From ebe6aa6d38dbfa2dde8b0617c656a4a07f5f52d5 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 10 Jun 2021 10:52:36 +0200 Subject: [PATCH 1/8] implemented datacite transformation also on master --- dhp-workflows/dhp-aggregation/pom.xml | 7 + .../DataciteToOAFTransformation.scala | 544 ++++++++ .../GenerateDataciteDatasetSpark.scala | 43 + .../project/PrepareProjects.java | 2 - .../actionmanager/datacite/datacite_filter | 28 + .../datacite/generate_dataset_params.json | 26 + .../actionmanager/datacite/hostedBy_map.json | 1032 ++++++++++++++ .../datacite/oozie_app/config-default.xml | 23 + .../datacite/oozie_app/workflow.xml | 46 + .../aggregation/AbstractVocabularyTest.java | 42 + .../datacite/DataciteToOAFTest.scala | 43 + .../dhp/actionmanager/datacite/datacite.json | 1 + .../eu/dnetlib/dhp/vocabulary/synonyms.txt | 1234 +++++++++++++++++ .../eu/dnetlib/dhp/vocabulary/terms.txt | 1080 +++++++++++++++ 14 files changed, 4149 insertions(+), 2 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/datacite_filter create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/hostedBy_map.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dentlib/dhp/aggregation/AbstractVocabularyTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/datacite.json create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/vocabulary/synonyms.txt create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/vocabulary/terms.txt diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index 4b16d9011..dc8e5b20b 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -37,6 +37,13 @@ dhp-schemas + + eu.dnetlib.dhp + dhp-graph-mapper + ${project.version} + + + net.sf.saxon diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala new file mode 100644 index 000000000..dace6e0de --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala @@ -0,0 +1,544 @@ +package eu.dnetlib.dhp.actionmanager.datacite + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup +import eu.dnetlib.dhp.schema.action.AtomicAction +import eu.dnetlib.dhp.schema.common.ModelConstants +import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Instance, KeyValue, Oaf, OafMapperUtils, OtherResearchProduct, Publication, Qualifier, Relation, Result, Software, StructuredProperty, Dataset => OafDataset} +import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Instance, KeyValue, Oaf, OtherResearchProduct, Publication, Qualifier, Relation, Result, Software, StructuredProperty, Dataset => OafDataset} +import eu.dnetlib.dhp.utils.DHPUtils +import org.apache.commons.lang3.StringUtils +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse + +import java.nio.charset.CodingErrorAction +import java.text.SimpleDateFormat +import java.time.LocalDate +import java.time.chrono.ThaiBuddhistDate +import java.time.format.DateTimeFormatter +import java.util.{Date, Locale} +import java.util.regex.Pattern +import scala.collection.JavaConverters._ +import scala.io.{Codec, Source} + +case class DataciteType(doi: String, timestamp: Long, isActive: Boolean, json: String) {} + +case class NameIdentifiersType(nameIdentifierScheme: Option[String], schemeUri: Option[String], nameIdentifier: Option[String]) {} + +case class CreatorType(nameType: Option[String], nameIdentifiers: Option[List[NameIdentifiersType]], name: Option[String], familyName: Option[String], givenName: Option[String], affiliation: Option[List[String]]) {} + +case class TitleType(title: Option[String], titleType: Option[String], lang: Option[String]) {} + +case class SubjectType(subject: Option[String], subjectScheme: Option[String]) {} + +case class DescriptionType(descriptionType: Option[String], description: Option[String]) {} + +case class FundingReferenceType(funderIdentifierType: Option[String], awardTitle: Option[String], awardUri: Option[String], funderName: Option[String], funderIdentifier: Option[String], awardNumber: Option[String]) {} + +case class DateType(date: Option[String], dateType: Option[String]) {} + +case class HostedByMapType(openaire_id: String, datacite_name: String, official_name: String, similarity: Option[Float]) {} + +object DataciteToOAFTransformation { + val UNKNOWN_REPOSITORY_ORIGINALID = "openaire____::1256f046-bf1f-4afc-8b47-d0b147148b18" + val DATACITE_ID = "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254" + + val DNET_DATACITE_DATE = "dnet:dataCite_date" + + val DNET_DATACITE_TITLE = "dnet:dataCite_title" + val SYSIMPORT_ACTIONSET = "sysimport:actionset" + val DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions" + + val PROVENANCE_ACTION_SET_QUALIFIER: Qualifier = OafMapperUtils.qualifier(SYSIMPORT_ACTIONSET, SYSIMPORT_ACTIONSET, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS) + + val MAIN_TITLE_QUALIFIER:Qualifier = OafMapperUtils.qualifier("main title","main title",DNET_DATACITE_TITLE,DNET_DATACITE_TITLE) + + implicit val codec: Codec = Codec("UTF-8") + codec.onMalformedInput(CodingErrorAction.REPLACE) + codec.onUnmappableCharacter(CodingErrorAction.REPLACE) + + val DOI_CLASS = "doi" + val SUBJ_CLASS = "keywords" + + + val j_filter: List[String] = { + val s = Source.fromInputStream(getClass.getResourceAsStream("datacite_filter")).mkString + s.lines.toList + } + + val mapper = new ObjectMapper() + val unknown_repository: HostedByMapType = HostedByMapType(UNKNOWN_REPOSITORY_ORIGINALID, ModelConstants.UNKNOWN_REPOSITORY.getValue, ModelConstants.UNKNOWN_REPOSITORY.getValue, Some(1.0F)) + + val dataInfo: DataInfo = generateDataInfo("0.9") + val DATACITE_COLLECTED_FROM: KeyValue = OafMapperUtils.keyValue(DATACITE_ID, "Datacite") + + val hostedByMap: Map[String, HostedByMapType] = { + val s = Source.fromInputStream(getClass.getResourceAsStream("hostedBy_map.json")).mkString + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: org.json4s.JValue = parse(s) + json.extract[Map[String, HostedByMapType]] + } + + val df_en: DateTimeFormatter = DateTimeFormatter.ofPattern("[MM-dd-yyyy][MM/dd/yyyy][dd-MM-yy][dd-MMM-yyyy][dd/MMM/yyyy][dd-MMM-yy][dd/MMM/yy][dd-MM-yy][dd/MM/yy][dd-MM-yyyy][dd/MM/yyyy][yyyy-MM-dd][yyyy/MM/dd]", Locale.ENGLISH) + val df_it: DateTimeFormatter = DateTimeFormatter.ofPattern("[dd-MM-yyyy][dd/MM/yyyy]", Locale.ITALIAN) + + val funder_regex: List[(Pattern, String)] = List( + (Pattern.compile("(info:eu-repo/grantagreement/ec/h2020/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda__h2020::"), + (Pattern.compile("(info:eu-repo/grantagreement/ec/fp7/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda_______::") + + ) + + val Date_regex: List[Pattern] = List( + //Y-M-D + Pattern.compile("(18|19|20)\\d\\d([- /.])(0[1-9]|1[012])\\2(0[1-9]|[12][0-9]|3[01])", Pattern.MULTILINE), + //M-D-Y + Pattern.compile("((0[1-9]|1[012])|([1-9]))([- /.])(0[1-9]|[12][0-9]|3[01])([- /.])(18|19|20)?\\d\\d", Pattern.MULTILINE), + //D-M-Y + Pattern.compile("(?:(?:31(/|-|\\.)(?:0?[13578]|1[02]|(?:Jan|Mar|May|Jul|Aug|Oct|Dec)))\\1|(?:(?:29|30)(/|-|\\.)(?:0?[1,3-9]|1[0-2]|(?:Jan|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec))\\2))(?:(?:1[6-9]|[2-9]\\d)?\\d{2})|(?:29(/|-|\\.)(?:0?2|(?:Feb))\\3(?:(?:(?:1[6-9]|[2-9]\\d)?(?:0[48]|[2468][048]|[13579][26])|(?:(?:16|[2468][048]|[3579][26])00))))|(?:0?[1-9]|1\\d|2[0-8])(/|-|\\.)(?:(?:0?[1-9]|(?:Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep))|(?:1[0-2]|(?:Oct|Nov|Dec)))\\4(?:(?:1[6-9]|[2-9]\\d)?\\d{2})", Pattern.MULTILINE), + //Y + Pattern.compile("(19|20)\\d\\d", Pattern.MULTILINE) + ) + + + def filter_json(json: String): Boolean = { + j_filter.exists(f => json.contains(f)) + } + + 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 embargo_end(embargo_end_date: String): Boolean = { + val dt = LocalDate.parse(embargo_end_date, DateTimeFormatter.ofPattern("[yyyy-MM-dd]")) + val td = LocalDate.now() + td.isAfter(dt) + } + + + def extract_date(input: String): Option[String] = { + val d = Date_regex.map(pattern => { + val matcher = pattern.matcher(input) + if (matcher.find()) + matcher.group(0) + else + null + } + ).find(s => s != null) + + if (d.isDefined) { + val a_date = if (d.get.length == 4) s"01-01-${d.get}" else d.get + try { + return Some(LocalDate.parse(a_date, df_en).toString) + } catch { + case _: Throwable => try { + return Some(LocalDate.parse(a_date, df_it).toString) + } catch { + case _: Throwable => + return None + } + } + } + d + } + + + def fix_thai_date(input:String, format:String) :String = { + try { + val a_date = LocalDate.parse(input,DateTimeFormatter.ofPattern(format)) + val d = ThaiBuddhistDate.of(a_date.getYear, a_date.getMonth.getValue, a_date.getDayOfMonth) + LocalDate.from(d).toString + } catch { + case _: Throwable => "" + } + } + + def getTypeQualifier(resourceType: String, resourceTypeGeneral: String, schemaOrg: String, vocabularies: VocabularyGroup): (Qualifier, Qualifier) = { + if (resourceType != null && resourceType.nonEmpty) { + val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceType) + if (typeQualifier != null) + return (typeQualifier, vocabularies.