forked from antonis.lempesis/dnet-hadoop
improved crossref mapping
This commit is contained in:
parent
5977f08e92
commit
157915988c
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@ -8,9 +8,11 @@ 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
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import scala.collection.JavaConverters._
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case class mappingAffiliation(name:String)
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case class mappingAuthor(given: Option[String], family: String, ORCID: Option[String], affiliation:Option[mappingAffiliation]) {}
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class Crossref2Oaf {
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//STATIC STRING
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@ -81,26 +83,22 @@ class Crossref2Oaf {
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"report" -> "0017 Report"
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)
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def convert(input: String, logger: Logger): Result = {
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def mappingResult(result: Result, json: JValue, cobjCategory:String): Result = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: json4s.JValue = parse(input)
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val objectType = (json \ "type").extractOrElse[String](null)
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val objectSubType = (json \ "subtype").extractOrElse[String](null)
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if (objectType == null)
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return null
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val result = generateItemFromType(objectType, objectSubType)
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if (result == null)
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return result
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val cOBJCategory = mappingCrossrefSubType.getOrElse(objectType, mappingCrossrefSubType.getOrElse(objectSubType, "0038 Other literature type"));
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logger.debug(mappingCrossrefType(objectType))
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logger.debug(cOBJCategory)
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//MAPPING Crossref DOI into PID
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val doi: String = (json \ "DOI").extract[String]
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result.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
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//MAPPING Crossref DOI into OriginalId
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result.setOriginalId(List(doi).asJava)
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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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result.setOriginalId(tmp.filter(id => id != null).asJava)
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//Set identifier as {50|60} | doiboost____::md5(DOI)
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result.setId(generateIdentifier(result, doi))
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@ -120,44 +118,162 @@ class Crossref2Oaf {
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val mainTitles = for {JString(title) <- json \ "title"} yield createSP(title, "main title", "dnet:dataCite_title")
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val originalTitles = for {JString(title) <- json \ "original-title"} yield createSP(title, "alternative title", "dnet:dataCite_title")
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val shortTitles = for {JString(title) <- json \ "short-title"} yield createSP(title, "alternative title", "dnet:dataCite_title")
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result.setTitle((mainTitles ::: originalTitles ::: shortTitles).asJava)
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val subtitles = for {JString(title) <- json \ "subtitle"} yield createSP(title, "subtitle", "dnet:dataCite_title")
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result.setTitle((mainTitles ::: originalTitles ::: shortTitles ::: subtitles).asJava)
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// DESCRIPTION
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val descriptionList = for {JString(description) <- json \ "abstract"} yield asField(description)
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result.setDescription(descriptionList.asJava)
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// Source
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val sourceList = for {JString(source) <- json \ "source"} yield asField(source)
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result.setSource(sourceList.asJava)
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//RELEVANT DATE Mapping
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val createdDate =generateDate((json \ "created" \"date-time").extract[String],(json \ "created"\"date-parts").extract[List[List[Int]]],"created", "dnet:dataCite_date" )
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val postedDate =generateDate((json \ "posted" \"date-time").extractOrElse[String](null),(json \ "posted"\"date-parts").extract[List[List[Int]]],"available", "dnet:dataCite_date" )
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val acceptedDate =generateDate((json \ "accepted" \"date-time").extractOrElse[String](null),(json \ "accepted"\"date-parts").extract[List[List[Int]]],"accepted", "dnet:dataCite_date" )
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val publishedPrintDate =generateDate((json \ "published-print" \"date-time").extractOrElse[String](null),(json \ "published-print"\"date-parts").extract[List[List[Int]]],"published-print", "dnet:dataCite_date" )
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val publishedOnlineDate =generateDate((json \ "published-online" \"date-time").extractOrElse[String](null),(json \ "published-online"\"date-parts").extract[List[List[Int]]],"published-online", "dnet:dataCite_date" )
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val createdDate = generateDate((json \ "created" \ "date-time").extract[String], (json \ "created" \ "date-parts").extract[List[List[Int]]], "created", "dnet:dataCite_date")
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val postedDate = generateDate((json \ "posted" \ "date-time").extractOrElse[String](null), (json \ "posted" \ "date-parts").extract[List[List[Int]]], "available", "dnet:dataCite_date")
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val acceptedDate = generateDate((json \ "accepted" \ "date-time").extractOrElse[String](null), (json \ "accepted" \ "date-parts").extract[List[List[Int]]], "accepted", "dnet:dataCite_date")
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val publishedPrintDate = generateDate((json \ "published-print" \ "date-time").extractOrElse[String](null), (json \ "published-print" \ "date-parts").extract[List[List[Int]]], "published-print", "dnet:dataCite_date")
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val publishedOnlineDate = generateDate((json \ "published-online" \ "date-time").extractOrElse[String](null), (json \ "published-online" \ "date-parts").extract[List[List[Int]]], "published-online", "dnet:dataCite_date")
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result.setRelevantdate(List(createdDate ,postedDate, acceptedDate,publishedOnlineDate, publishedPrintDate).asJava)
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val issuedDate = extractDate((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(asField(issuedDate))
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}
