forked from D-Net/dnet-hadoop
Merge pull request 'Crossref Enhancements:' (#511) from crossref_mapping_improvement into beta
Reviewed-on: D-Net/dnet-hadoop#511
This commit is contained in:
commit
77308ed525
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@ -37,7 +37,7 @@ case class mappingAuthor(
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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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affiliation: Option[List[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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@ -457,15 +457,14 @@ case object Crossref2Oaf {
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}
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//Mapping Author
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val authorList: List[mappingAuthor] =
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(json \ "author").extract[List[mappingAuthor]].filter(a => a.family.isDefined)
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val authorList: List[mappingAuthor] = (json \ "author").extract[List[mappingAuthor]].filter(a => a.family.isDefined)
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val sorted_list = authorList.sortWith((a: mappingAuthor, b: mappingAuthor) =>
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a.sequence.isDefined && a.sequence.get.equalsIgnoreCase("first")
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)
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result.setAuthor(sorted_list.zipWithIndex.map { case (a, index) =>
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generateAuhtor(a.given.orNull, a.family.get, a.ORCID.orNull, index)
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generateAuthor(a.given.orNull, a.family.get, a.ORCID.orNull, index, a.affiliation)
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}.asJava)
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// Mapping instance
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@ -504,18 +503,6 @@ case object Crossref2Oaf {
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)
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}
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val is_review = json \ "relation" \ "is-review-of" \ "id"
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if (is_review != JNothing) {
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instance.setInstancetype(
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OafMapperUtils.qualifier(
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"0015",
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"peerReviewed",
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ModelConstants.DNET_REVIEW_LEVELS,
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ModelConstants.DNET_REVIEW_LEVELS
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)
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)
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}
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if (doi.startsWith("10.3410") || doi.startsWith("10.12703"))
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instance.setHostedby(
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@ -569,17 +556,24 @@ case object Crossref2Oaf {
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result
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}
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def generateIdentifier(oaf: Result, doi: String): String = {
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val id = DHPUtils.md5(doi.toLowerCase)
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s"50|doiboost____|$id"
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}
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def generateAuhtor(given: String, family: String, orcid: String, index: Int): Author = {
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private def generateAuthor(given: String, family: String, orcid: String, index: Int, affiliation: Option[List[mappingAffiliation]]): Author = {
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val a = new Author
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a.setName(given)
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a.setSurname(family)
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a.setFullname(s"$given $family")
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a.setRank(index + 1)
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// Adding Raw affiliation if it's defined
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if (affiliation.isDefined) {
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a.setRawAffiliationString(affiliation.get.map(a => a.name).asJava)
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}
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if (StringUtils.isNotBlank(orcid))
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a.setPid(
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List(
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@ -705,11 +699,21 @@ case object Crossref2Oaf {
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val objectType = (json \ "type").extractOrElse[String](null)
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if (objectType == null)
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return resultList
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val typology = getTypeQualifier(objectType, vocabularies)
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// If the item has a relations is-review-of, then we force it to a peer-review
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val is_review = json \ "relation" \ "is-review-of" \ "id"
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var force_to_review = false
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if (is_review != JNothing) {
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force_to_review = true
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}
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val typology = getTypeQualifier(if (force_to_review) "peer-review" else objectType, vocabularies)
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if (typology == null)
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return List()
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val result = generateItemFromType(typology._2)
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if (result == null)
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return List()
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@ -757,33 +761,6 @@ case object Crossref2Oaf {
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else
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resultList
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}
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// if (uw != null) {
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// result.getCollectedfrom.add(createUnpayWallCollectedFrom())
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// val i: Instance = new Instance()
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// i.setCollectedfrom(createUnpayWallCollectedFrom())
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// if (uw.best_oa_location != null) {
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//
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// i.setUrl(List(uw.best_oa_location.url).asJava)
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// if (uw.best_oa_location.license.isDefined) {
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// i.setLicense(field[String](uw.best_oa_location.license.get, null))
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// }
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//
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// val colour = get_unpaywall_color(uw.oa_status)
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// if (colour.isDefined) {
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// val a = new AccessRight
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// a.setClassid(ModelConstants.ACCESS_RIGHT_OPEN)
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// a.setClassname(ModelConstants.ACCESS_RIGHT_OPEN)
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// a.setSchemeid(ModelConstants.DNET_ACCESS_MODES)
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// a.setSchemename(ModelConstants.DNET_ACCESS_MODES)
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// a.setOpenAccessRoute(colour.get)
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// i.setAccessright(a)
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// }
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// i.setPid(result.getPid)
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// result.getInstance().add(i)
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// }
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// }
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}
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private def createCiteRelation(source: Result, targetPid: String, targetPidType: String): List[Relation] = {
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@ -0,0 +1,232 @@
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{
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"indexed": {
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"date-parts": [
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[
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2022,
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4,
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3
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]
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],
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"date-time": "2022-04-03T01:45:59Z",
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"timestamp": 1648950359167
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},
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"reference-count": 0,
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"publisher": "American Society of Clinical Oncology (ASCO)",