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid)) + } + if (schemaOrg != null && schemaOrg.nonEmpty) { + val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, schemaOrg) + if (typeQualifier != null) + return (typeQualifier, vocabularies.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid)) + + } + if (resourceTypeGeneral != null && resourceTypeGeneral.nonEmpty) { + val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceTypeGeneral) + if (typeQualifier != null) + return (typeQualifier, vocabularies.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid)) + + } + null + } + + + def getResult(resourceType: String, resourceTypeGeneral: String, schemaOrg: String, vocabularies: VocabularyGroup): Result = { + val typeQualifiers: (Qualifier, Qualifier) = getTypeQualifier(resourceType, resourceTypeGeneral, schemaOrg, vocabularies) + if (typeQualifiers == null) + return null + val i = new Instance + i.setInstancetype(typeQualifiers._1) + typeQualifiers._2.getClassname match { + case "dataset" => + val r = new OafDataset + r.setInstance(List(i).asJava) + return r + case "publication" => + val r = new Publication + r.setInstance(List(i).asJava) + return r + case "software" => + val r = new Software + r.setInstance(List(i).asJava) + return r + case "other" => + val r = new OtherResearchProduct + r.setInstance(List(i).asJava) + return r + } + null + } + + + def available_date(input: String): Boolean = { + + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: org.json4s.JValue = parse(input) + val l: List[String] = for { + JObject(dates) <- json \\ "dates" + JField("dateType", JString(dateTypes)) <- dates + } yield dateTypes + + l.exists(p => p.equalsIgnoreCase("available")) + + } + + + def OPEN_ACCESS_RIGHT = { + val result = new Qualifier + result.setClassid("OPEN") + result.setClassid("OPEN") + result.setSchemeid(ModelConstants.DNET_ACCESS_MODES) + result.setSchemename(ModelConstants.DNET_ACCESS_MODES) + result + } + + + + /** + * As describe in ticket #6377 + * when the result come from figshare we need to remove subject + * and set Access rights OPEN. + * @param r + */ + def fix_figshare(r: Result): Unit = { + + if (r.getInstance() != null) { + val hosted_by_figshare = r.getInstance().asScala.exists(i => i.getHostedby != null && "figshare".equalsIgnoreCase(i.getHostedby.getValue)) + if (hosted_by_figshare) { + r.getInstance().asScala.foreach(i => i.setAccessright(OPEN_ACCESS_RIGHT)) + val l: List[StructuredProperty] = List() + r.setSubject(l.asJava) + } + } + + + } + + def generateOAFDate(dt: String, q: Qualifier): StructuredProperty = { + OafMapperUtils.structuredProperty(dt, q, null) + } + + def generateRelation(sourceId: String, targetId: String, relClass: String, cf: KeyValue, di: DataInfo): Relation = { + + val r = new Relation + r.setSource(sourceId) + r.setTarget(targetId) + r.setRelType(ModelConstants.RESULT_PROJECT) + r.setRelClass(relClass) + r.setSubRelType(ModelConstants.OUTCOME) + r.setCollectedfrom(List(cf).asJava) + r.setDataInfo(di) + r + + + } + + def get_projectRelation(awardUri: String, sourceId: String): List[Relation] = { + val match_pattern = funder_regex.find(s => s._1.matcher(awardUri).find()) + + if (match_pattern.isDefined) { + val m = match_pattern.get._1 + val p = match_pattern.get._2 + val grantId = m.matcher(awardUri).replaceAll("$2") + val targetId = s"$p${DHPUtils.md5(grantId)}" + List( + generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo), + generateRelation(targetId, sourceId, "produces", DATACITE_COLLECTED_FROM, dataInfo) + ) + } + else + List() + + } + + + def generateOAF(input: String, ts: Long, dateOfCollection: Long, vocabularies: VocabularyGroup): List[Oaf] = { + if (filter_json(input)) + return List() + + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json = parse(input) + + val resourceType = (json \ "attributes" \ "types" \ "resourceType").extractOrElse[String](null) + val resourceTypeGeneral = (json \ "attributes" \ "types" \ "resourceTypeGeneral").extractOrElse[String](null) + val schemaOrg = (json \ "attributes" \ "types" \ "schemaOrg").extractOrElse[String](null) + + val doi = (json \ "attributes" \ "doi").extract[String] + if (doi.isEmpty) + return List() + + //Mapping type based on vocabularies dnet:publication_resource and dnet:result_typologies + val result = getResult(resourceType, resourceTypeGeneral, schemaOrg, vocabularies) + if (result == null) + return List() + + + val doi_q = OafMapperUtils.qualifier("doi", "doi", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES) + val pid = OafMapperUtils.structuredProperty(doi, doi_q, dataInfo) + result.setPid(List(pid).asJava) + result.setId(OafMapperUtils.createOpenaireId(50, s"datacite____::$doi", true)) + result.setOriginalId(List(doi).asJava) + + val d = new Date(dateOfCollection * 1000) + val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US) + + + result.setDateofcollection(ISO8601FORMAT.format(d)) + result.setDateoftransformation(ISO8601FORMAT.format(ts)) + result.setDataInfo(dataInfo) + + val creators = (json \\ "creators").extractOrElse[List[CreatorType]](List()) + + + val authors = creators.zipWithIndex.map { case (c, idx) => + val a = new Author + a.setFullname(c.name.orNull) + a.setName(c.givenName.orNull) + a.setSurname(c.familyName.orNull) + if (c.nameIdentifiers != null && c.nameIdentifiers.isDefined && c.nameIdentifiers.get != null) { + a.setPid(c.nameIdentifiers.get.map(ni => { + val q = if (ni.nameIdentifierScheme.isDefined) vocabularies.getTermAsQualifier(ModelConstants.DNET_PID_TYPES, ni.nameIdentifierScheme.get.toLowerCase()) else null + if (ni.nameIdentifier != null && ni.nameIdentifier.isDefined) { + OafMapperUtils.structuredProperty(ni.nameIdentifier.get, q, dataInfo) + } + else + null + + } + ) + .asJava) + } + if (c.affiliation.isDefined) + a.setAffiliation(c.affiliation.get.filter(af => af.nonEmpty).map(af => OafMapperUtils.field(af, dataInfo)).asJava) + a.setRank(idx + 1) + a + } + + + val titles: List[TitleType] = (json \\ "titles").extractOrElse[List[TitleType]](List()) + + result.setTitle(titles.filter(t => t.title.nonEmpty).map(t => { + if (t.titleType.isEmpty) { + OafMapperUtils.structuredProperty(t.title.get, MAIN_TITLE_QUALIFIER, null) + } else { + OafMapperUtils.structuredProperty(t.title.get, t.titleType.get, t.titleType.get, DNET_DATACITE_TITLE, DNET_DATACITE_TITLE, null) + } + }).asJava) + + if (authors == null || authors.isEmpty || !authors.exists(a => a != null)) + return List() + result.setAuthor(authors.asJava) + + val dates = (json \\ "dates").extract[List[DateType]] + val publication_year = (json \\ "publicationYear").extractOrElse[String](null) + + val i_date = dates + .filter(d => d.date.isDefined && d.dateType.isDefined) + .find(d => d.dateType.get.equalsIgnoreCase("issued")) + .map(d => extract_date(d.date.get)) + val a_date: Option[String] = dates + .filter(d => d.date.isDefined && d.dateType.isDefined && d.dateType.get.equalsIgnoreCase("available")) + .map(d => extract_date(d.date.get)) + .find(d => d != null && d.isDefined) + .map(d => d.get) + + if (a_date.isDefined) { + if(doi.startsWith("10.14457")) + result.setEmbargoenddate(OafMapperUtils.field(fix_thai_date(a_date.get,"[yyyy-MM-dd]"), null)) + else + result.setEmbargoenddate(OafMapperUtils.field(a_date.get, null)) + } + if (i_date.isDefined && i_date.get.isDefined) { + if(doi.startsWith("10.14457")) { + result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get,"[yyyy-MM-dd]"), null)) + result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get,"[yyyy-MM-dd]"), null)) + } + else { + result.setDateofacceptance(OafMapperUtils.field(i_date.get.get, null)) + result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(i_date.get.get, null)) + } + } + else if (publication_year != null) { + if(doi.startsWith("10.14457")) { + result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year","[dd-MM-yyyy]"), null)) + result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year","[dd-MM-yyyy]"), null)) + + } else { + result.setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null)) + result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null)) + } + } + + + result.setRelevantdate(dates.filter(d => d.date.isDefined && d.dateType.isDefined) + .map(d => (extract_date(d.date.get), d.dateType.get)) + .filter(d => d._1.isDefined) + .map(d => (d._1.get, vocabularies.getTermAsQualifier(DNET_DATACITE_DATE, d._2.toLowerCase()))) + .filter(d => d._2 != null) + .map(d => generateOAFDate(d._1, d._2)).asJava) + + val subjects = (json \\ "subjects").extract[List[SubjectType]] + + result.setSubject(subjects.filter(s => s.subject.nonEmpty) + .map(s => + OafMapperUtils.structuredProperty(s.subject.get, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, null) + ).asJava) + + + result.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava) + + val descriptions = (json \\ "descriptions").extract[List[DescriptionType]] + + result.setDescription( + descriptions + .filter(d => d.description.isDefined). + map(d => + OafMapperUtils.field(d.description.get, null) + ).filter(s => s != null).asJava) + + + val publisher = (json \\ "publisher").extractOrElse[String](null) + if (publisher != null) + result.setPublisher(OafMapperUtils.field(publisher, null)) + + + val language: String = (json \\ "language").extractOrElse[String](null) + + if (language != null) + result.setLanguage(vocabularies.getSynonymAsQualifier(ModelConstants.DNET_LANGUAGES, language)) + + + val instance = result.getInstance().get(0) + + val client = (json \ "relationships" \ "client" \\ "id").extractOpt[String] + + val accessRights: List[String] = for { + JObject(rightsList) <- json \\ "rightsList" + JField("rightsUri", JString(rightsUri)) <- rightsList + } yield rightsUri + + val aRights: Option[Qualifier] = accessRights.map(r => { + vocabularies.getSynonymAsQualifier(ModelConstants.DNET_ACCESS_MODES, r) + }).find(q => q != null).map(q => { + val a = new Qualifier + a.setClassid(q.getClassid) + a.setClassname(q.getClassname) + a.setSchemeid(q.getSchemeid) + a.setSchemename(q.getSchemename) + a + }) + + + val access_rights_qualifier = if (aRights.isDefined) aRights.get else OafMapperUtils.qualifier(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE, ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES) + + if (client.isDefined) { + val hb = hostedByMap.getOrElse(client.get.toUpperCase(), unknown_repository) + instance.setHostedby(OafMapperUtils.keyValue(generateDSId(hb.openaire_id), hb.official_name)) + instance.setCollectedfrom(DATACITE_COLLECTED_FROM) + instance.setUrl(List(s"https://dx.doi.org/$doi").asJava) + instance.setAccessright(access_rights_qualifier) + val license = accessRights + .find(r => r.startsWith("http") && r.matches(".*(/licenses|/publicdomain|unlicense\\.org/|/legal-and-data-protection-notices|/download/license|/open-government-licence).*")) + if (license.isDefined) + instance.setLicense(OafMapperUtils.field(license.get, null)) + } + + val awardUris: List[String] = for { + JObject(fundingReferences) <- json \\ "fundingReferences" + JField("awardUri", JString(awardUri)) <- fundingReferences + } yield awardUri + + val relations: List[Relation] = awardUris.flatMap(a => get_projectRelation(a, result.getId)).filter(r => r != null) + fix_figshare(result) + if (relations != null && relations.nonEmpty) { + List(result) ::: relations + } + else + List(result) + } + + def generateDataInfo(trust: String): DataInfo = { + val di = new DataInfo + di.setDeletedbyinference(false) + di.setInferred(false) + di.setInvisible(false) + di.setTrust(trust) + di.setProvenanceaction(PROVENANCE_ACTION_SET_QUALIFIER) + di + } + + def generateDSId(input: String): String = { + val b = StringUtils.substringBefore(input, "::") + val a = StringUtils.substringAfter(input, "::") + s"10|$b::${DHPUtils.md5(a)}" + } + + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala new file mode 100644 index 000000000..c99bfcdb3 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala @@ -0,0 +1,43 @@ +package eu.dnetlib.dhp.actionmanager.datacite +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup +import eu.dnetlib.dhp.schema.oaf.Oaf +import eu.dnetlib.dhp.utils.ISLookupClientFactory +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +import scala.io.Source + +object GenerateDataciteDatasetSpark { + + val log: Logger = LoggerFactory.getLogger(GenerateDataciteDatasetSpark.getClass) + + def main(args: Array[String]): Unit = { + val conf = new SparkConf + val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json")).mkString) + parser.parseArgument(args) + val master = parser.get("master") + val sourcePath = parser.get("sourcePath") + val targetPath = parser.get("targetPath") + val isLookupUrl: String = parser.get("isLookupUrl") + log.info("isLookupUrl: {}", isLookupUrl) + + val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl) + val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService) + val spark: SparkSession = SparkSession.builder().config(conf) + .appName(GenerateDataciteDatasetSpark.getClass.getSimpleName) + .master(master) + .getOrCreate() + + implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] + + import spark.implicits._ + + spark.read.load(sourcePath).as[DataciteType] + .filter(d => d.isActive) + .flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies)) + .filter(d => d != null) + .write.mode(SaveMode.Overwrite).save(targetPath) + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java index 07786d62d..aac5b8345 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java @@ -18,7 +18,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; - import eu.dnetlib.dhp.actionmanager.project.utils.CSVProject; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; @@ -33,7 +32,6 @@ public class PrepareProjects { private static final Logger log = LoggerFactory.getLogger(PrepareProgramme.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/datacite_filter b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/datacite_filter new file mode 100644 index 000000000..ad80d6998 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/datacite_filter @@ -0,0 +1,28 @@ +TUBYDI - Assistir Filmes e Series Online Grátis +123Movies +WATCH FULL MOVIE +Movierulz +Full Movie Online +MOVIé WatcH +The King of Staten Island 2020 Online For Free +Watch Train to Busan 2 2020 online for free +Sixth Sense Movie Novelization +Film Complet streaming vf gratuit en ligne +watch now free +LIVE stream watch +LIVE stream UFC +RBC Heritage live stream +MLBStreams Free +NFL Live Stream +Live Stream Free +Royal Ascot 2020 Live Stream +TV Shows Full Episodes Official +FuboTV +Gomovies +Online Free Trial Access +123watch +DÜŞÜK HAPI +Bebek Düşürme Yöntemleri +WHATSAP İLETİŞİM +Cytotec +düşük hapı \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json new file mode 100644 index 000000000..e2fbe6d90 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "s", + "paramLongName": "sourcePath", + "paramDescription": "the source mdstore path", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target mdstore path", + "paramRequired": true + }, + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "the master name", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "isLookupUrl", + "paramDescription": "the isLookup URL", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/hostedBy_map.