53,19 @@ public class XmlRecordFactoryTest {
System.out.println(doc.asXML()); System.out.println(doc.asXML());
Assertions.assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid")); assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid"));
Assertions.assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending")); assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending"));
Assertions.assertEquals("0000-0001-9613-9956", doc.valueOf("//creator[@rank = '2']/@orcid")); assertEquals("0000-0001-9613-9956", doc.valueOf("//creator[@rank = '2']/@orcid"));
Assertions.assertEquals("", doc.valueOf("//creator[@rank = '2']/@orcid_pending")); assertEquals("", doc.valueOf("//creator[@rank = '2']/@orcid_pending"));
Assertions.assertEquals("doi", doc.valueOf("//instance/pid/@classid")); assertEquals("doi", doc.valueOf("//instance/pid/@classid"));
Assertions.assertEquals("10.1109/TED.2018.2853550", doc.valueOf("//instance/pid/text()")); assertEquals("10.1109/TED.2018.2853550", doc.valueOf("//instance/pid/text()"));
Assertions.assertEquals("doi", doc.valueOf("//instance/alternateidentifier/@classid")); assertEquals("doi", doc.valueOf("//instance/alternateidentifier/@classid"));
Assertions.assertEquals("10.5689/LIB.2018.2853550", doc.valueOf("//instance/alternateidentifier/text()")); assertEquals("10.5689/LIB.2018.2853550", doc.valueOf("//instance/alternateidentifier/text()"));
// TODO add assertions based of values extracted from the XML record
assertEquals(3, doc.selectNodes("//instance").size());
} }
@Test @Test
@ -96,7 +96,7 @@ public class XmlRecordFactoryTest {
final Document doc = new SAXReader().read(new StringReader(xml)); final Document doc = new SAXReader().read(new StringReader(xml));
assertNotNull(doc); assertNotNull(doc);
System.out.println(doc.asXML()); System.out.println(doc.asXML());
Assertions.assertEquals("2021-01-01", doc.valueOf("//validated/@date")); assertEquals("2021-01-01", doc.valueOf("//validated/@date"));
} }
@Test @Test

View File

@ -412,9 +412,800 @@
"value": "" "value": ""
}, },
"url": [ "url": [
"http://juuli.fi/Record/0331473718",
"http://dx.doi.org/10.1109/TED.2018.2853550" "http://dx.doi.org/10.1109/TED.2018.2853550"
] ]
},
{
"pid": [
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "",
"classname": "",
"schemeid": "",
"schemename": ""
},
"trust": ""
},
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1109/TED.2018.2853550"
}
],
"alternateIdentifier": [
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "",
"classname": "",
"schemeid": "",
"schemename": ""
},
"trust": ""
},
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.5689/LIB.2018.2853550"
}
],
"accessright": {
"classid": "CLOSED",
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