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"issue": "18_suppl",
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"content-domain": {
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"domain": [],
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"crossmark-restriction": false
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},
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"short-container-title": [
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"JCO"
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],
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"published-print": {
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"date-parts": [
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[
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2007,
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6,
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20
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]
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]
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},
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"abstract": "<jats:p> 3507 </jats:p><jats:p> Purpose: To detect IGF-1R on circulating tumor cells (CTCs) as a biomarker in the clinical development of a monoclonal human antibody, CP-751,871, targeting IGF-1R. Experimental Design: An automated sample preparation and analysis system for enumerating CTCs (Celltracks) was adapted for detecting IGF-1R positive CTCs with a diagnostic antibody targeting a different IGF-1R epitope to CP-751,871. This assay was utilized in three phase I trials of CP-751,871 as a single agent or with chemotherapy and was validated using cell lines and blood samples from healthy volunteers and patients with metastatic carcinoma. Results: There was no interference between the analytical and therapeutic antibodies. CP-751,871 was well tolerated as a single agent, and in combination with docetaxel or carboplatin and paclitaxel, at doses ranging from 0.05 mg/kg to 20 mg/kg. Eighty patients were enrolled on phase 1 studies of CP-751,871, with 47 (59%) patients having CTCs detected during the study. Prior to treatment 26 patients (33%) had CTCs, with 23 having detectable IGF-1R positive CTCs. CP-751,871 alone, and CP-751,871 with cytotoxic chemotherapy, decreased CTCs and IGF-1R positive CTCs; these increased towards the end of the 21-day cycle in some patients, falling again with retreatment. CTCs were commonest in advanced hormone refractory prostate cancer (11/20). Detectable IGF-1R expression on CTCs before treatment with CP-751,871 and docetaxel was associated with a higher frequency of PSA decline by more than 50% (6/10 vs 2/8 patients). A relationship was observed between sustained falls in CTCs counts and PSA declines by more than 50%. Conclusions: IGF-1R expression is detectable by immunofluorescence on CTCs. These data support the further evaluation of CTCs in pharmacodynamic studies and patient selection, particularly in advanced prostate cancer. </jats:p><jats:p> No significant financial relationships to disclose. </jats:p>",
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"DOI": "10.1200/jco.2007.25.18_suppl.3507",
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"type": "journal-article",
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"created": {
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"date-parts": [
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[
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2020,
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3,
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6
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]
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],
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"date-time": "2020-03-06T20:50:42Z",
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"timestamp": 1583527842000
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},
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"page": "3507-3507",
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"source": "Crossref",
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"is-referenced-by-count": 0,
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"title": [
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"Circulating tumor cells expressing the insulin growth factor-1 receptor (IGF-1R): Method of detection, incidence and potential applications"
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],
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"prefix": "10.1200",
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"volume": "25",
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"author": [
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{
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"given": "J. S.",
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"family": "de Bono",
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"sequence": "first",
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"affiliation": [
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{
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"name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
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}
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]
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},
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{
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"given": "A.",
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"family": "Adjei",
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"sequence": "additional",
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"affiliation": [
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{
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"name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
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}
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]
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},
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{
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"given": "G.",
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"family": "Attard",
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"sequence": "additional",
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"affiliation": [
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{
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"name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
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}
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]
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},
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{
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"given": "M.",
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"family": "Pollak",
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"sequence": "additional",
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"affiliation": [
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{
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"name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
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}
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]
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},
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{
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"given": "P.",
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"family": "Fong",
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"sequence": "additional",
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"affiliation": [
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{
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"name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
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}
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]
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},
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{
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"given": "P.",
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"family": "Haluska",
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"sequence": "additional",
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"affiliation": [
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{
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"name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
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}
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]
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},
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{
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"given": "L.",
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"family": "Roberts",
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"sequence": "additional",
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"affiliation": [
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{
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"name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
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}
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]
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},
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{
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"given": "D.",
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"family": "Chainese",
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"sequence": "additional",
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"affiliation": [
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{
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"name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
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}
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]