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/hostedBy_map.json new file mode 100644 index 000000000..47a0c1ee4 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/hostedBy_map.json @@ -0,0 +1,1032 @@ +{ + "SND.QOG": { + "openaire_id": "re3data_____::r3d100012231", + "datacite_name": "Quality of Government Institute", + "official_name": "Quality of Government Institute's Data", + "similarity": 0.8985507246376812 + }, + "GESIS.CESSDA": { + "openaire_id": "re3data_____::r3d100010202", + "datacite_name": "CESSDA ERIC", + "official_name": "CESSDA ERIC" + }, + "BL.CRAN": { + "openaire_id": "re3data_____::r3d100012068", + "datacite_name": "Cranfield University", + "official_name": "Cranfield Online Research Data" + }, + "SUL.OPENNEURO": { + "openaire_id": "re3data_____::r3d100010924", + "datacite_name": "OpenNeuro", + "official_name": "OpenNeuro" + }, + "UNAVCO.UNAVCO": { + "openaire_id": "re3data_____::r3d100010872", + "datacite_name": "UNAVCO", + "official_name": "UNAVCO" + }, + "SUL.SDR": { + "openaire_id": "re3data_____::r3d100010710", + "datacite_name": "Stanford Digital Repository", + "official_name": "Stanford Digital Repository" + }, + "DK.ICES": { + "openaire_id": "re3data_____::r3d100011288", + "datacite_name": "International Council for the Exploration of the Sea (ICES)", + "official_name": "International Council for the Exploration of the Sea datasets", + "similarity": 0.8833333333333333 + }, + "CISTI.DFOSCIMR": { + "openaire_id": "re3data_____::r3d100012039", + "datacite_name": "Bedford Institute of Oceanography - Fisheries and Oceans Canada - Ocean Data and Information Section", + "official_name": "Bedford Institute of Oceanography - Oceanographic Databases" + }, + "CSIC.DIGITAL": { + "openaire_id": "re3data_____::r3d100011076", + "datacite_name": "Digital CSIC", + "official_name": "DIGITAL.CSIC" + }, + "TIB.PANGAEA": { + "openaire_id": "re3data_____::r3d100010134", + "datacite_name": "PANGAEA", + "official_name": "PANGAEA" + }, + "PSU.DATACOM": { + "openaire_id": "re3data_____::r3d100010477", + "datacite_name": "Data Commons", + "official_name": "ANU Data Commons", + "similarity": 0.8571428571428571 + }, + "ANDS.CENTRE72": { + "openaire_id": "re3data_____::r3d100010451", + "datacite_name": "PARADISEC", + "official_name": "Pacific and Regional Archive for Digital Sources in Endangered Cultures" + }, + "BL.OXDB": { + "openaire_id": "re3data_____::r3d100011653", + "datacite_name": "Oxford University Library Service Databank", + "official_name": "DataBank, Bodleian Libraries, University of Oxford" + }, + "BL.STANDREW": { + "openaire_id": "re3data_____::r3d100012411", + "datacite_name": "University of St Andrews", + "official_name": "St Andrews Research portal - Research Data" + }, + "TIB.BAFG": { + "openaire_id": "re3data_____::r3d100011664", + "datacite_name": "Bundesanstalt für Gewässerkunde", + "official_name": "Geoportal der BFG" + }, + "CRUI.UNIBO": { + "openaire_id": "re3data_____::r3d100012604", + "datacite_name": "Università degli Studi di Bologna", + "official_name": "AMS Acta" + }, + "GDCC.ODUM-LIBRARY": { + "openaire_id": "re3data_____::r3d100000005", + "datacite_name": "UNC Libraries", + "official_name": "UNC Dataverse" + }, + "RG.RG": { + "openaire_id": "re3data_____::r3d100012227", + "datacite_name": "ResearchGate", + "official_name": "ResearchGate" + }, + "TIB.EUMETSAT": { + "openaire_id": "re3data_____::r3d100010232", + "datacite_name": "EUMETSAT", + "official_name": "Eumetsat" + }, + "SND.SMHI": { + "openaire_id": "re3data_____::r3d100011776", + "datacite_name": "Swedish Meteorological and Hydrological Institute open data", + "official_name": "Swedish Meteorological and Hydrological Institute open data" + }, + "NOAA.NCEI": { + "openaire_id": "re3data_____::r3d100011801", + "datacite_name": "National Oceanic and Atmospheric Administration (NOAA) National Centers for Environmental Information (NCEI)", + "official_name": "NCEI" + }, + "TIB.WDCC": { + "openaire_id": "re3data_____::r3d100010299", + "datacite_name": "World Data Center for Climate", + "official_name": "World Data Center for Climate" + }, + "CNGB.GIGADB": { + "openaire_id": "re3data_____::r3d100010478", + "datacite_name": "GigaDB", + "official_name": "GigaDB" + }, + "DELFT.VLIZ": { + "openaire_id": "re3data_____::r3d100010661", + "datacite_name": "Vlaams Instituut voor de Zee", + "official_name": "Flanders Marine Institute" + }, + "NUS.SB": { + "openaire_id": "re3data_____::r3d100012564", + "datacite_name": "National University of Singapore", + "official_name": "ScholarBank@NUS" + }, + "EDI.EDI": { + "openaire_id": "re3data_____::r3d100010272", + "datacite_name": "Environmental Data Initiative", + "official_name": "Environmental Data Initiative Repository" + }, + "INIST.ADISP": { + "openaire_id": "re3data_____::r3d100010494", + "datacite_name": "Quetelet PROGEDO Diffusion", + "official_name": "Quetelet PROGEDO Diffusion" + }, + "GESIS.SHARE": { + "openaire_id": "re3data_____::r3d100010430", + "datacite_name": "SHARE - ERIC", + "official_name": "Survey of Health, Ageing and Retirement in Europe" + }, + "ANDS.CENTRE-1": { + "openaire_id": "re3data_____::r3d100010864", + "datacite_name": "Griffith University", + "official_name": "Griffith University Research Data Repository" + }, + "BL.READING": { + "openaire_id": "re3data_____::r3d100012064", + "datacite_name": "University of Reading", + "official_name": "University of Reading Research Data Archive" + }, + "CORNELL.CISER": { + "openaire_id": "re3data_____::r3d100011056", + "datacite_name": "CISER Data Archive", + "official_name": "CISER Data Archive" + }, + "DRYAD.DRYAD": { + "openaire_id": "re3data_____::r3d100000044", + "datacite_name": "DRYAD", + "official_name": "DRYAD" + }, + "CDL.PISCO": { + "openaire_id": "re3data_____::r3d100010947", + "datacite_name": "Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO)", + "official_name": "Partnership for Interdisciplinary Studies of Coastal Oceans" + }, + "IEEE.DATAPORT": { + "openaire_id": "re3data_____::r3d100012569", + "datacite_name": "IEEE DataPort", + "official_name": "IEEE DataPort" + }, + "DELFT.MAASTRO": { + "openaire_id": "re3data_____::r3d100011086", + "datacite_name": "MAASTRO Clinic", + "official_name": "CancerData.org" + }, + "USGS.PROD": { + "openaire_id": "re3data_____::r3d100010054", + "datacite_name": "USGS DOI Tool Production Environment", + "official_name": "U.S. Geological Survey" + }, + "GDCC.ODUM-DV": { + "openaire_id": "re3data_____::r3d100000005", + "datacite_name": "Odum Institute Dataverse", + "official_name": "UNC Dataverse" + }, + "CDL.SDSCSG": { + "openaire_id": "re3data_____::r3d100011690", + "datacite_name": "UCSD Signaling Gateway", + "official_name": "UCSD Signaling gateway" + }, + "ORBIS.NKN": { + "openaire_id": "re3data_____::r3d100011587", + "datacite_name": "Northwest Knowledge Network", + "official_name": "Northwest Knowledge Network" + }, + "ANDS.CENTRE63": { + "openaire_id": "re3data_____::r3d100010918", + "datacite_name": "Test: Atlas of Living Australia", + "official_name": "Atlas of Living Australia", + "similarity": 0.8928571428571429 + }, + "SML.TALKBANK": { + "openaire_id": "re3data_____::r3d100010887", + "datacite_name": "TalkBank", + "official_name": "TalkBank" + }, + "CORNELL.LIBRARY": { + "openaire_id": "re3data_____::r3d100012322", + "datacite_name": "Cornell University Library", + "official_name": "eCommons - Cornell's digital repository" + }, + "BL.SOTON": { + "openaire_id": "re3data_____::r3d100011245", + "datacite_name": "University of Southampton", + "official_name": "University of Southampton Institutional Research Repository" + }, + "GESIS.DB-BANK": { + "openaire_id": "re3data_____::r3d100012252", + "datacite_name": "Forschungsdaten- und Servicezentrum der Bundesbank", + "official_name": "Forschungsdaten- und Servicezentrum der Bundesbank" + }, + "ANDS.CENTRE68": { + "openaire_id": "re3data_____::r3d100010918", + "datacite_name": "Atlas of Living Australia", + "official_name": "Atlas of Living Australia" + }, + "ANDS.CENTRE69": { + "openaire_id": "re3data_____::r3d100010914", + "datacite_name": "Australian Ocean Data Network", + "official_name": "Australian Ocean Data Network Portal" + }, + "INIST.CDS": { + "openaire_id": "re3data_____::r3d100010584", + "datacite_name": "Strasbourg Astronomical Data Center", + "official_name": "Strasbourg Astronomical Data Center" + }, + "BL.NHM": { + "openaire_id": "re3data_____::r3d100011675", + "datacite_name": "Natural History Museum, London", + "official_name": "Natural