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result.setRelevantdate(List(createdDate, postedDate, acceptedDate, publishedOnlineDate, publishedPrintDate).filter(p => p != null).asJava)
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//Mapping AUthor
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val authorList:List[mappingAuthor] = (json \ "author").extract[List[mappingAuthor]]
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result.setAuthor(authorList.map(a => generateAuhtor(a.given.orNull, a.family, a.ORCID.orNull)).asJava)
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// Mapping instance
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val instance = new Instance()
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val license = for {
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JString(lic) <- json \ "license" \ "URL"
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} yield asField(lic)
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val l = license.filter(d => StringUtils.isNotBlank(d.getValue))
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if (l.nonEmpty)
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instance.setLicense(l.head)
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instance.setAccessright(createQualifier("Restricted", "dnet:access_modes"))
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result.setInstance(List(instance).asJava)
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instance.setInstancetype(createQualifier(cobjCategory.substring(0,4), cobjCategory.substring(5), "dnet:publication_resource", "dnet:publication_resource"))
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instance.setCollectedfrom(createCollectedFrom())
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if (StringUtils.isNotBlank(issuedDate)) {
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instance.setDateofacceptance(asField(issuedDate))
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}
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val s: String =(json \ "URL").extract[String]
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val links:List[String] = ((for {JString(url) <-json \ "link" \ "URL"} yield url) ::: List(s)).filter(p =>p != null).distinct
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if (links.nonEmpty)
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instance.setUrl(links.asJava)
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result
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}
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def generateDate(dt: String, datePart: List[List[Int]], classId: String, schemeId: String): StructuredProperty = {
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def generateAuhtor(given:String, family:String, orcid:String):Author = {
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val a =new Author
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a.setName(given)
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a.setSurname(family)
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a.setFullname(s"${given} ${family}")
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if (StringUtils.isNotBlank(orcid))
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a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava)
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a
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}
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def convert(input: String, logger: Logger): Result = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: json4s.JValue = parse(input)
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val objectType = (json \ "type").extractOrElse[String](null)
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val objectSubType = (json \ "subtype").extractOrElse[String](null)
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if (objectType == null)
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return null
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val result = generateItemFromType(objectType, objectSubType)
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if (result == null)
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return result
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val cOBJCategory = mappingCrossrefSubType.getOrElse(objectType, mappingCrossrefSubType.getOrElse(objectSubType, "0038 Other literature type"));
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logger.debug(mappingCrossrefType(objectType))
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logger.debug(cOBJCategory)
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mappingResult(result, json, cOBJCategory)
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result match {
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case publication: Publication => convertPublication(publication)
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case dataset: Dataset => convertDataset(dataset)
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}
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result
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}
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def convertDataset(dataset: Dataset): Unit = {
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}
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def convertPublication(publication: Publication, json: JValue, cobjCategory:String): Unit = {
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val containerTitles = for {JString(ct) <- json \ "container-title"} yield ct
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//Mapping book
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if (cobjCategory.toLowerCase.contains("book")) {
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val ISBN = for {JString(isbn) <- json \ "ISBN"} yield isbn
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if (ISBN.nonEmpty && containerTitles.nonEmpty) {
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val source = s"${containerTitles.head} ISBN: ${ISBN.head}"
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if (publication.getSource != null) {
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val l: List[Field[String]] = publication.getSource.asScala.toList
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val ll: List[Field[String]] = l ::: List(asField(source))
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publication.setSource(ll.asJava)
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}
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else
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publication.setSource(List(asField(source)).asJava)
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}
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} else {
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val issn =
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}
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// Mapping other types of publications
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}
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def extractDate(dt: String, datePart: List[List[Int]]): String = {
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if (StringUtils.isNotBlank(dt))
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return createSP(dt, classId, schemeId)
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return dt
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if (datePart != null && datePart.size == 1) {
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val res = datePart.head
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if (res.size == 3) {
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val dp = f"${res.head}-${res(1)}%02d-${res(2)}%02d"
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println(dp)
