1031 lines
36 KiB
Scala
1031 lines
36 KiB
Scala
package eu.dnetlib.dhp.collection.crossref
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.oaf._
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.{field, qualifier, structuredProperty, subject}
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import eu.dnetlib.dhp.schema.oaf.utils.{
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DoiCleaningRule,
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GraphCleaningFunctions,
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IdentifierFactory,
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OafMapperUtils,
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PidType
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}
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import eu.dnetlib.dhp.utils.DHPUtils
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import org.apache.commons.lang.StringUtils
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import org.json4s
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import org.json4s.DefaultFormats
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import org.json4s.JsonAST._
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import org.json4s.jackson.JsonMethods._
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import org.slf4j.{Logger, LoggerFactory}
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import java.time.LocalDate
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import java.time.format.DateTimeFormatter
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import java.util
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import scala.collection.JavaConverters._
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import scala.collection.mutable
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import scala.io.Source
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import scala.util.matching.Regex
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case class CrossrefDT(doi: String, json: String, timestamp: Long) {}
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case class mappingAffiliation(name: String) {}
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case class mappingAuthor(
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given: Option[String],
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family: Option[String],
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sequence: Option[String],
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ORCID: Option[String],
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affiliation: Option[mappingAffiliation]
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) {}
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case class funderInfo(id: String, uri: String, name: String, synonym: List[String]) {}
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case class mappingFunder(name: String, DOI: Option[String], award: Option[List[String]]) {}
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case class CrossrefResult(oafType: String, body: String) {}
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case class UnpayWall(doi: String, is_oa: Boolean, best_oa_location: UnpayWallOALocation, oa_status: String) {}
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case class UnpayWallOALocation(license: Option[String], url: String, host_type: Option[String]) {}
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case object Crossref2Oaf {
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val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
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val mapper = new ObjectMapper
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val irishFunder: List[funderInfo] = {
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val s = Source
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.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/irish_funder.json"))
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.mkString
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: org.json4s.JValue = parse(s)
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json.extract[List[funderInfo]]
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}
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val invalidName = List(
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",",
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"none none",
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"none, none",
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"none &na;",
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"(:null)",
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"test test test",
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"test test",
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"test",
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"&na; &na;"
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)
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def getIrishId(doi: String): Option[String] = {
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val id = doi.split("/").last
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irishFunder
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.find(f => id.equalsIgnoreCase(f.id) || (f.synonym.nonEmpty && f.synonym.exists(s => s.equalsIgnoreCase(id))))
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.map(f => f.id)
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}
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def createCrossrefCollectedFrom(): KeyValue = {
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val cf = new KeyValue
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cf.setValue("Crossref");
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cf.setKey(ModelConstants.CROSSREF_ID)
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cf
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}
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def createUnpayWallCollectedFrom(): KeyValue = {
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val cf = new KeyValue
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cf.setValue("UnpayWall")
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cf.setKey(s"10|openaire____:${DHPUtils.md5("UnpayWall".toLowerCase)}")
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cf
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}
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def generateDataInfo(): DataInfo = {
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generateDataInfo("0.91")
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}
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def generateDataInfo(trust: String): DataInfo = {
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val di = new DataInfo
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di.setDeletedbyinference(false)
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di.setInferred(false)
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di.setInvisible(false)
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di.setTrust(trust)
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di.setProvenanceaction(
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OafMapperUtils.qualifier(
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ModelConstants.SYSIMPORT_ACTIONSET,
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ModelConstants.SYSIMPORT_ACTIONSET,
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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ModelConstants.DNET_PROVENANCE_ACTIONS
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)
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)
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di
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}
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def getOpenAccessQualifier(): AccessRight = {
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OafMapperUtils.accessRight(
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ModelConstants.ACCESS_RIGHT_OPEN,
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"Open Access",
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ModelConstants.DNET_ACCESS_MODES,
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ModelConstants.DNET_ACCESS_MODES
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)
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}
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def getRestrictedQualifier(): AccessRight = {
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OafMapperUtils.accessRight(
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"RESTRICTED",
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"Restricted",
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ModelConstants.DNET_ACCESS_MODES,
