From 507e42102a7bd697dcf9fcf8fd3b86e5a039aa5e Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Mon, 21 Jun 2021 09:36:40 +0200 Subject: [PATCH] added pdb to oaf class --- .../aggregation/AbstractVocabularyTest.java | 14 +- .../dhp/actionmanager/datacite/record.json | 2 +- .../eu/dnetlib/dhp/transform/synonyms.txt | 1235 +++++++++++++++++ .../eu/dnetlib/dhp/transform/terms.txt | 1080 ++++++++++++++ .../java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala | 16 +- 5 files changed, 2336 insertions(+), 11 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/aggregation/AbstractVocabularyTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/aggregation/AbstractVocabularyTest.java index 8e0f0ce4b..9735c80b0 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/aggregation/AbstractVocabularyTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/aggregation/AbstractVocabularyTest.java @@ -6,13 +6,13 @@ import static org.mockito.Mockito.lenient; import java.io.IOException; import java.util.Collections; import java.util.List; +import java.util.Objects; import org.apache.commons.io.IOUtils; import org.mockito.Mock; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.transformation.TransformationFactory; -import eu.dnetlib.dhp.transformation.TransformationJobTest; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -34,16 +34,22 @@ public abstract class AbstractVocabularyTest { private static List vocs() throws IOException { return IOUtils - .readLines(TransformationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/terms.txt")); + .readLines( + Objects + .requireNonNull( + AbstractVocabularyTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/terms.txt"))); } private static List synonyms() throws IOException { return IOUtils - .readLines(TransformationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/synonyms.txt")); + .readLines( + Objects + .requireNonNull( + AbstractVocabularyTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/synonyms.txt"))); } protected void mockupTrasformationRule(final String trule, final String path) throws Exception { - final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path)); + final String trValue = IOUtils.toString(Objects.requireNonNull(this.getClass().getResourceAsStream(path))); lenient() .when(isLookUpService.quickSearchProfile(String.format(TransformationFactory.TRULE_XQUERY, trule))) diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record.json index c66498fac..3ae10be73 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record.json +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record.json @@ -1 +1 @@ -{"relationships": {"client": {"data": {"type": "clients", "id": "figshare.ars"}}}, "attributes": {"partCount": 0, "contributors": [], "versionCount": 0, "titles": [{"title": "Occurrence Download"}], "descriptions": [{"lang": "eng", "descriptionType": "Abstract", "description": "A dataset containing 2452 species occurrences available in GBIF matching the query: { \"TaxonKey\" : [ \"is Indotyphlops braminus (Daudin, 1803)\" ] } The dataset includes 2452 records from 48 constituent datasets: 8 records from India Biodiversity Portal publication grade dataset. 6 records from UCM Amphibian and Reptile Collection (Arctos). 577 records from iNaturalist Research-grade Observations. 5 records from NCSM Herpetology Collection. 4 records from Vertebrate Zoology Division - Herpetology, Yale Peabody Museum. 4 records from Asian Herpetological Collection - IICT. 11 records from WildNet - Queensland Wildlife Data. 68 records from Australian Museum provider for OZCAM. 33 records from Geographically tagged INSDC sequences. 8 records from LACM Vertebrate Collection. 19 records from Herpetology. 88 records from KUBI Herpetology Collection. 187 records from The reptiles and amphibians collection (RA) of the Mus\u00e9um national d'Histoire Naturelle (MNHN - Paris). 36 records from Queensland Museum provider for OZCAM. 46 records from DAYO: Invasive Alien Reptiles in the Philippines. 33 records from MVZ Herp Collection (Arctos). 22 records from BYU Herpetology Collection. 1 records from Atlas des amphibiens et reptiles de Martinique. 2 records from University of Alberta Museum of Zoology Amphibian and Reptile Collection (UAMZ). 2 records from NMNH Paleobiology Specimen Records. 23 records from South Australian Museum Australia provider for OZCAM. 30 records from Fauna Atlas N.T.. 302 records from Museum of Comparative Zoology, Harvard University. 9 records from Herpetology Collection NRM. 397 records from University of Florida Herpetology. 40 records from Western Australian Museum provider for OZCAM. 1 records from Collection Herpetology SMF. 16 records from TNHC Herpetology Collection. 28 records from International Barcode of Life project (iBOL). 26 records from Base de donn\u00e9es de NOI \u2013 JDD_HISTORIQUE. 24 records from Naturalis Biodiversity Center (NL) - Amphibia and Reptilia. 242 records from Field Museum of Natural History (Zoology) Amphibian and Reptile Collection. 18 records from Australian National Wildlife Collection provider for OZCAM. 1 records from Herpetology. 1 records from Donn\u00e9es naturalistes d'Olivier ESCUDER. 12 records from Reptile Specimens. 1 records from Lund Museum of Zoology (MZLU). 2 records from Donn\u00e9es d'occurrences Esp\u00e8ces issues de l'inventaire des ZNIEFF. 