From 288ec0b7d6c6214cd996d34f3c7f604d00ca45e5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 28 Jun 2023 09:15:37 +0200 Subject: [PATCH] [doiboost] merged workflow from branch beta --- .../orcidnodoi/oaf/PublicationToOaf.java | 2 +- .../doiboost/DoiBoostMappingUtil.scala | 22 + .../doiboost/crossref/Crossref2Oaf.scala | 32 +- .../dnetlib/doiboost/mag/MagDataModel.scala | 12 +- .../crossref/publication_license_embargo.json | 3006 ++++++++--------- .../crossref/CrossrefMappingTest.scala | 46 + 6 files changed, 1578 insertions(+), 1542 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java index f92040c24..ba7c7dd01 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -554,7 +554,7 @@ public class PublicationToOaf implements Serializable { private KeyValue createCollectedFrom() { KeyValue cf = new KeyValue(); cf.setValue(ModelConstants.ORCID.toUpperCase()); - cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a"); + cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "cd0f74b5955dc87fd0605745c4b49ee8"); return cf; } diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala index 20471973a..4789093cd 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala @@ -391,6 +391,28 @@ object DoiBoostMappingUtil { di } + def createSubject(value: String, classId: String, schemeId: String): Subject = { + val s = new Subject + s.setQualifier(OafMapperUtils.qualifier(classId, classId, schemeId, schemeId)) + s.setValue(value) + s + + } + + def createSubject( + value: String, + classId: String, + className: String, + schemeId: String, + schemeName: String + ): Subject = { + val s = new Subject + s.setQualifier(OafMapperUtils.qualifier(classId, className, schemeId, schemeName)) + s.setValue(value) + s + + } + def createSP( value: String, classId: String, diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 1b1b384cc..9c63b709b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -201,7 +201,7 @@ case object Crossref2Oaf { if (subjectList.nonEmpty) { result.setSubject( - subjectList.map(s => createSP(s, "keywords", ModelConstants.DNET_SUBJECT_TYPOLOGIES)).asJava + subjectList.map(s => createSubject(s, "keyword", ModelConstants.DNET_SUBJECT_TYPOLOGIES)).asJava ) } @@ -370,10 +370,40 @@ case object Crossref2Oaf { 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 + } resultList = resultList ::: List(result) resultList } + 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, diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala index 18ba864ce..9a0b0d845 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala @@ -2,7 +2,7 @@ package eu.dnetlib.doiboost.mag import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory -import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty} +import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty, Subject} import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.DoiBoostMappingUtil._ import org.json4s @@ -210,8 +210,8 @@ case object ConversionUtil { val className = "Microsoft Academic Graph classification" val classid = "MAG" - val p: List[StructuredProperty] = fieldOfStudy.subjects.flatMap(s => { - val s1 = createSP( + val p: List[Subject] = fieldOfStudy.subjects.flatMap(s => { + val s1 = createSubject( s.DisplayName, classid, className, @@ -219,10 +219,10 @@ case object ConversionUtil { ModelConstants.DNET_SUBJECT_TYPOLOGIES ) val di = DoiBoostMappingUtil.generateDataInfo(s.Score.toString) - var resList: List[StructuredProperty] = List(s1) + var resList: List[Subject] = List(s1) if (s.MainType.isDefined) { val maintp = s.MainType.get - val s2 = createSP( + val s2 = createSubject( s.MainType.get, classid, className, @@ -232,7 +232,7 @@ case object ConversionUtil { s2.setDataInfo(di) resList = resList ::: List(s2) if (maintp.contains(".")) { - val s3 = createSP( + val s3 = createSubject( maintp.split("\\.").head, classid, className, diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json index 788946fea..b66147b2d 100644 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json @@ -1,1537 +1,1475 @@ { -"indexed": { -"date-parts": [ -[ -2021, -7, -2 -] -], -"date-time": "2021-07-02T07:30:10Z", -"timestamp": 1625211010708 -}, -"reference-count": 83, -"publisher": "Springer Science and Business Media LLC", -"issue": "5", -"license": [ -{ -"URL": "https://www.springer.com/tdm", -"start": { -"date-parts": [ -[ -2021, -2, -22 -] -], -"date-time": "2021-02-22T00:00:00Z", -"timestamp": 1613952000000 -}, -"delay-in-days": 0, -"content-version": "tdm" -}, -{ -"URL": "https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model", -"start": { -"date-parts": [ -[ -2021, -2, -22 -] -], -"date-time": "2021-02-22T00:00:00Z", -"timestamp": 1613952000000 -}, -"delay-in-days": 0, -"content-version": "vor" -} -], -"content-domain": { -"domain": [ -"link.springer.com" -], -"crossmark-restriction": false -}, -"short-container-title": [ -"Nat Astron" -], -"published-print": { -"date-parts": [ -[ -2021, -5 -] -] -}, -"DOI": "10.1038/s41550-020-01295-8", -"type": "journal-article", -"created": { -"date-parts": [ -[ -2021, -2, -22 -] -], -"date-time": "2021-02-22T17:03:42Z", -"timestamp": 1614013422000 -}, -"page": "510-518", -"update-policy": "http://dx.doi.org/10.1007/springer_crossmark_policy", -"source": "Crossref", -"is-referenced-by-count": 6, -"title": [ -"A tidal disruption event coincident with a high-energy neutrino" -], -"prefix": "10.1038", -"volume": "5", -"author": [ -{ -"ORCID": "http://orcid.org/0000-0003-2434-0387", -"authenticated-orcid": false, -"given": "Robert", -"family": "Stein", -"sequence": "first", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-3859-8074", -"authenticated-orcid": false, -"given": "Sjoert van", -"family": "Velzen", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0001-8594-8666", -"authenticated-orcid": false, -"given": "Marek", -"family": "Kowalski", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Anna", -"family": "Franckowiak", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-3703-5154", -"authenticated-orcid": false, -"given": "Suvi", -"family": "Gezari", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-3124-2814", -"authenticated-orcid": false, -"given": "James C. A.", -"family": "Miller-Jones", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Sara", -"family": "Frederick", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-0466-3779", -"authenticated-orcid": false, -"given": "Itai", -"family": "Sfaradi", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Michael F.", -"family": "Bietenholz", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-5936-1156", -"authenticated-orcid": false, -"given": "Assaf", -"family": "Horesh", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Rob", -"family": "Fender", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-2403-4582", -"authenticated-orcid": false, -"given": "Simone", -"family": "Garrappa", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-2184-6430", -"authenticated-orcid": false, -"given": "Tomás", -"family": "Ahumada", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Igor", -"family": "Andreoni", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Justin", -"family": "Belicki", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0001-8018-5348", -"authenticated-orcid": false, -"given": "Eric C.", -"family": "Bellm", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Markus", -"family": "Böttcher", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Valery", -"family": "Brinnel", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Rick", -"family": "Burruss", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-1673-970X", -"authenticated-orcid": false, -"given": "S. Bradley", -"family": "Cenko", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-8262-2924", -"authenticated-orcid": false, -"given": "Michael W.", -"family": "Coughlin", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-2292-0441", -"authenticated-orcid": false, -"given": "Virginia", -"family": "Cunningham", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Andrew", -"family": "Drake", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Glennys R.", -"family": "Farrar", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Michael", -"family": "Feeney", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Ryan J.", -"family": "Foley", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-3653-5598", -"authenticated-orcid": false, -"given": "Avishay", -"family": "Gal-Yam", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "V. Zach", -"family": "Golkhou", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-4163-4996", -"authenticated-orcid": false, -"given": "Ariel", -"family": "Goobar", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-3168-0139", -"authenticated-orcid": false, -"given": "Matthew J.", -"family": "Graham", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Erica", -"family": "Hammerstein", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-3367-3415", -"authenticated-orcid": false, -"given": "George", -"family": "Helou", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-9878-7889", -"authenticated-orcid": false, -"given": "Tiara", -"family": "Hung", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Mansi M.", -"family": "Kasliwal", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-5740-7747", -"authenticated-orcid": false, -"given": "Charles D.", -"family": "Kilpatrick", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-5105-344X", -"authenticated-orcid": false, -"given": "Albert K. H.", -"family": "Kong", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-6540-1484", -"authenticated-orcid": false, -"given": "Thomas", -"family": "Kupfer", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-2451-5482", -"authenticated-orcid": false, -"given": "Russ R.", -"family": "Laher", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-2242-0244", -"authenticated-orcid": false, -"given": "Ashish A.", -"family": "Mahabal", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-8532-9395", -"authenticated-orcid": false, -"given": "Frank J.", -"family": "Masci", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-0280-7484", -"authenticated-orcid": false, -"given": "Jannis", -"family": "Necker", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0001-8342-6274", -"authenticated-orcid": false, -"given": "Jakob", -"family": "Nordin", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Daniel A.", -"family": "Perley", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-8121-2560", -"authenticated-orcid": false, -"given": "Mickael", -"family": "Rigault", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-7788-628X", -"authenticated-orcid": false, -"given": "Simeon", -"family": "Reusch", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Hector", -"family": "Rodriguez", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-7559-315X", -"authenticated-orcid": false, -"given": "César", -"family": "Rojas-Bravo", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0001-7648-4142", -"authenticated-orcid": false, -"given": "Ben", -"family": "Rusholme", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-4401-0430", -"authenticated-orcid": false, -"given": "David L.", -"family": "Shupe", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0001-9898-5597", -"authenticated-orcid": false, -"given": "Leo P.", -"family": "Singer", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-1546-6615", -"authenticated-orcid": false, -"given": "Jesper", -"family": "Sollerman", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Maayane T.", -"family": "Soumagnac", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Daniel", -"family": "Stern", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Kirsty", -"family": "Taggart", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Jakob", -"family": "van Santen", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Charlotte", -"family": "Ward", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Patrick", -"family": "Woudt", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0001-6747-8509", -"authenticated-orcid": false, -"given": "Yuhan", -"family": "Yao", -"sequence": "additional", -"affiliation": [ - -] -} -], -"member": "297", -"published-online": { -"date-parts": [ -[ -2021, -2, -22 -] -] -}, -"reference": [ -{ -"key": "1295_CR1", -"doi-asserted-by": "crossref", -"first-page": "P03012", -"DOI": "10.1088/1748-0221/12/03/P03012", -"volume": "12", -"author": "MG Aartsen", -"year": "2017", -"unstructured": "Aartsen, M. G. et al. The IceCube Neutrino Observatory: instrumentation and online systems. J. Instrum. 12, P03012 (2017).", -"journal-title": "J. Instrum." -}, -{ -"key": "1295_CR2", -"unstructured": "Stein, R. IceCube-191001A—IceCube observation of a high-energy neutrino candidate event. GCN Circ. 25913 (2019)." -}, -{ -"key": "1295_CR3", -"doi-asserted-by": "crossref", -"first-page": "018002", -"DOI": "10.1088/1538-3873/aaecbe", -"volume": "131", -"author": "EC Bellm", -"year": "2019", -"unstructured": "Bellm, E. C. et al. The Zwicky Transient Facility: system overview, performance, and first results. Publ. Astron. Soc. Pac. 131, 018002 (2019).", -"journal-title": "Publ. Astron. Soc. Pac." -}, -{ -"key": "1295_CR4", -"doi-asserted-by": "crossref", -"first-page": "533", -"DOI": "10.1016/j.astropartphys.2007.03.005", -"volume": "27", -"author": "M Kowalski", -"year": "2007", -"unstructured": "Kowalski, M. & Mohr, A. Detecting neutrino transients with optical follow-up observations. Astropart. Phys. 27, 533–538 (2007).", -"journal-title": "Astropart. Phys." -}, -{ -"key": "1295_CR5", -"doi-asserted-by": "crossref", -"first-page": "329", -"DOI": "10.1088/0004-637X/693/1/329", -"volume": "693", -"author": "GR Farrar", -"year": "2009", -"unstructured": "Farrar, G. R. & Gruzinov, A. Giant AGN flares and cosmic ray bursts. Astrophys. J. 693, 329–332 (2009).", -"journal-title": "Astrophys. J." -}, -{ -"key": "1295_CR6", -"doi-asserted-by": "crossref", -"first-page": "1354", -"DOI": "10.1093/mnras/stx863", -"volume": "469", -"author": "L Dai", -"year": "2017", -"unstructured": "Dai, L. & Fang, K. Can tidal disruption events produce the IceCube neutrinos? Mon. Not. R. Astron. Soc. 469, 1354–1359 (2017).", -"journal-title": "Mon. Not. R. Astron. Soc." -}, -{ -"key": "1295_CR7", -"doi-asserted-by": "crossref", -"first-page": "114", -"DOI": "10.3847/1538-4357/ab44ca", -"volume": "886", -"author": "K Hayasaki", -"year": "2019", -"unstructured": "Hayasaki, K. & Yamazaki, R. 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