diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala index a19c6fb12..90b65c8f7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala @@ -199,7 +199,7 @@ object BioDBToOAF { d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO)) } val relevant_dates: List[StructuredProperty] = dates.filter(d => !d.date_info.contains("entry version")) - .map(date => OafMapperUtils.structuredProperty(date.date, "UNKNOWN", "UNKNOWN", ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, DATA_INFO)) + .map(date => OafMapperUtils.structuredProperty(date.date, ModelConstants.UNKNOWN, ModelConstants.UNKNOWN, ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, DATA_INFO)) if (relevant_dates != null && relevant_dates.nonEmpty) d.setRelevantdate(relevant_dates.asJava) d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO)) @@ -218,12 +218,12 @@ object BioDBToOAF { if (references_pmid != null && references_pmid.nonEmpty) { - val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if (i_date.isDefined) i_date.get.date else null) + val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null) rel.getCollectedfrom List(d, rel) } else if (references_doi != null && references_doi.nonEmpty) { - val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if (i_date.isDefined) i_date.get.date else null) + val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null) List(d, rel) } else @@ -243,7 +243,7 @@ object BioDBToOAF { rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava) rel.setDataInfo(DATA_INFO) - rel.setRelType("resultResult") + rel.setRelType(ModelConstants.RESULT_RESULT) rel.setSubRelType(subRelType) rel.setRelClass(relClass) @@ -263,7 +263,7 @@ object BioDBToOAF { def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date:String): Relation = { - createRelation(pid,pidType,sourceId,collectedFrom, "supplement","IsSupplementTo", date) + createRelation(pid,pidType,sourceId,collectedFrom, ModelConstants.SUPPLEMENT, ModelConstants.IS_SUPPLEMENT_TO, date) } @@ -392,6 +392,6 @@ object BioDBToOAF { i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO)) d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO)) - List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"),"relationship", "isRelatedTo", GraphCleaningFunctions.cleanDate(input.date))) + List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, GraphCleaningFunctions.cleanDate(input.date))) } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PubMedToOaf.scala index ae4a72062..9a49deebc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PubMedToOaf.scala @@ -16,7 +16,7 @@ object PubMedToOaf { ) def createResult(cobjQualifier: Qualifier, vocabularies: VocabularyGroup): Result = { - val result_typologies = getVocabularyTerm("dnet:result_typologies", vocabularies, cobjQualifier.getClassid) + val result_typologies = getVocabularyTerm(ModelConstants.DNET_RESULT_TYPOLOGIES, vocabularies, cobjQualifier.getClassid) result_typologies.getClassid match { case "dataset" => new Dataset case "publication" => new Publication @@ -68,11 +68,11 @@ object PubMedToOaf { //else We have to find a terms that match the vocabulary otherwise we discard it val ja = article.getPublicationTypes.asScala.find(s => "Journal Article".equalsIgnoreCase(s.getValue)) if (ja.isDefined) { - val cojbCategory = getVocabularyTerm("dnet:publication_resource", vocabularies, ja.get.getValue) + val cojbCategory = getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, ja.get.getValue) i.setInstancetype(cojbCategory) } else { val i_type = article.getPublicationTypes.asScala - .map(s => getVocabularyTerm("dnet:publication_resource", vocabularies, s.getValue)) + .map(s => getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue)) .find(q => q != null) if (i_type.isDefined) i.setInstancetype(i_type.get) @@ -112,7 +112,7 @@ object PubMedToOaf { if (article.getLanguage != null) { - val term = vocabularies.getSynonymAsQualifier("dnet:languages", article.getLanguage) + val term = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_LANGUAGES, article.getLanguage) if (term != null) result.setLanguage(term) } diff --git a/pom.xml b/pom.xml index fc4a8a21b..433c88093 100644 --- a/pom.xml +++ b/pom.xml @@ -741,7 +741,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.7.14] + [2.7.15] [4.0.3] [6.0.5] [3.1.6]