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if (dp.length == 10) {
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return dp
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}
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}
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}
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null
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}
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def generateDate(dt: String, datePart: List[List[Int]], classId: String, schemeId: String): StructuredProperty = {
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val dp = extractDate(dt, datePart)
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if (StringUtils.isNotBlank(dp))
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return createSP(dp, classId, schemeId)
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}
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}
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}
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null
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}
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@ -206,15 +322,19 @@ class Crossref2Oaf {
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}
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def createQualifier(cls: String, sch: String): Qualifier = {
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def createQualifier(clsName: String,clsValue: String, schName: String, schValue: String): Qualifier = {
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val q = new Qualifier
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q.setClassid(cls)
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q.setClassname(cls)
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q.setSchemeid(sch)
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q.setSchemename(sch)
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q.setClassid(clsName)
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q.setClassname(clsValue)
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q.setSchemeid(schName)
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q.setSchemename(schValue)
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q
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}
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def createQualifier(cls: String, sch: String): Qualifier = {
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createQualifier(cls, cls, sch, sch)
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}
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def generateItemFromType(objectType: String, objectSubType: String): Result = {
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if (mappingCrossrefType.contains(objectType)) {
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@ -226,4 +346,4 @@ class Crossref2Oaf {
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null
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}
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}
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}
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@ -30,9 +30,9 @@ public class DoiBoostTest {
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}
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@Test
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public void testConvertCrossRef2Oaf() throws IOException {
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public void testConvertPreprintCrossRef2Oaf() throws IOException {
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final String json = IOUtils.toString(getClass().getResourceAsStream("pc.json"));
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final String json = IOUtils.toString(getClass().getResourceAsStream("article.json"));
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ObjectMapper mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT);
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assertNotNull(json);
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assertFalse(StringUtils.isBlank(json));
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@ -73,13 +73,79 @@ public class DoiBoostTest {
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assertTrue(
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result.getRelevantdate().stream()
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.anyMatch(d -> d.getQualifier().getClassid().equalsIgnoreCase("created")));
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// assertTrue(
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// result.getRelevantdate().stream()
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// .anyMatch(
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// d ->
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// d.getQualifier().getClassid().equalsIgnoreCase("available")));
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// assertTrue(
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// result.getRelevantdate().stream()
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// .anyMatch(d ->
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// d.getQualifier().getClassid().equalsIgnoreCase("accepted")));
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assertTrue(
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result.getRelevantdate().stream()
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.anyMatch(
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d -> d.getQualifier().getClassid().equalsIgnoreCase("available")));
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d ->
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d.getQualifier()
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.getClassid()
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.equalsIgnoreCase("published-online")));
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// assertTrue(
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// result.getRelevantdate().stream()
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// .anyMatch(
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// d ->
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// d.getQualifier()
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// .getClassid()
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// .equalsIgnoreCase("published-print")));
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logger.info(mapper.writeValueAsString(result));
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}
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@Test
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public void testConvertBooktCrossRef2Oaf() throws IOException {
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final String json = IOUtils.toString(getClass().getResourceAsStream("book.json"));
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ObjectMapper mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT);
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assertNotNull(json);
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assertFalse(StringUtils.isBlank(json));
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Crossref2Oaf cf = new Crossref2Oaf();
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final Result result = cf.convert(json, logger);
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assertNotNull(result);
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logger.info(mapper.writeValueAsString(result));
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assertNotNull(result.getDataInfo(), "Datainfo test not null Failed");
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assertNotNull(
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result.getDataInfo().getProvenanceaction(),
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"DataInfo/Provenance test not null Failed");