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ModelConstants.DNET_ACCESS_MODES
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)
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}
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def getUnknownQualifier(): AccessRight = {
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OafMapperUtils.accessRight(
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ModelConstants.UNKNOWN,
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ModelConstants.NOT_AVAILABLE,
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ModelConstants.DNET_ACCESS_MODES,
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ModelConstants.DNET_ACCESS_MODES
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)
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}
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def getEmbargoedAccessQualifier(): AccessRight = {
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OafMapperUtils.accessRight(
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"EMBARGO",
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"Embargo",
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ModelConstants.DNET_ACCESS_MODES,
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ModelConstants.DNET_ACCESS_MODES
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)
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}
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def getClosedAccessQualifier(): AccessRight = {
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OafMapperUtils.accessRight(
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"CLOSED",
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"Closed Access",
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ModelConstants.DNET_ACCESS_MODES,
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ModelConstants.DNET_ACCESS_MODES
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)
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}
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def decideAccessRight(lic: Field[String], date: String): AccessRight = {
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if (lic == null) {
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//Default value Unknown
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return getUnknownQualifier()
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}
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val license: String = lic.getValue
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//CC licenses
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if (
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license.startsWith("cc") ||
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license.startsWith("http://creativecommons.org/licenses") ||
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license.startsWith("https://creativecommons.org/licenses") ||
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//ACS Publications Author choice licenses (considered OPEN also by Unpaywall)
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license.equals("http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html") ||
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license.equals("http://pubs.acs.org/page/policy/authorchoice_termsofuse.html") ||
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license.equals("http://pubs.acs.org/page/policy/authorchoice_ccbyncnd_termsofuse.html") ||
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//APA (considered OPEN also by Unpaywall)
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license.equals("http://www.apa.org/pubs/journals/resources/open-access.aspx")
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) {
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val oaq: AccessRight = getOpenAccessQualifier()
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oaq.setOpenAccessRoute(OpenAccessRoute.hybrid)
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return oaq
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}
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//OUP (BUT ONLY AFTER 12 MONTHS FROM THE PUBLICATION DATE, OTHERWISE THEY ARE EMBARGOED)
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if (
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license.equals(
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"https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model"
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)
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) {
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val now = java.time.LocalDate.now
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try {
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val pub_date = LocalDate.parse(date, DateTimeFormatter.ofPattern("yyyy-MM-dd"))
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if (((now.toEpochDay - pub_date.toEpochDay) / 365.0) > 1) {
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val oaq: AccessRight = getOpenAccessQualifier()
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oaq.setOpenAccessRoute(OpenAccessRoute.hybrid)
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return oaq
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} else {
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return getEmbargoedAccessQualifier()
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}
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} catch {
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case e: Exception => {
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try {
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val pub_date =
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LocalDate.parse(date, DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'"))
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if (((now.toEpochDay - pub_date.toEpochDay) / 365.0) > 1) {
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val oaq: AccessRight = getOpenAccessQualifier()
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oaq.setOpenAccessRoute(OpenAccessRoute.hybrid)
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return oaq
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} else {
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return getEmbargoedAccessQualifier()
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}
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} catch {
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case ex: Exception => return getClosedAccessQualifier()
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}
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}
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}
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}
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getClosedAccessQualifier()
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}
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def isValidAuthorName(fullName: String): Boolean = {
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if (fullName == null || fullName.isEmpty)
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return false
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if (invalidName.contains(fullName.toLowerCase.trim))
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return false
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true
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}
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def filterResult(publication: Result): Boolean = {
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//Case empty publication
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if (publication == null)
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return false
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if (publication.getId == null || publication.getId.isEmpty)
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return false
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//Case publication with no title
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if (publication.getTitle == null || publication.getTitle.size == 0)
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return false
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val s = publication.getTitle.asScala.count(p =>
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p.getValue != null
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&& p.getValue.nonEmpty && !p.getValue.equalsIgnoreCase("[NO TITLE AVAILABLE]")
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)
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if (s == 0)
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return false
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// fixes #4360 (test publisher)
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val publisher =
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if (publication.getPublisher != null) publication.getPublisher.getValue else null
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if (
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publisher != null && (publisher.equalsIgnoreCase("Test accounts") || publisher
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.equalsIgnoreCase("CrossRef Test Account"))
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) {
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return false;
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}
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//RELAXED this constraint
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//Publication with no Author
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if (publication.getAuthor == null || publication.getAuthor.size() == 0)
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return true
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//filter invalid author
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val authors = publication.getAuthor.asScala.map(s => {
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if (s.getFullname.nonEmpty) {
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s.getFullname
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} else
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s"${s.getName} ${s.getSurname}"
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})
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val c = authors.count(isValidAuthorName)
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if (c == 0)
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return false
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// fixes #4368
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if (
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authors.count(s => s.equalsIgnoreCase("Addie Jackson")) > 0 && "Elsevier BV".equalsIgnoreCase(
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publication.getPublisher.getValue
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)
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)
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return false
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true
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}
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def get_unpaywall_color(input: String): Option[OpenAccessRoute] = {
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if (input == null || input.equalsIgnoreCase("close"))
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return None
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if (input.equalsIgnoreCase("green"))
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return Some(OpenAccessRoute.green)
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if (input.equalsIgnoreCase("bronze"))
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return Some(OpenAccessRoute.bronze)
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if (input.equalsIgnoreCase("hybrid"))
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return Some(OpenAccessRoute.hybrid)
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else
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return Some(OpenAccessRoute.gold)
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}
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def get_color(input: String): Option[OpenAccessRoute] = {
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if (input == null || input.equalsIgnoreCase("closed"))
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return None
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if (input.equalsIgnoreCase("green"))
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return Some(OpenAccessRoute.green)
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if (input.equalsIgnoreCase("bronze"))
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return Some(OpenAccessRoute.bronze)
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if (input.equalsIgnoreCase("hybrid"))
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return Some(OpenAccessRoute.hybrid)
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else
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return Some(OpenAccessRoute.gold)
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}
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def mappingResult(result: Result, json: JValue, instanceType: Qualifier, originalType: String): Result = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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//MAPPING Crossref DOI into PID
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val doi: String = DoiCleaningRule.normalizeDoi((json \ "DOI").extract[String])
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result.setPid(
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List(
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structuredProperty(
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doi,
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qualifier(
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PidType.doi.toString,
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PidType.doi.toString,
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ModelConstants.DNET_PID_TYPES,
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ModelConstants.DNET_PID_TYPES
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),
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null
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)
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).asJava
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)
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//MAPPING Crossref DOI into OriginalId
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//and Other Original Identifier of dataset like clinical-trial-number
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val clinicalTrialNumbers = for (JString(ctr) <- json \ "clinical-trial-number") yield ctr
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val alternativeIds = for (JString(ids) <- json \ "alternative-id") yield ids
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val tmp = clinicalTrialNumbers ::: alternativeIds ::: List(doi)
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val originalIds = new util.ArrayList(tmp.filter(id => id != null).asJava)
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result.setOriginalId(originalIds)
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// Add DataInfo
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result.setDataInfo(generateDataInfo())
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result.setLastupdatetimestamp((json \ "indexed" \ "timestamp").extract[Long])
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result.setDateofcollection((json \ "indexed" \ "date-time").extract[String])
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result.setCollectedfrom(List(createCrossrefCollectedFrom()).asJava)
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// Publisher ( Name of work's publisher mapped into Result/Publisher)
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val publisher = (json \ "publisher").extractOrElse[String](null)
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if (publisher != null && publisher.nonEmpty)
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result.setPublisher(field(publisher, null))
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// TITLE
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val mainTitles =
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for { JString(title) <- json \ "title" if title.nonEmpty } yield {
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structuredProperty(title, ModelConstants.MAIN_TITLE_QUALIFIER, null)
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}
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val originalTitles = for {
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JString(title) <- json \ "original-title" if title.nonEmpty
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} yield structuredProperty(title, ModelConstants.ALTERNATIVE_TITLE_QUALIFIER, null)
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val shortTitles = for {
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JString(title) <- json \ "short-title" if title.nonEmpty
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} yield structuredProperty(title, ModelConstants.ALTERNATIVE_TITLE_QUALIFIER, null)
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val subtitles =
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for { JString(title) <- json \ "subtitle" if title.nonEmpty } yield structuredProperty(