History Museum, Data Portal" + }, + "BL.ADS": { + "openaire_id": "re3data_____::r3d100000006", + "datacite_name": "Archaeology Data Service", + "official_name": "Archaeology Data Service" + }, + "GDCC.JHU": { + "openaire_id": "re3data_____::r3d100011836", + "datacite_name": "Johns Hopkins University Library", + "official_name": "Johns Hopkins Data Archive Dataverse Network" + }, + "BL.ED": { + "openaire_id": "re3data_____::r3d100000047", + "datacite_name": "University of Edinburgh", + "official_name": "Edinburgh DataShare" + }, + "BL.EXETER": { + "openaire_id": "re3data_____::r3d100011202", + "datacite_name": "University of Exeter", + "official_name": "Open Research Exeter" + }, + "BL.NCL": { + "openaire_id": "re3data_____::r3d100012408", + "datacite_name": "Newcastle University", + "official_name": "NCL Data" + }, + "BROWN.BDR": { + "openaire_id": "re3data_____::r3d100011654", + "datacite_name": "Brown Digital Repository", + "official_name": "Brown Digital Repository" + }, + "GDCC.SYR-QDR": { + "openaire_id": "re3data_____::r3d100011038", + "datacite_name": "Syracuse University Qualitative Data Repository", + "official_name": "Qualitative Data Repository" + }, + "BL.BRISTOL": { + "openaire_id": "re3data_____::r3d100011099", + "datacite_name": "University of Bristol", + "official_name": "data.bris Research Data Repository" + }, + "DATACITE.DATACITE": { + "openaire_id": "openaire____::datacite", + "datacite_name": "DataCite", + "official_name": "Datacite" + }, + "ESTDOI.KEEL": { + "openaire_id": "re3data_____::r3d100011941", + "datacite_name": "Keeleressursid. The Center of Estonian Language Resources", + "official_name": "Center of Estonian Language Resources" + }, + "BL.ESSEX": { + "openaire_id": "re3data_____::r3d100012405", + "datacite_name": "University of Essex", + "official_name": "Research Data at Essex" + }, + "PURDUE.MDF": { + "openaire_id": "re3data_____::r3d100012080", + "datacite_name": "Univ Chicago Materials Data Facility", + "official_name": "Materials Data Facility" + }, + "DELFT.KNMI": { + "openaire_id": "re3data_____::r3d100011879", + "datacite_name": "KNMI Data Centre", + "official_name": "KNMI Data Centre" + }, + "CUL.CIESIN": { + "openaire_id": "re3data_____::r3d100010207", + "datacite_name": "Center for International Earth Science Information Network", + "official_name": "Center for International Earth Science Information Network" + }, + "WISC.NEOTOMA": { + "openaire_id": "re3data_____::r3d100011761", + "datacite_name": "Neotoma Paleoecological Database", + "official_name": "Neotoma Paleoecology Database", + "similarity": 0.9180327868852459 + }, + "IRIS.IRIS": { + "openaire_id": "re3data_____::r3d100010268", + "datacite_name": "Incorporated Research Institutions for Seismology", + "official_name": "Incorporated Research Institutions for Seismology" + }, + "ANDS.CENTRE50": { + "openaire_id": "re3data_____::r3d100012378", + "datacite_name": "Analysis and Policy Observatory", + "official_name": "Analysis and Policy Observatory" + }, + "FAO.RING": { + "openaire_id": "re3data_____::r3d100012571", + "datacite_name": "CIARD RING", + "official_name": "CIARD Ring" + }, + "CUL.R2R": { + "openaire_id": "re3data_____::r3d100010735", + "datacite_name": "Rolling Deck to Repository", + "official_name": "Rolling Deck to Repository" + }, + "DEMO.GRIIDC": { + "openaire_id": "re3data_____::r3d100011571", + "datacite_name": "Gulf of Mexico Research Initiative Information and Data Cooperative", + "official_name": "Gulf of Mexico Research Initiative Information and Data Cooperative" + }, + "ANDS.CENTRE-6": { + "openaire_id": "re3data_____::r3d100012268", + "datacite_name": "Curtin University", + "official_name": "Curtin University Research Data Collection" + }, + "ANDS.CENTRE-5": { + "openaire_id": "re3data_____::r3d100012013", + "datacite_name": "TERN Central Portal", + "official_name": "TERN Data Discovery portal" + }, + "FIGSHARE.UCT": { + "openaire_id": "re3data_____::r3d100012633", + "datacite_name": "University of Cape Town (UCT)", + "official_name": "ZivaHub" + }, + "BIBSYS.UIT-ORD": { + "openaire_id": "re3data_____::r3d100012538", + "datacite_name": "DataverseNO", + "official_name": "DataverseNO" + }, + "CISTI.CADC": { + "openaire_id": "re3data_____::r3d100000016", + "datacite_name": "Canadian Astronomy Data Centre", + "official_name": "The Canadian Astronomy Data Centre", + "similarity": 0.9375 + }, + "BL.CCDC": { + "openaire_id": "re3data_____::r3d100010197", + "datacite_name": "The Cambridge Crystallographic Data Centre", + "official_name": "The Cambridge Structural Database" + }, + "BL.UCLD": { + "openaire_id": "re3data_____::r3d100012417", + "datacite_name": "University College London", + "official_name": "UCL Discovery" + }, + "GESIS.RKI": { + "openaire_id": "re3data_____::r3d100010436", + "datacite_name": "'Health Monitoring' Research Data Centre at the Robert Koch Institute", + "official_name": "'Health Monitoring' Research Data Centre at the Robert Koch Institute" + }, + "BL.DRI": { + "openaire_id": "re3data_____::r3d100011805", + "datacite_name": "Digital Repository of Ireland", + "official_name": "Digital Repository of Ireland" + }, + "TIB.KIT-IMK": { + "openaire_id": "re3data_____::r3d100011956", + "datacite_name": "Institute for Meteorology and Climate Research - Atmospheric Trace Gases and Remote Sensing", + "official_name": "CARIBIC" + }, + "DOINZ.LANDCARE": { + "openaire_id": "re3data_____::r3d100011662", + "datacite_name": "Landcare Research New Zealand Ltd", + "official_name": "Landcare Research Data Repository" + }, + "DEMO.EMORY": { + 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Atmosphere", + "similarity": 0.9642857142857143 + }, + "ZBMED.DSMZ": { + "openaire_id": "re3data_____::r3d100010219", + "datacite_name": "DSMZ", + "official_name": "DSMZ" + }, + "DOINZ.NZAU": { + "openaire_id": "re3data_____::r3d100012110", + "datacite_name": "University of Auckland Data Publishing and Discovery Service", + "official_name": "University of Auckland Data Repository" + }, + "INIST.RESIF": { + "openaire_id": "re3data_____::r3d100012222", + "datacite_name": "Réseau sismologique et géodésique français", + "official_name": "RESIF Seismic Data Portal" + }, + "CDL.NCEAS": { + "openaire_id": "re3data_____::r3d100010093", + "datacite_name": "National Center for Ecological Analysis and Synthesis (NCEAS)", + "official_name": "National Center for Ecological Analysis and Synthesis Data Repository" + }, + "ZBMED.EMP": { + "openaire_id": "re3data_____::r3d100010234", + "datacite_name": "eyeMoviePedia", + "official_name": "eyeMoviePedia" + }, + "ZBMED.BIOFRESH": { + "openaire_id": "re3data_____::r3d100011651", + "datacite_name": "Project BioFresh, Leibniz-Institute of Freshwater Ecology and Inland Fisheries", + "official_name": "Freshwater Biodiversity Data Portal" + }, + "INIST.IFREMER": { + "openaire_id": "re3data_____::r3d100011867", + "datacite_name": "Institut Français de Recherche pour l'Exploitation de la Mer", + "official_name": "SEANOE" + }, + "ETHZ.SICAS": { + "openaire_id": "re3data_____::r3d100011560", + "datacite_name": "SICAS", + "official_name": "Sicas Medical Image Repository" + }, + "SND.SND": { + "openaire_id": "re3data_____::r3d100010146", + "datacite_name": "Swedish National Data Service", + "official_name": "Swedish National Data Service" + }, + "DELFT.EASY": { + "openaire_id": "re3data_____::r3d100011201", + "datacite_name": "DANS", + "official_name": "DataverseNL" + }, + "WH.WHOAS": { + "openaire_id": "re3data_____::r3d100010423", + "datacite_name": "Woods Hole Open Access Server", + "official_name": "Woods Hole Open Access Server" + }, + "DATACITE.UCSC": { + "openaire_id": "re3data_____::r3d100010243", + "datacite_name": "UCSC Genome Browser", + "official_name": "UCSC Genome Browser" + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/config-default.xml new file mode 100644 index 000000000..dd3c32c62 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/config-default.xml @@ -0,0 +1,23 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml new file mode 100644 index 000000000..1851c815f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml @@ -0,0 +1,46 @@ + + + + mainPath + the working path of Datacite