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assertFalse(
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StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getClassid()),
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"DataInfo/Provenance/classId test not null Failed");
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assertFalse(
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StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getClassname()),
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"DataInfo/Provenance/className test not null Failed");
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assertFalse(
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StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getSchemeid()),
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"DataInfo/Provenance/SchemeId test not null Failed");
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assertFalse(
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StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getSchemename()),
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"DataInfo/Provenance/SchemeName test not null Failed");
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assertNotNull(result.getCollectedfrom(), "CollectedFrom test not null Failed");
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assertTrue(result.getCollectedfrom().size() > 0);
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assertTrue(
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result.getCollectedfrom().stream()
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.anyMatch(
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c ->
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c.getKey()
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.equalsIgnoreCase(
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"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")));
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assertTrue(
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result.getCollectedfrom().stream()
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.anyMatch(c -> c.getValue().equalsIgnoreCase("crossref")));
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assertTrue(
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result.getRelevantdate().stream()
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.anyMatch(d -> d.getQualifier().getClassid().equalsIgnoreCase("accepted")));
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.anyMatch(d -> d.getQualifier().getClassid().equalsIgnoreCase("created")));
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assertTrue(
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result.getRelevantdate().stream()
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.anyMatch(
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@ -94,8 +160,6 @@ public class DoiBoostTest {
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d.getQualifier()
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.getClassid()
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.equalsIgnoreCase("published-print")));
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logger.info(mapper.writeValueAsString(result));
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}
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@Test
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@ -0,0 +1,174 @@
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{
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"DOI": "10.26850/1678-4618eqj.v35.1.2010.p41-46",
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"issued": {
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"date-parts": [
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[
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2018,
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1,
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15
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]
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]
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},
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"abstract": "<jats:p>A qualitative spot-test and tandem quantitative analysis of dipyrone in the bulk drugand in pharmaceutical preparations is proposed. The formation of a reddish-violet\u00a0 color indicates a positive result. In sequence a quantitative procedure can be performed in the same flask. The quantitative results obtained were statistically compared with those obtained with the method indicated by the Brazilian\u00a0 Pharmacopoeia, using the Student\u2019s t and the F tests. Considering the concentration in a 100 \u03bcL aliquot, the qualitative visual limit of detection is about 5\u00d710-6 g; instrumental LOD \u2245 1.4\u00d710-4 mol L-1 ; LOQ \u2245 4.5\u00d710-4 mol L-1.</jats:p>",
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"prefix": "10.26850",
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"author": [
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{
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"authenticated-orcid": false,
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"given": "Matthieu",
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"family": "Tubino",
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"sequence": "first",
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"affiliation": [],
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"ORCID": "http://orcid.org/0000-0002-1987-3907"
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},
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{
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"affiliation": [],
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"given": "A. C.",
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"family": "Biondo",
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"sequence": "additional"
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},
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{
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"authenticated-orcid": false,
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"given": "Marta Maria Duarte Carvalho",
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"family": "Vila",
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"sequence": "additional",
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"affiliation": [],
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"ORCID": "http://orcid.org/0000-0002-0198-7076"
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},
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{
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"authenticated-orcid": false,
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"given": "Leonardo",
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"family": "Pezza",
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"sequence": "additional",
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"affiliation": [],
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"ORCID": "http://orcid.org/0000-0003-0197-7369"
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},
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{
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"authenticated-orcid": false,
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"given": "Helena Redigolo",
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"family": "Pezza",
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"sequence": "additional",
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"affiliation": [],
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"ORCID": "http://orcid.org/0000-0001-5564-1639"
|
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Loading…
Reference in New Issue