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title,
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ModelConstants.SUBTITLE_QUALIFIER,
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null
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)
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result.setTitle((mainTitles ::: originalTitles ::: shortTitles ::: subtitles).asJava)
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// DESCRIPTION
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val descriptionList =
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for { JString(description) <- json \ "abstract" } yield field[String](description, null)
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result.setDescription(descriptionList.asJava)
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// Source
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val sourceList = for {
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JString(source) <- json \ "source" if source != null && source.nonEmpty
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} yield field(source, null)
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result.setSource(sourceList.asJava)
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//RELEVANT DATE Mapping
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val createdDate = generateDate(
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(json \ "created" \ "date-time").extract[String],
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(json \ "created" \ "date-parts").extract[List[List[Int]]],
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"created",
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ModelConstants.DNET_DATACITE_DATE
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)
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val postedDate = generateDate(
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(json \ "posted" \ "date-time").extractOrElse[String](null),
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(json \ "posted" \ "date-parts").extract[List[List[Int]]],
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"available",
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ModelConstants.DNET_DATACITE_DATE
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)
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val acceptedDate = generateDate(
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(json \ "accepted" \ "date-time").extractOrElse[String](null),
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(json \ "accepted" \ "date-parts").extract[List[List[Int]]],
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"accepted",
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ModelConstants.DNET_DATACITE_DATE
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)
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val publishedPrintDate = generateDate(
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(json \ "published-print" \ "date-time").extractOrElse[String](null),
|
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(json \ "published-print" \ "date-parts").extract[List[List[Int]]],
|
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"published-print",
|
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ModelConstants.DNET_DATACITE_DATE
|
||
)
|
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val publishedOnlineDate = generateDate(
|
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(json \ "published-online" \ "date-time").extractOrElse[String](null),
|
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(json \ "published-online" \ "date-parts").extract[List[List[Int]]],
|
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"published-online",
|
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ModelConstants.DNET_DATACITE_DATE
|
||
)
|
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|
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val issuedDate = extractDate(
|
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(json \ "issued" \ "date-time").extractOrElse[String](null),
|
||
(json \ "issued" \ "date-parts").extract[List[List[Int]]]
|
||
)
|
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if (StringUtils.isNotBlank(issuedDate)) {
|
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result.setDateofacceptance(field(issuedDate, null))
|
||
} else {
|
||
result.setDateofacceptance(field(createdDate.getValue, null))
|
||
}
|
||
result.setRelevantdate(
|
||
List(createdDate, postedDate, acceptedDate, publishedOnlineDate, publishedPrintDate)
|
||
.filter(p => p != null)
|
||
.asJava
|
||
)
|
||
|
||
//Mapping Subject
|
||
val subjectList: List[String] = (json \ "subject").extractOrElse[List[String]](List())
|
||
|
||
if (subjectList.nonEmpty) {
|
||
result.setSubject(
|
||
subjectList.map(s => subject(s, ModelConstants.SUBTITLE_QUALIFIER, null)).asJava
|
||
)
|
||
}
|
||
|
||
//Mapping Author
|
||
val authorList: List[mappingAuthor] =
|
||
(json \ "author").extract[List[mappingAuthor]].filter(a => a.family.isDefined)
|
||
|
||
val sorted_list = authorList.sortWith((a: mappingAuthor, b: mappingAuthor) =>
|
||
a.sequence.isDefined && a.sequence.get.equalsIgnoreCase("first")
|
||
)
|
||
|
||
result.setAuthor(sorted_list.zipWithIndex.map { case (a, index) =>
|
||
generateAuhtor(a.given.orNull, a.family.get, a.ORCID.orNull, index)
|
||
}.asJava)
|
||
|
||
// Mapping instance
|
||
val instance = new Instance()
|
||
val license = for {
|
||
JObject(license) <- json \ "license"
|
||
JField("URL", JString(lic)) <- license
|
||
JField("content-version", JString(content_version)) <- license
|
||
} yield (field[String](lic, null), content_version)
|
||
val l = license.filter(d => StringUtils.isNotBlank(d._1.getValue))
|
||
if (l.nonEmpty) {
|
||
if (l exists (d => d._2.equals("vor"))) {
|
||
for (d <- l) {
|
||
if (d._2.equals("vor")) {
|
||
instance.setLicense(d._1)
|
||
}
|
||
}
|
||
} else {
|
||
instance.setLicense(l.head._1)
|
||
}
|
||
}
|
||
|
||
// Ticket #6281 added pid to Instance
|
||
instance.setPid(result.getPid)
|
||
|
||
val has_review = json \ "relation" \ "has-review" \ "id"
|
||
|
||
if (has_review != JNothing) {
|
||
instance.setRefereed(
|
||
OafMapperUtils.qualifier(
|
||
"0001",
|
||
"peerReviewed",
|
||
ModelConstants.DNET_REVIEW_LEVELS,
|
||
ModelConstants.DNET_REVIEW_LEVELS
|
||
)
|
||
)
|
||
}
|
||
|
||
instance.setAccessright(
|
||
decideAccessRight(instance.getLicense, result.getDateofacceptance.getValue)
|
||
)
|
||
instance.setInstancetype(instanceType)
|
||
|
||
//ADD ORIGINAL TYPE to the mapping
|
||
val itm = new InstanceTypeMapping
|
||
itm.setOriginalType(originalType)
|
||
itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1)
|
||
instance.setInstanceTypeMapping(List(itm).asJava)
|
||
|
||
instance.setCollectedfrom(createCrossrefCollectedFrom())
|
||
if (StringUtils.isNotBlank(issuedDate)) {
|
||
instance.setDateofacceptance(field(issuedDate, null))
|
||
} else {
|
||
instance.setDateofacceptance(field(createdDate.getValue, null))
|
||
}
|
||
val s: List[String] = List("https://doi.org/" + doi)
|
||
// val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null && p.toLowerCase().contains(doi.toLowerCase())).distinct
|
||
// if (links.nonEmpty) {
|
||
// instance.setUrl(links.asJava)
|
||
// }
|
||
if (s.nonEmpty) {
|
||
instance.setUrl(s.asJava)
|
||
}
|
||
|
||
result.setInstance(List(instance).asJava)
|
||
|
||
//IMPORTANT
|
||
//The old method result.setId(generateIdentifier(result, doi))
|
||
//is replaced using IdentifierFactory, but the old identifier
|
||
//is preserved among the originalId(s)
|
||
val oldId = generateIdentifier(result, doi)
|
||
result.setId(oldId)
|
||
|
||
val newId = IdentifierFactory.createDOIBoostIdentifier(result)
|
||
if (!oldId.equalsIgnoreCase(newId)) {
|
||
result.getOriginalId.add(oldId)
|
||
}
|
||
result.setId(newId)
|
||
|
||
if (result.getId == null)
|
||
null
|
||
else
|
||
result
|
||
}
|
||
|
||
def generateIdentifier(oaf: Result, doi: String): String = {
|
||
val id = DHPUtils.md5(doi.toLowerCase)
|
||
s"50|doiboost____|$id"
|
||
}
|
||
|
||
def generateAuhtor(given: String, family: String, orcid: String, index: Int): Author = {
|
||
val a = new Author
|
||
a.setName(given)
|
||
a.setSurname(family)
|
||
a.setFullname(s"$given $family")
|
||
a.setRank(index + 1)
|
||
if (StringUtils.isNotBlank(orcid))
|
||
a.setPid(
|
||
List(
|
||
structuredProperty(
|
||
orcid,
|
||
qualifier(
|
||
ModelConstants.ORCID_PENDING,
|
||
ModelConstants.ORCID_PENDING,
|
||
ModelConstants.DNET_PID_TYPES,
|
||
ModelConstants.DNET_PID_TYPES
|
||
),
|
||
generateDataInfo()
|
||
)
|
||
).asJava
|
||
)
|
||
|
||
a
|
||
}
|
||
|
||
/** *
|
||
* Use the vocabulary dnet:publication_resource to find a synonym to one of these terms and get the instance.type.