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},
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{
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"given": "L.",
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"family": "Terstappen",
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"sequence": "additional",
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"affiliation": [
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{
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"name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
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}
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]
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},
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{
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"given": "A.",
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"family": "Gualberto",
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"sequence": "additional",
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"affiliation": [
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{
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"name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
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}
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]
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}
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],
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"member": "233",
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"container-title": [
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"Journal of Clinical Oncology"
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],
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"original-title": [],
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"language": "en",
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"deposited": {
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"date-parts": [
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[
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2020,
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3,
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6
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]
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],
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"date-time": "2020-03-06T20:51:03Z",
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"timestamp": 1583527863000
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},
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"score": 1,
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"resource": {
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"primary": {
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"URL": "http://ascopubs.org/doi/10.1200/jco.2007.25.18_suppl.3507"
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}
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},
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"subtitle": [],
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"short-title": [],
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"issued": {
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"date-parts": [
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[
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2007,
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6,
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20
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]
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]
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},
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"references-count": 0,
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"journal-issue": {
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"issue": "18_suppl",
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"published-print": {
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"date-parts": [
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[
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2007,
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6,
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20
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]
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]
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}
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},
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"alternative-id": [
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"10.1200/jco.2007.25.18_suppl.3507"
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],
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"URL": "http://dx.doi.org/10.1200/jco.2007.25.18_suppl.3507",
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"relation": {},
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"ISSN": [
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"0732-183X",
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"1527-7755"
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],
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"issn-type": [
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{
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"value": "0732-183X",
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"type": "print"
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},
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{
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"value": "1527-7755",
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"type": "electronic"
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}
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],
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"subject": [],
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"published": {
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"date-parts": [
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[
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2007,
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6,
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20
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]
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]
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}
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}
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@ -3,12 +3,15 @@ package eu.dnetlib.dhp.collection.crossref
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
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import eu.dnetlib.dhp.collection.crossref.Crossref2Oaf.TransformationType
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import eu.dnetlib.dhp.schema.oaf.Publication
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import org.apache.commons.io.IOUtils
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import org.junit.jupiter.api.{BeforeEach, Test}
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import org.junit.jupiter.api.{Assertions, BeforeEach, Test}
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import org.junit.jupiter.api.extension.ExtendWith
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import org.mockito.junit.jupiter.MockitoExtension
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import org.slf4j.{Logger, LoggerFactory}
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import scala.collection.JavaConverters.asScalaBufferConverter
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@ExtendWith(Array(classOf[MockitoExtension]))
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class CrossrefMappingTest extends AbstractVocabularyTest {
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@ -25,8 +28,28 @@ class CrossrefMappingTest extends AbstractVocabularyTest {
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val input =
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IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/issn_pub.json"), "utf-8")
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println(Crossref2Oaf.convert(input, vocabularies, TransformationType.All))
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Crossref2Oaf.convert(input, vocabularies, TransformationType.All).foreach(record => {
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Assertions.assertNotNull(record)
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})
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}
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@Test
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def mappingAffiliation(): Unit = {
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val input =
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IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/affiliationTest.json"), "utf-8")
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val data = Crossref2Oaf.convert(input, vocabularies, TransformationType.OnlyResult)
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data.foreach(record => {
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Assertions.assertNotNull(record)
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Assertions.assertTrue(record.isInstanceOf[Publication])
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val publication = record.asInstanceOf[Publication]
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publication.getAuthor.asScala.foreach(author => {
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Assertions.assertNotNull(author.getRawAffiliationString)
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Assertions.assertTrue(author.getRawAffiliationString.size()>0)
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})
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})
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println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(data.head))
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}
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}
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|
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