stores + + + isLookupUrl + The IS lookUp service endopoint + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn-cluster + cluster + TransformJob + eu.dnetlib.dhp.actionmanager.datacite.GenerateDataciteDatasetSpark + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${mainPath}/datacite_dump + --targetPath${mainPath}/datacite_oaf_production + --isLookupUrl${isLookupUrl} + --masteryarn-cluster + + + + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dentlib/dhp/aggregation/AbstractVocabularyTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dentlib/dhp/aggregation/AbstractVocabularyTest.java new file mode 100644 index 000000000..1340af22e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dentlib/dhp/aggregation/AbstractVocabularyTest.java @@ -0,0 +1,42 @@ +package eu.dentlib.dhp.aggregation; +import static org.mockito.Mockito.lenient; + +import java.io.IOException; +import java.util.Collections; +import java.util.List; +import java.util.Objects; + +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; +import org.apache.commons.io.IOUtils; +import org.mockito.Mock; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +public abstract class AbstractVocabularyTest { + + @Mock + protected ISLookUpService isLookUpService; + + protected VocabularyGroup vocabularies; + + public void setUpVocabulary() throws ISLookUpException, IOException { + lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); + + lenient() + .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) + .thenReturn(synonyms()); + vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService); + } + + private static List vocs() throws IOException { + return IOUtils + .readLines(Objects.requireNonNull(AbstractVocabularyTest.class.getResourceAsStream("/eu/dnetlib/dhp/vocabulary/terms.txt"))); + } + + private static List synonyms() throws IOException { + return IOUtils + .readLines(Objects.requireNonNull(AbstractVocabularyTest.class.getResourceAsStream("/eu/dnetlib/dhp/vocabulary/synonyms.txt"))); + } + + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala new file mode 100644 index 000000000..aa57d470a --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala @@ -0,0 +1,43 @@ +package eu.dnetlib.dhp.actionmanager.datacite + + +import eu.dentlib.dhp.aggregation.AbstractVocabularyTest +import eu.dnetlib.dhp.schema.oaf.Oaf +import org.junit.jupiter.api.extension.ExtendWith +import org.junit.jupiter.api.{BeforeEach, Test} +import org.mockito.junit.jupiter.MockitoExtension +import org.codehaus.jackson.map.ObjectMapper + +import scala.io.Source + +@ExtendWith(Array(classOf[MockitoExtension])) +class DataciteToOAFTest extends AbstractVocabularyTest{ + + + @BeforeEach + def setUp() :Unit = { + + super.setUpVocabulary() + } + + @Test + def testMapping() :Unit = { + val record =Source.fromInputStream(getClass.getResourceAsStream("datacite.json")).mkString + + + + val mapper = new ObjectMapper() + val res:List[Oaf] =DataciteToOAFTransformation.generateOAF(record, 0L,0L, vocabularies ) + println (mapper.defaultPrettyPrintingWriter().writeValueAsString(res.head)) + + + } + @Test + def testDate():Unit = { + + println(DataciteToOAFTransformation.fix_thai_date("01-01-2561","[dd-MM-yyyy]")) + println(DataciteToOAFTransformation.fix_thai_date("2561-01-01","[yyyy-MM-dd]")) + + } + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/datacite.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/datacite.json new file mode 100644 index 000000000..cd1ccca1d --- /dev/null +++ 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Academic Graph Identifier +dnet:pid_types @=@ dnet:pid_types @=@ oai @=@ Open Archives Initiative +dnet:pid_types @=@ dnet:pid_types @=@ orcid @=@ Open Researcher and Contributor ID +dnet:pid_types @=@ dnet:pid_types @=@ PANGAEA @=@ PANGAEA +dnet:pid_types @=@ dnet:pid_types @=@ epo_nr_epodoc @=@ Patent application number in EPODOC format +dnet:pid_types @=@ dnet:pid_types @=@ UNKNOWN @=@ UNKNOWN +dnet:pid_types @=@ dnet:pid_types @=@ VIAF @=@ Virtual International Authority File +dnet:pid_types @=@ dnet:pid_types @=@ arXiv @=@ arXiv +dnet:pid_types @=@ dnet:pid_types @=@ doi @=@ doi +dnet:pid_types @=@ dnet:pid_types @=@ grid @=@ grid +dnet:pid_types @=@ dnet:pid_types @=@ info:eu-repo/dai @=@ info:eu-repo/dai +dnet:pid_types @=@ dnet:pid_types @=@ orcidworkid @=@ orcid workid +dnet:pid_types @=@ dnet:pid_types @=@ pmc @=@ pmc +dnet:pid_types @=@ dnet:pid_types @=@ pmid @=@ pmid +dnet:pid_types @=@ dnet:pid_types @=@ urn @=@ urn +dnet:pid_types @=@ dnet:pid_types @=@ who @=@ WHO Identifier +dnet:pid_types @=@ dnet:pid_types @=@ drks @=@ DRKS Identifier +dnet:pid_types @=@ dnet:pid_types @=@ handle @=@ Handle +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/ACM @=@ An ACM classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/ARXIV @=@ An ARXIV classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/DDC @=@ A Dewey Decimal classification term (DDC) that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/JEL @=@ A Journal of Economic Literature (JEL) classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/OPENACCESS_VERSION @=@ An Open Access versions of your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_REFERENCED_BY @=@ A dataset referenced by your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/REFERENCES @=@ A dataset that refers to your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_RELATED_TO @=@ A dataset related to your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_TO @=@ A dataset that supplements your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PUBLICATION/IS_RELATED_TO @=@ A publication related to your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PUBLICATION/REFERENCES @=@ A publication referenced by your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PUBLICATION/IS_REFERENCED_BY @=@ A publication that refers to your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_BY @=@ A publication that is supplemented by your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_TO @=@ A publication that supplements your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SOFTWARE @=@ A software referred by your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/OPENACCESS_VERSION @=@ Another Open Access version of a publication +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/PID @=@ Another persistent identifier associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/MESHEUROPMC @=@ A classification term from the Medical Subject Headings (MeSH) that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/ABSTRACT @=@ An abstract describing among your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PUBLICATION_DATE @=@ A date of publication missing in your content +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PID @=@ A persistent identifier associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/ACM @=@ Another ACM classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/ARXIV @=@ Another ARXIV classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/DDC @=@ Another Dewey Decimal classification term (DDC) that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/JEL @=@ Another Journal of Economic Literature (JEL) classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/MESHEUROPMC @=@ Another classification term from the Medical Subject Headings (MeSH) that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PROJECT @=@ A project reference that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_BY @=@ A dataset that is supplemented by your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/AUTHOR/ORCID @=@ An Open Researcher and Contributor ID (ORCID) that can be associated to an author of your publications +dnet:review_levels @=@ dnet:review_levels @=@ 0000 @=@ Unknown +dnet:review_levels @=@ dnet:review_levels @=@ 0002 @=@ nonPeerReviewed +dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed \ No newline at end of file From 42ff7a5665d9f0c3064c5b8573220ec40863fc9a Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 10 Jun 2021 14:31:06 +0200 Subject: [PATCH 2/8] some fix to the pom to compile scala --- dhp-workflows/dhp-aggregation/pom.xml | 37 +++++++++++--- .../datacite/oozie_app/workflow.xml | 2 +- .../aggregation/AbstractVocabularyTest.java | 48 +++++++++++-------- 3 files changed, 60 insertions(+), 27 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index dc8e5b20b..b202abccf 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -7,6 +7,37 @@ 1.2.4-SNAPSHOT dhp-aggregation + + + + + net.alchim31.maven + scala-maven-plugin + 4.0.1 + + + scala-compile-first + initialize + + add-source + compile + + + + scala-test-compile + process-test-resources + + testCompile + + + + + ${scala.version} + + + + + @@ -24,12 +55,6 @@ eu.dnetlib.dhp dhp-common ${project.version} - - - com.sun.xml.bind - jaxb-core - - diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml index 1851c815f..48c05d56a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml @@ -34,7 +34,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --sourcePath${mainPath}/datacite_dump - --targetPath${mainPath}/datacite_oaf_production + --targetPath${mainPath}/production/datacite_oaf --isLookupUrl${isLookupUrl} --masteryarn-cluster diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dentlib/dhp/aggregation/AbstractVocabularyTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dentlib/dhp/aggregation/AbstractVocabularyTest.java index 1340af22e..ff507c3d0 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dentlib/dhp/aggregation/AbstractVocabularyTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dentlib/dhp/aggregation/AbstractVocabularyTest.java @@ -1,4 +1,6 @@ + package eu.dentlib.dhp.aggregation; + import static org.mockito.Mockito.lenient; import java.io.IOException; @@ -6,37 +8,43 @@ import java.util.Collections; import java.util.List; import java.util.Objects; -import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import org.apache.commons.io.IOUtils; import org.mockito.Mock; + +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public abstract class AbstractVocabularyTest { - @Mock - protected ISLookUpService isLookUpService; + @Mock + protected ISLookUpService isLookUpService; - protected VocabularyGroup vocabularies; + protected VocabularyGroup vocabularies; - public void setUpVocabulary() throws ISLookUpException, IOException { - lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); + public void setUpVocabulary() throws ISLookUpException, IOException { + lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); - lenient() - .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) - .thenReturn(synonyms()); - vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService); - } + lenient() + .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) + .thenReturn(synonyms()); + vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService); + } - private static List vocs() throws IOException { - return IOUtils - .readLines(Objects.requireNonNull(AbstractVocabularyTest.class.getResourceAsStream("/eu/dnetlib/dhp/vocabulary/terms.txt"))); - } - - private static List synonyms() throws IOException { - return IOUtils - .readLines(Objects.requireNonNull(AbstractVocabularyTest.class.getResourceAsStream("/eu/dnetlib/dhp/vocabulary/synonyms.txt"))); - } + private static List vocs() throws IOException { + return IOUtils + .readLines( + Objects + .requireNonNull( + AbstractVocabularyTest.class.getResourceAsStream("/eu/dnetlib/dhp/vocabulary/terms.txt"))); + } + private static List synonyms() throws IOException { + return IOUtils + .readLines( + Objects + .requireNonNull( + AbstractVocabularyTest.class.getResourceAsStream("/eu/dnetlib/dhp/vocabulary/synonyms.txt"))); + } } From 9ca438d9b1ab2ebee9896b94b3544cb0bfac87f8 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 10 Jun 2021 14:59:45 +0200 Subject: [PATCH 3/8] imported from branch stable_ids generation of Actionset datacite --- .../datacite/ExportActionSetJobNode.scala | 40 ++++++++++++++++ .../datacite/exportDataset_parameters.json | 21 +++++++++ .../oozie_app/config-default.xml | 23 ++++++++++ .../datacite_export/oozie_app/workflow.xml | 46 +++++++++++++++++++ 4 files changed, 130 insertions(+) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala new file mode 100644 index 000000000..42241c773 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala @@ -0,0 +1,40 @@ +package eu.dnetlib.dhp.actionmanager.datacite +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.Oaf +import org.apache.hadoop.io.Text +import org.apache.hadoop.io.compress.GzipCodec +import org.apache.hadoop.mapred.SequenceFileOutputFormat +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +import scala.io.Source + +object ExportActionSetJobNode { + + val log: Logger = LoggerFactory.getLogger(ExportActionSetJobNode.getClass) + + def main(args: Array[String]): Unit = { + val conf = new SparkConf + val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json")).mkString) + parser.parseArgument(args) + val master = parser.get("master") + val sourcePath = parser.get("sourcePath") + val targetPath = parser.get("targetPath") + + val spark: SparkSession = SparkSession.builder().config(conf) + .appName(ExportActionSetJobNode.getClass.getSimpleName) + .master(master) + .getOrCreate() + implicit val resEncoder: 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 =>DataciteToOAFTransformation.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]) + + + } + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json new file mode 100644 index 000000000..63e080337 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json @@ -0,0 +1,21 @@ +[ + { + "paramName": "s", + "paramLongName": "sourcePath", + "paramDescription": "the source mdstore path", + "paramRequired": true + }, + + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target mdstore path", + "paramRequired": true + }, + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "the master name", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/config-default.xml new file mode 100644 index 000000000..dd3c32c62 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/config-default.xml @@ -0,0 +1,23 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/workflow.xml new file mode 100644 index 000000000..c4c260b96 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/workflow.xml @@ -0,0 +1,46 @@ + + + + sourcePath + the working path of Datacite stores + + + outputPath + the path of Datacite ActionSet + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + yarn-cluster + cluster + ExportDataset + eu.dnetlib.dhp.actionmanager.datacite.ExportActionSetJobNode + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${sourcePath} + --targetPath${outputPath} + --masteryarn-cluster + + + + + + + From 6208b04f1d8518e10bee49eff3d417aa6d58a336 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 16 Jun 2021 14:56:26 +0200 Subject: [PATCH 4/8] smarter DatePicker for ISO dates on dateofacceptance --- .../eu/dnetlib/dhp/oa/dedup/DatePicker.java | 3 +- .../dnetlib/dhp/oa/dedup/DatePickerTest.java | 44 +++++++++++++++++++ 2 files changed, 46 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatePickerTest.java diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DatePicker.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DatePicker.java index 70fb2cc5b..3a789c14c 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DatePicker.