|
||
* Using the dnet:result_typologies vocabulary, we look up the instance.type synonym
|
||
* to generate one of the following main entities:
|
||
* - publication
|
||
* - dataset
|
||
* - software
|
||
* - otherresearchproduct
|
||
*
|
||
* @param resourceType
|
||
* @param vocabularies
|
||
* @return
|
||
*/
|
||
def getTypeQualifier(
|
||
resourceType: String,
|
||
vocabularies: VocabularyGroup
|
||
): (Qualifier, Qualifier, String) = {
|
||
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
|
||
),
|
||
resourceType
|
||
)
|
||
}
|
||
null
|
||
}
|
||
|
||
def extract_doi(input: String): CrossrefDT = {
|
||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||
lazy val json: json4s.JValue = parse(input)
|
||
CrossrefDT(doi = (json \ "DOI").extract[String].toLowerCase, json = input, 0)
|
||
}
|
||
|
||
def convert(input: CrossrefDT, uw: UnpayWall, vocabularies: VocabularyGroup): List[CrossrefResult] = {
|
||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||
lazy val json: json4s.JValue = parse(input.json)
|
||
|
||
var resultList: List[CrossrefResult] = List()
|
||
|
||
val objectType = (json \ "type").extractOrElse[String](null)
|
||
if (objectType == null)
|
||
return resultList
|
||
val typology = getTypeQualifier(objectType, vocabularies)
|
||
|
||
if (typology == null)
|
||
return List()
|
||
|
||
val result = generateItemFromType(typology._2)
|
||
if (result == null)
|
||
return List()
|
||
|
||
mappingResult(result, json, typology._1, typology._3)
|
||
|
||
if (result == null || result.getId == null)
|
||
return List()
|
||
|
||
val funderList: List[mappingFunder] =
|
||
(json \ "funder").extractOrElse[List[mappingFunder]](List())
|
||
|
||
if (funderList.nonEmpty) {
|
||
resultList = resultList ::: mappingFunderToRelations(
|
||
funderList,
|
||
result.getId,
|
||
createCrossrefCollectedFrom(),
|
||
result.getDataInfo,
|
||
result.getLastupdatetimestamp
|
||
).map(s => CrossrefResult(s.getClass.getSimpleName, mapper.writeValueAsString(s)))
|
||
}
|
||
|
||
result match {
|
||
case publication: Publication => convertPublication(publication, json, typology._1)
|
||
case dataset: Dataset => convertDataset(dataset)
|
||
}
|
||
|
||
val doisReference: List[String] = for {
|
||
JObject(reference_json) <- json \ "reference"
|
||
JField("DOI", JString(doi_json)) <- reference_json
|
||
} yield doi_json
|
||
|
||
if (doisReference != null && doisReference.nonEmpty) {
|
||
val citation_relations: List[Relation] = generateCitationRelations(doisReference, result)
|
||
resultList = resultList ::: citation_relations.map(s =>
|
||
CrossrefResult(s.getClass.getSimpleName, mapper.writeValueAsString(s))
|
||
)
|
||
}
|
||
|
||
if (uw != null) {
|
||
result.getCollectedfrom.add(createUnpayWallCollectedFrom())
|
||
val i: Instance = new Instance()
|
||
i.setCollectedfrom(createUnpayWallCollectedFrom())
|
||
if (uw.best_oa_location != null) {
|
||
|
||
i.setUrl(List(uw.best_oa_location.url).asJava)
|
||
if (uw.best_oa_location.license.isDefined) {
|
||
i.setLicense(field[String](uw.best_oa_location.license.get, null))
|
||
}
|
||
|
||
val colour = get_unpaywall_color(uw.oa_status)
|
||
if (colour.isDefined) {
|
||
val a = new AccessRight
|
||
a.setClassid(ModelConstants.ACCESS_RIGHT_OPEN)
|
||
a.setClassname(ModelConstants.ACCESS_RIGHT_OPEN)
|
||
a.setSchemeid(ModelConstants.DNET_ACCESS_MODES)
|
||
a.setSchemename(ModelConstants.DNET_ACCESS_MODES)
|
||
a.setOpenAccessRoute(colour.get)
|
||
i.setAccessright(a)
|
||
}
|
||
i.setPid(result.getPid)
|
||
result.getInstance().add(i)
|
||
}
|
||
}
|
||
if (!filterResult(result))
|
||
List()
|
||
else
|
||
resultList ::: List(result).map(s => CrossrefResult(s.getClass.getSimpleName, mapper.writeValueAsString(s)))
|
||
|
||
}
|
||
|
||
private def createCiteRelation(source: Result, targetPid: String, targetPidType: String): List[Relation] = {
|
||
|
||
val targetId = IdentifierFactory.idFromPid("50", targetPidType, targetPid, true)
|
||
|
||
val from = new Relation
|
||
from.setSource(source.getId)
|
||
from.setTarget(targetId)
|
||
from.setRelType(ModelConstants.RESULT_RESULT)
|
||
from.setRelClass(ModelConstants.CITES)
|
||
from.setSubRelType(ModelConstants.CITATION)
|
||
from.setCollectedfrom(source.getCollectedfrom)
|
||