6 records from Museums Victoria provider for OZCAM. 3 records from Questagame weekly feed. 78 records from Northern Territory Museum and Art Gallery provider for OZCAM. 1 records from SysTax - Zoological Collections. 11 records from UMZC Zoological Specimens. 1 records from AUMNH Herpetology Voucher Collection. 1 records from Tissues Specimens. 10 records from Apoyo a las colecciones biol\u00f3gicas de la Facultad de Ciencias de la UNAM: Fase 1 (MZFC_HE). 4 records from HerpMapper. 4 records from ALA species sightings and OzAtlas. 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Xu","nameType":"Personal","givenName":"Xu","familyName":"Huang","affiliation":[],"nameIdentifiers":[]},{"name":"Guo, Zhixiong","nameType":"Personal","givenName":"Zhixiong","familyName":"Guo","nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0003-0481-2738","nameIdentifierScheme":"ORCID"}],"affiliation":[]}],"titles":[{"title":"High thermal conductance across c-BN/diamond interface"}],"publisher":"Rutgers University","container":{},"publicationYear":2099,"subjects":[{"subject":"Diamond"},{"subject":"Cubic boron nitride"},{"subject":"Thermal conductivity"},{"subject":"Interface"},{"subject":"Phonon"},{"subject":"Thermal conductance"}],"contributors":[],"dates":[{"date":"2099-12-31","dateType":"Accepted"},{"date":"2099","dateType":"Issued"}],"language":"en","types":{"ris":"RPRT","bibtex":"article","citeproc":"article-journal","schemaOrg":"ScholarlyArticle","resourceType":"Accepted 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Diamond, a superhard material with ultrahigh thermal conductivity at room temperature, is desirable for microelectronics thermal management. Cubic polymorph of boron nitride (c-BN) is a promising material due to wide bandgap and diamond like structure and properties. To understand the nature in thermal transport of diamond, c-BN and the most commonly used silicon (Si) semiconductor, ab initio phonon Boltzmann transport equations are employed to investigate lattice vibrational properties of these three materials. At 300 K, the predicted thermal conductivity of Si, diamond and c-BN reached 142, 2112, and 736 W/(m��K), respectively. What's more, heat transport phenomena across the interfaces of Si/diamond, c-BN/diamond and Si/c-BN are unfolded. In comparison, the interfacial thermal conductance of c-BN/diamond is ten-fold of Si/diamond; besides, the thermal conductance across Si/c-BN interface is 20.2% larger than that of Si/diamond at 300 K and 18.9% larger at 340 K. These findings provide us new vision and potential solution to heat dissipation of high-local-power density devices, shedding light on future thermal management of c-BN and diamond related electronics.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://scholarship.libraries.rutgers.edu/discovery/fulldisplay/alma991031549917804646/01RUT_INST:ResearchRepository","contentUrl":null,"metadataVersion":1,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2020-06-30T21:12:19Z","registered":"2020-07-02T16:45:07Z","published":null,"updated":"2021-01-14T18:24:19Z"},"relationships":{"client":{"data":{"id":"rutgers.lib","type":"clients"}}}} \ No newline at end of file diff --git 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@=@ dataset @=@ dataset +dnet:externalReference_typologies @=@ dnet:externalReference_typologies @=@ software @=@ software +datacite:id_typologies @=@ datacite:id_typologies @=@ ARK @=@ ARK +datacite:id_typologies @=@ datacite:id_typologies @=@ DOI @=@ DOI +datacite:id_typologies @=@ datacite:id_typologies @=@ EAN13 @=@ EAN13 +datacite:id_typologies @=@ datacite:id_typologies @=@ EISSN @=@ EISSN +datacite:id_typologies @=@ datacite:id_typologies @=@ Handle @=@ Handle +datacite:id_typologies @=@ datacite:id_typologies @=@ ISBN @=@ ISBN +datacite:id_typologies @=@ datacite:id_typologies @=@ ISSN @=@ ISSN +datacite:id_typologies @=@ datacite:id_typologies @=@ ISTC @=@ ISTC +datacite:id_typologies @=@ datacite:id_typologies @=@ LISSN @=@ LISSN +datacite:id_typologies @=@ datacite:id_typologies @=@ LSID @=@ LSID +datacite:id_typologies @=@ datacite:id_typologies @=@ PURL @=@ PURL +datacite:id_typologies @=@ datacite:id_typologies @=@ UNKNOWN @=@ UNKNOWN +datacite:id_typologies @=@ datacite:id_typologies @=@ UPC @=@ UPC +datacite:id_typologies @=@ datacite:id_typologies @=@ URL @=@ URL +datacite:id_typologies @=@ datacite:id_typologies @=@ URN @=@ URN +dnet:pid_types @=@ dnet:pid_types @=@ actrn @=@ ACTRN Identifier +dnet:pid_types @=@ dnet:pid_types @=@ nct @=@ ClinicalTrials.gov Identifier +dnet:pid_types @=@ dnet:pid_types @=@ euctr @=@ EU Clinical Trials Register +dnet:pid_types @=@ dnet:pid_types @=@ epo_id @=@ European Patent Office application ID +dnet:pid_types @=@ dnet:pid_types @=@ gsk @=@ GSK Identifier +dnet:pid_types @=@ dnet:pid_types @=@ GeoPass @=@ Geographic Location-Password Scheme +dnet:pid_types @=@ dnet:pid_types @=@ GBIF @=@ Global Biodiversity Information Facility +dnet:pid_types @=@ dnet:pid_types @=@ isrctn @=@ ISRCTN Identifier +dnet:pid_types @=@ dnet:pid_types @=@ ISNI @=@ International Standard Name Identifier +dnet:pid_types @=@ dnet:pid_types @=@ jprn @=@ JPRN Identifier +dnet:pid_types @=@ dnet:pid_types @=@ mag_id @=@ Microsoft Academic Graph Identifier +dnet:pid_types @=@ dnet:pid_types @=@ oai @=@ Open Archives Initiative +dnet:pid_types @=@ dnet:pid_types @=@ orcid @=@ Open Researcher and Contributor ID +dnet:pid_types @=@ dnet:pid_types @=@ PANGAEA @=@ PANGAEA +dnet:pid_types @=@ dnet:pid_types @=@ epo_nr_epodoc @=@ Patent application number in EPODOC format +dnet:pid_types @=@ dnet:pid_types @=@ UNKNOWN @=@ UNKNOWN +dnet:pid_types @=@ dnet:pid_types @=@ VIAF @=@ Virtual International Authority File +dnet:pid_types @=@ dnet:pid_types @=@ arXiv @=@ arXiv +dnet:pid_types @=@ dnet:pid_types @=@ doi @=@ doi +dnet:pid_types @=@ dnet:pid_types @=@ grid @=@ grid +dnet:pid_types @=@ dnet:pid_types @=@ info:eu-repo/dai @=@ info:eu-repo/dai +dnet:pid_types @=@ dnet:pid_types @=@ orcidworkid @=@ orcid workid +dnet:pid_types @=@ dnet:pid_types @=@ pmc @=@ pmc +dnet:pid_types @=@ dnet:pid_types @=@ pmid @=@ pmid +dnet:pid_types @=@ dnet:pid_types @=@ urn @=@ urn +dnet:pid_types @=@ dnet:pid_types @=@ who @=@ WHO Identifier +dnet:pid_types @=@ dnet:pid_types @=@ drks @=@ DRKS Identifier +dnet:pid_types @=@ dnet:pid_types @=@ handle @=@ Handle +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/ACM @=@ An ACM classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/ARXIV @=@ An ARXIV classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/DDC @=@ A Dewey Decimal classification term (DDC) that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/JEL @=@ A Journal of Economic Literature (JEL) classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/OPENACCESS_VERSION @=@ An Open Access versions of your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_REFERENCED_BY @=@ A dataset referenced by your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/REFERENCES @=@ A dataset that refers to your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_RELATED_TO @=@ A dataset related to your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_TO @=@ A dataset that supplements your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PUBLICATION/IS_RELATED_TO @=@ A publication related to your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PUBLICATION/REFERENCES @=@ A publication referenced by your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PUBLICATION/IS_REFERENCED_BY @=@ A publication that refers to your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_BY @=@ A publication that is supplemented by your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_TO @=@ A publication that supplements your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SOFTWARE @=@ A software referred by your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/OPENACCESS_VERSION @=@ Another Open Access version of a publication +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/PID @=@ Another persistent identifier associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/MESHEUROPMC @=@ A classification term from the Medical Subject Headings (MeSH) that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/ABSTRACT @=@ An abstract describing among your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PUBLICATION_DATE @=@ A date of publication missing in your content +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PID @=@ A persistent identifier associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/ACM @=@ Another ACM classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/ARXIV @=@ Another ARXIV classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/DDC @=@ Another Dewey Decimal classification term (DDC) that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/JEL @=@ Another Journal of Economic Literature (JEL) classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/MESHEUROPMC @=@ Another classification term from the Medical Subject Headings (MeSH) that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PROJECT @=@ A project reference that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_BY @=@ A dataset that is supplemented by your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/AUTHOR/ORCID @=@ An Open Researcher and Contributor ID (ORCID) that can be associated to an author of your publications +dnet:review_levels @=@ dnet:review_levels @=@ 0000 @=@ Unknown +dnet:review_levels @=@ dnet:review_levels @=@ 0002 @=@ nonPeerReviewed +dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala index 6294c3b98..e255a2270 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala @@ -1,13 +1,14 @@ package eu.dnetlib.dhp.sx.bio +import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils -import eu.dnetlib.dhp.schema.oaf.{Dataset, Oaf} +import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Oaf} import org.json4s.DefaultFormats -import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.jackson.JsonMethods.parse - +import scala.collection.JavaConverters._ object PDBToOAF { + val dataInfo: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9") def convert(input:String):List[Oaf]= { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json = parse(input) @@ -18,13 +19,16 @@ object PDBToOAF { val d = new Dataset - d.setPid(List(OafMapperUtils.structuredProperty())) + d.setPid( + List( + OafMapperUtils.structuredProperty(pdb, "pdb", "pdb", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES,dataInfo) + ).asJava + ) - - List() + List(d) }