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DatePicker.java @@ -18,7 +18,7 @@ import eu.dnetlib.dhp.schema.oaf.Field; public class DatePicker { - private static final String DATE_PATTERN = "\\d{4}-\\d{2}-\\d{2}"; + private static final String DATE_PATTERN = "^(\\d{4})-(\\d{2})-(\\d{2})"; private static final String DATE_DEFAULT_SUFFIX = "01-01"; private static final int YEAR_LB = 1300; private static final int YEAR_UB = Year.now().getValue() + 5; @@ -28,6 +28,7 @@ public class DatePicker { final Map frequencies = dateofacceptance .parallelStream() .filter(StringUtils::isNotBlank) + .map(d -> substringBefore(d, "T")) .collect(Collectors.toConcurrentMap(w -> w, w -> 1, Integer::sum)); if (frequencies.isEmpty()) { diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatePickerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatePickerTest.java new file mode 100644 index 000000000..7c58c375a --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatePickerTest.java @@ -0,0 +1,44 @@ + +package eu.dnetlib.dhp.oa.dedup; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.util.Collection; + +import org.junit.jupiter.api.Test; + +import com.clearspring.analytics.util.Lists; + +public class DatePickerTest { + + Collection dates = Lists.newArrayList(); + + @Test + public void testPickISO() { + dates.add("2016-01-01T12:00:00Z"); + dates.add("2016-06-16T12:00:00Z"); + dates.add("2020-01-01T12:00:00Z"); + dates.add("2020-10-01T12:00:00Z"); + assertEquals("2020-10-01", DatePicker.pick(dates).getValue()); + } + + @Test + public void testPickSimple() { + dates.add("2016-01-01"); + dates.add("2016-06-16"); + dates.add("2020-01-01"); + dates.add("2020-10-01"); + assertEquals("2020-10-01", DatePicker.pick(dates).getValue()); + } + + @Test + public void testPickFrequent() { + dates.add("2016-02-01"); + dates.add("2016-02-01"); + dates.add("2016-02-01"); + dates.add("2020-10-01"); + assertEquals("2016-02-01", DatePicker.pick(dates).getValue()); + } + +} From a3948c1f6eeb958cb66a5fe212b8055c33a4ccff Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 18 Jun 2021 15:14:08 +0200 Subject: [PATCH 5/8] cleanup old doiboost workflows --- .../dhp/doiboost/oozie_app/config-default.xml | 42 -- .../dhp/doiboost/oozie_app/workflow.xml | 372 ------------------ 2 files changed, 414 deletions(-) delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml deleted file mode 100644 index 508202e30..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - oozie.launcher.mapreduce.user.classpath.first - true - - - hive_metastore_uris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - spark2YarnHistoryServerAddress - http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 - - - spark2EventLogDir - /user/spark/spark2ApplicationHistory - - - spark2ExtraListeners - "com.cloudera.spark.lineage.NavigatorAppListener" - - - spark2SqlQueryExecutionListeners - "com.cloudera.spark.lineage.NavigatorQueryListener" - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml deleted file mode 100644 index 77aa595f5..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml +++ /dev/null @@ -1,372 +0,0 @@ - - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorIntersectionMemory - memory for individual executor - - - - sparkExecutorCores - number of cores used by single executor - - - - - - workingPath - the working Path - - - - hostedByMapPath - the hostedByMap Path - - - outputPath - the Path of the sequence file action set - - - - - - inputPathCrossref - the Crossref input path - - - crossrefTimestamp - Timestamp for the Crossref incremental Harvesting - - - esServer - elasticsearch server url for the Crossref Harvesting - - - esIndex - elasticsearch index name for the Crossref Harvesting - - - - - MAGDumpPath - the MAG dump working path - - - - inputPathMAG - the MAG working path - - - - - - inputPathUnpayWall - the UnpayWall working path - - - - - inputPathOrcid - the ORCID input path - - - - workingPathOrcid - the ORCID working path - - - - - - ${jobTracker} - ${nameNode} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - ${wf:conf('resumeFrom') eq 'ConvertCrossrefToOAF'} - ${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'} - ${wf:conf('resumeFrom') eq 'PreprocessMag'} - ${wf:conf('resumeFrom') eq 'PreprocessUW'} - ${wf:conf('resumeFrom') eq 'PreprocessORCID'} - ${wf:conf('resumeFrom') eq 'CreateDOIBoost'} - ${wf:conf('resumeFrom') eq 'GenerateActionSet'} - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - eu.dnetlib.doiboost.crossref.CrossrefImporter - --targetPath${inputPathCrossref}/index_update - --namenode${nameNode} - --esServer${esServer} - --esIndex${esIndex} - --timestamp${crossrefTimestamp} - - - - - - - - - - - yarn-cluster - cluster - GenerateCrossrefDataset - eu.dnetlib.doiboost.crossref.CrossrefDataset - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --workingPath${inputPathCrossref} - --masteryarn-cluster - - - - - - - - - - - - - - - - - - - - - - - - - - - - - yarn-cluster - cluster - Convert Mag to Dataset - eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${MAGDumpPath} - --targetPath${inputPathMAG}/dataset - --masteryarn-cluster - - - - - - - - - yarn-cluster - cluster - ConvertCrossrefToOAF - eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${inputPathCrossref}/crossref_ds - --targetPath${workingPath} - --masteryarn-cluster - - - - - - - - yarn-cluster - cluster - Convert Mag to OAF Dataset - eu.dnetlib.doiboost.mag.SparkProcessMAG - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorIntersectionMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${inputPathMAG}/dataset - --workingPath${inputPathMAG}/process - --targetPath${workingPath} - --masteryarn-cluster - - - - - - - - - - yarn-cluster - cluster - Convert UnpayWall to Dataset - eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${inputPathUnpayWall}/uw_extracted - --targetPath${workingPath}/uwPublication - --masteryarn-cluster - - - - - - - - - yarn-cluster - cluster - Convert ORCID to Dataset - eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${inputPathOrcid} - --workingPath${workingPathOrcid} - --targetPath${workingPath}/orcidPublication - --masteryarn-cluster - - - - - - - - - yarn-cluster - cluster - Create DOIBoost Infospace - eu.dnetlib.doiboost.SparkGenerateDoiBoost - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorIntersectionMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --hostedByMapPath${hostedByMapPath} - --affiliationPath${inputPathMAG}/dataset/Affiliations - --paperAffiliationPath${inputPathMAG}/dataset/PaperAuthorAffiliations - --workingPath${workingPath} - --masteryarn-cluster - - - - - - - - - yarn-cluster - cluster - Generate DOIBoost ActionSet - eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --dbPublicationPath${workingPath}/doiBoostPublicationFiltered - --dbDatasetPath${workingPath}/crossrefDataset - --crossRefRelation${workingPath}/crossrefRelation - --dbaffiliationRelationPath${workingPath}/doiBoostPublicationAffiliation - --dbOrganizationPath${workingPath}/doiBoostOrganization - --targetPath${workingPath}/actionDataSet - --sFilePath${outputPath} - --masteryarn-cluster - - - - - - - \ No newline at end of file From c0d2b62e46ed1e88412862b28ad11c40a3343c6d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 18 Jun 2021 15:57:41 +0200 Subject: [PATCH 6/8] [doiboost] added missing implicit Encoder --- .../java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala index 01bf9dd62..ee3229f1f 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala @@ -33,9 +33,9 @@ object SparkMapDumpIntoOAF { implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] implicit val mapEncoderRelatons: Encoder[Relation] = Encoders.kryo[Relation] implicit val mapEncoderDatasets: Encoder[oaf.Dataset] = Encoders.kryo[OafDataset] + implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT] val targetPath = parser.get("targetPath") - import spark.implicits._ spark.read.load(parser.get("sourcePath")).as[CrossrefDT] .flatMap(k => Crossref2Oaf.convert(k.json)) From 6b8c3573813d6e2493c82ed0124e8054a409fe12 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 18 Jun 2021 16:08:45 +0200 Subject: [PATCH 7/8] removed extra whitespace at the end of the file --- .../datacite_export/oozie_app/{workflow.xml => workflow.xml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/{workflow.xml => workflow.xml} (100%) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/workflow.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/workflow.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite_export/oozie_app/workflow.xml From 59c36eb185f2eabebf4626f1f66fac1575493ca9 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 21 Jun 2021 10:41:47 +0200 Subject: [PATCH 8/8] check if pid is null (to avoid NullPointerException) --- .../src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java index 0b602b774..72b60e1d2 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java @@ -115,6 +115,8 @@ public class AuthorMerger { } public static String pidToComparableString(StructuredProperty pid) { + if (pid == null) + return ""; return (pid.getQualifier() != null ? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : "" : "")