from.setDataInfo(source.getDataInfo)
|
||
from.setLastupdatetimestamp(source.getLastupdatetimestamp)
|
||
|
||
List(from)
|
||
}
|
||
|
||
def generateCitationRelations(dois: List[String], result: Result): List[Relation] = {
|
||
dois.flatMap(d => createCiteRelation(result, d, "doi"))
|
||
}
|
||
|
||
def mappingFunderToRelations(
|
||
funders: List[mappingFunder],
|
||
sourceId: String,
|
||
cf: KeyValue,
|
||
di: DataInfo,
|
||
ts: Long
|
||
): List[Relation] = {
|
||
|
||
val queue = new mutable.Queue[Relation]
|
||
|
||
def snsfRule(award: String): String = {
|
||
val tmp1 = StringUtils.substringAfter(award, "_")
|
||
val tmp2 = StringUtils.substringBefore(tmp1, "/")
|
||
logger.debug(s"From $award to $tmp2")
|
||
tmp2
|
||
|
||
}
|
||
|
||
def extractECAward(award: String): String = {
|
||
val awardECRegex: Regex = "[0-9]{4,9}".r
|
||
if (awardECRegex.findAllIn(award).hasNext)
|
||
return awardECRegex.findAllIn(award).max
|
||
null
|
||
}
|
||
|
||
def generateRelation(sourceId: String, targetId: String, relClass: String): Relation = {
|
||
|
||
val r = new Relation
|
||
r.setSource(sourceId)
|
||
r.setTarget(targetId)
|
||
r.setRelType(ModelConstants.RESULT_PROJECT)
|
||
r.setRelClass(relClass)
|
||
r.setSubRelType(ModelConstants.OUTCOME)
|
||
r.setCollectedfrom(List(cf).asJava)
|
||
r.setDataInfo(di)
|
||
r.setLastupdatetimestamp(ts)
|
||
r
|
||
|
||
}
|
||
|
||
def generateSimpleRelationFromAward(
|
||
funder: mappingFunder,
|
||
nsPrefix: String,
|
||
extractField: String => String
|
||
): Unit = {
|
||
if (funder.award.isDefined && funder.award.get.nonEmpty)
|
||
funder.award.get
|
||
.map(extractField)
|
||
.filter(a => a != null && a.nonEmpty)
|
||
.foreach(award => {
|
||
val targetId = getProjectId(nsPrefix, DHPUtils.md5(award))
|
||
queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
|
||
queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
|
||
})
|
||
}
|
||
|
||
def getProjectId(nsPrefix: String, targetId: String): String = {
|
||
s"40|$nsPrefix::$targetId"
|
||
}
|
||
|
||
if (funders != null)
|
||
funders.foreach(funder => {
|
||
if (funder.DOI.isDefined && funder.DOI.get.nonEmpty) {
|
||
|
||
if (getIrishId(funder.DOI.get).isDefined) {
|
||
val nsPrefix = getIrishId(funder.DOI.get).get.padTo(12, '_')
|
||
val targetId = getProjectId(nsPrefix, "1e5e62235d094afd01cd56e65112fc63")
|
||
queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
|
||
queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
|
||
}
|
||
|
||
funder.DOI.get match {
|
||
case "10.13039/100010663" | "10.13039/100010661" | "10.13039/501100007601" | "10.13039/501100000780" |
|
||
"10.13039/100010665" =>
|
||
generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward)
|
||
case "10.13039/100011199" | "10.13039/100004431" | "10.13039/501100004963" | "10.13039/501100000780" =>
|
||
generateSimpleRelationFromAward(funder, "corda_______", extractECAward)
|
||
case "10.13039/501100000781" =>
|
||
generateSimpleRelationFromAward(funder, "corda_______", extractECAward)
|
||
generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward)
|
||
generateSimpleRelationFromAward(funder, "corda_____he", extractECAward)
|
||
case "10.13039/100000001" => generateSimpleRelationFromAward(funder, "nsf_________", a => a)
|
||
case "10.13039/501100001665" => generateSimpleRelationFromAward(funder, "anr_________", a => a)
|
||
case "10.13039/501100002341" => generateSimpleRelationFromAward(funder, "aka_________", a => a)
|
||
case "10.13039/501100001602" =>
|
||
generateSimpleRelationFromAward(funder, "sfi_________", a => a.replace("SFI", ""))
|
||
case "10.13039/501100000923" => generateSimpleRelationFromAward(funder, "arc_________", a => a)
|
||
case "10.13039/501100000038" =>
|
||
val targetId = getProjectId("nserc_______", "1e5e62235d094afd01cd56e65112fc63")
|
||
queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
|
||
queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
|
||
case "10.13039/501100000155" =>
|
||
val targetId = getProjectId("sshrc_______", "1e5e62235d094afd01cd56e65112fc63")
|
||
queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
|
||
queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
|
||
case "10.13039/501100000024" =>
|
||
val targetId = getProjectId("cihr________", "1e5e62235d094afd01cd56e65112fc63")
|
||
queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
|
||
queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
|
||
|
||
case "10.13039/100020031" =>
|
||
val targetId = getProjectId("tara________", "1e5e62235d094afd01cd56e65112fc63")
|
||
queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
|
||
queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
|
||
|
||
case "10.13039/501100005416" => generateSimpleRelationFromAward(funder, "rcn_________", a => a)
|
||
case "10.13039/501100002848" => generateSimpleRelationFromAward(funder, "conicytf____", a => a)
|
||
case "10.13039/501100003448" => generateSimpleRelationFromAward(funder, "gsrt________", extractECAward)
|
||
case "10.13039/501100010198" => generateSimpleRelationFromAward(funder, "sgov________", a => a)
|
||
case "10.13039/501100004564" => generateSimpleRelationFromAward(funder, "mestd_______", extractECAward)
|
||
case "10.13039/501100003407" =>
|
||
generateSimpleRelationFromAward(funder, "miur________", a => a)
|
||
val targetId = getProjectId("miur________", "1e5e62235d094afd01cd56e65112fc63")
|
||
queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
|
||
queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
|
||
case "10.13039/501100006588" | "10.13039/501100004488" =>
|
||
generateSimpleRelationFromAward(
|
||
funder,
|
||
"irb_hr______",
|
||
a => a.replaceAll("Project No.", "").replaceAll("HRZZ-", "")
|
||
)
|
||
case "10.13039/501100006769" => generateSimpleRelationFromAward(funder, "rsf_________", a => a)
|
||
case "10.13039/501100001711" => generateSimpleRelationFromAward(funder, "snsf________", snsfRule)
|
||
case "10.13039/501100004410" => generateSimpleRelationFromAward(funder, "tubitakf____", a => a)
|
||
case "10.13039/100004440" =>
|
||
generateSimpleRelationFromAward(funder, "wt__________", a => a)
|
||
val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63")
|
||
queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
|
||
queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
|
||
//ASAP
|
||
case "10.13039/100018231" => generateSimpleRelationFromAward(funder, "asap________", a => a)
|
||
//CHIST-ERA
|
||
case "10.13039/501100001942" =>
|
||
val targetId = getProjectId("chistera____", "1e5e62235d094afd01cd56e65112fc63")
|
||
queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
|
||
queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
|
||
//HE
|
||
case "10.13039/100018693" | "10.13039/100018694" | "10.13039/100019188" | "10.13039/100019180" |
|
||
"10.13039/100018695" | "10.13039/100019185" | "10.13039/100019186" | "10.13039/100019187" =>
|
||
generateSimpleRelationFromAward(funder, "corda_____he", extractECAward)
|
||
//FCT
|
||
case "10.13039/501100001871" =>
|
||
generateSimpleRelationFromAward(funder, "fct_________", a => a)
|
||
//NHMRC
|
||
case "10.13039/501100000925" =>
|
||
generateSimpleRelationFromAward(funder, "nhmrc_______", a => a)
|
||
//NIH
|
||
case "10.13039/100000002" =>
|
||
generateSimpleRelationFromAward(funder, "nih_________", a => a)
|
||
//NWO
|
||
case "10.13039/501100003246" =>
|
||
generateSimpleRelationFromAward(funder, "nwo_________", a => a)
|
||
//UKRI
|
||
case "10.13039/100014013" | "10.13039/501100000267" | "10.13039/501100000268" | "10.13039/501100000269" |
|
||
"10.13039/501100000266" | "10.13039/501100006041" | "10.13039/501100000265" | "10.13039/501100000270" |
|
||
"10.13039/501100013589" | "10.13039/501100000271" =>
|
||
generateSimpleRelationFromAward(funder, "ukri________", a => a)
|
||
|
||
case _ => logger.debug("no match for " + funder.DOI.get)
|
||
|
||
}
|
||
|
||
} else {
|
||
funder.name match {
|
||
case "European Union’s Horizon 2020 research and innovation program" =>
|
||
generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward)
|
||
case "European Union's" =>
|
||
generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward)
|
||
generateSimpleRelationFromAward(funder, "corda_______", extractECAward)
|
||
generateSimpleRelationFromAward(funder, "corda_____he", extractECAward)
|
||
case "The French National Research Agency (ANR)" | "The French National Research Agency" =>
|
||
generateSimpleRelationFromAward(funder, "anr_________", a => a)
|
||
case "CONICYT, Programa de Formación de Capital Humano Avanzado" =>
|
||
generateSimpleRelationFromAward(funder, "conicytf____", a => a)
|
||
case "Wellcome Trust Masters Fellowship" =>
|
||
generateSimpleRelationFromAward(funder, "wt__________", a => a)
|
||
val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63")
|
||
queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
|
||
queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
|
||
case _ => logger.debug("no match for " + funder.name)
|
||
|
||
}
|
||
}
|
||
|
||
})
|
||
queue.toList
|
||
}
|
||
|
||
def convertDataset(dataset: Dataset): Unit = {
|
||
// TODO check if there are other info to map into the Dataset
|
||
}
|
||
|
||
def convertPublication(publication: Publication, json: JValue, cobjCategory: Qualifier): Unit = {
|
||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||
val containerTitles = for { JString(ct) <- json \ "container-title" } yield ct
|
||
|
||
//Mapping book
|
||
if (cobjCategory.getClassname.toLowerCase.contains("book")) {
|
||
val ISBN = for { JString(isbn) <- json \ "ISBN" } yield isbn
|
||
if (ISBN.nonEmpty && containerTitles.nonEmpty) {
|
||
val source = s"${containerTitles.head} ISBN: ${ISBN.head}"
|
||
if (publication.getSource != null) {
|
||
val l: List[Field[String]] = publication.getSource.asScala.toList
|
||
val ll: List[Field[String]] = l ::: List(field(source, null))
|
||
publication.setSource(ll.asJava)
|
||
} else
|
||
publication.setSource(List(field(source, null)).asJava)
|
||
}
|
||
} else {
|
||
// Mapping Journal
|
||
|
||
val issnInfos = for {
|
||
JArray(issn_types) <- json \ "issn-type"
|
||
JObject(issn_type) <- issn_types
|
||
JField("type", JString(tp)) <- issn_type
|
||
JField("value", JString(vl)) <- issn_type
|
||
} yield Tuple2(tp, vl)
|
||
|
||
val volume = (json \ "volume").extractOrElse[String](null)
|
||
if (containerTitles.nonEmpty) {
|
||
val journal = new Journal
|
||
journal.setName(containerTitles.head)
|
||
if (issnInfos.nonEmpty) {
|
||
|
||
issnInfos.foreach(tp => {
|
||
tp._1 match {
|
||
case "electronic" => journal.setIssnOnline(tp._2)
|
||
case "print" => journal.setIssnPrinted(tp._2)
|
||
}
|
||
})
|
||
}
|
||
journal.setVol(volume)
|
||
val page = (json \ "page").extractOrElse[String](null)
|
||
if (page != null) {
|
||
val pp = page.split("-")
|
||
if (pp.nonEmpty)
|
||
journal.setSp(pp.head)
|
||
if (pp.size > 1)
|
||
journal.setEp(pp(1))
|
||
}
|
||
publication.setJournal(journal)
|
||
}
|
||
}
|
||
}
|
||
|
||
def extractDate(dt: String, datePart: List[List[Int]]): String = {
|
||
if (StringUtils.isNotBlank(dt))
|
||
return GraphCleaningFunctions.cleanDate(dt)
|
||
if (datePart != null && datePart.size == 1) {
|
||
val res = datePart.head
|
||
if (res.size == 3) {
|
||
val dp = f"${res.head}-${res(1)}%02d-${res(2)}%02d"
|
||
if (dp.length == 10) {
|
||
return GraphCleaningFunctions.cleanDate(dp)
|
||
}
|
||
} else if (res.size == 2) {
|
||
val dp = f"${res.head}-${res(1)}%02d-01"
|
||
return GraphCleaningFunctions.cleanDate(dp)
|
||
} else if (res.size == 1) {
|
||
return GraphCleaningFunctions.cleanDate(s"${res.head}-01-01")
|
||
}
|
||
}
|
||
null
|
||
|
||
}
|
||
|
||
def generateDate(
|
||
dt: String,
|
||
datePart: List[List[Int]],
|
||
classId: String,
|
||
schemeId: String
|
||
): StructuredProperty = {
|
||
val dp = extractDate(dt, datePart)
|
||
if (StringUtils.isNotBlank(dp))
|
||
return structuredProperty(dp, qualifier(classId, classId, schemeId, schemeId), null)
|
||
null
|
||
}
|
||
|
||
def generateItemFromType(objectType: Qualifier): Result = {
|
||
if (objectType.getClassid.equalsIgnoreCase("publication")) {
|
||
val item = new Publication
|
||
item.setResourcetype(objectType)
|
||
return item
|
||
} else if (objectType.getClassid.equalsIgnoreCase("dataset")) {
|
||
val item = new Dataset
|
||
item.setResourcetype(objectType)
|
||
return item
|
||
} else if (objectType.getClassid.equalsIgnoreCase("software")) {
|
||
val item = new Software
|
||
item.setResourcetype(objectType)
|
||
return item
|
||
} else if (objectType.getClassid.equalsIgnoreCase("OtherResearchProduct")) {
|
||
val item = new OtherResearchProduct
|
||
item.setResourcetype(objectType)
|
||
return item
|
||
}
|
||
null
|
||
}
|
||
|
||
}
|