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dnet-hadoop
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mergin with branch beta

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Miriam Baglioni 2021-08-03 10:47:11 +02:00
parent 461b8a29a0 e826aae848
commit 100e54e6c8
3 changed files with 11 additions and 11 deletions
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12
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala
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@ -199,7 +199,7 @@ object BioDBToOAF {
d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO)) d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
} }
val relevant_dates: List[StructuredProperty] = dates.filter(d => !d.date_info.contains("entry version")) 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) if (relevant_dates != null && relevant_dates.nonEmpty)
d.setRelevantdate(relevant_dates.asJava) d.setRelevantdate(relevant_dates.asJava)
d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO)) d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
@ -218,12 +218,12 @@ object BioDBToOAF {
if (references_pmid != null && references_pmid.nonEmpty) { 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 rel.getCollectedfrom
List(d, rel) List(d, rel)
} }
else if (references_doi != null && references_doi.nonEmpty) { 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) List(d, rel)
} }
else else
@ -243,7 +243,7 @@ object BioDBToOAF {
rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava) rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava)
rel.setDataInfo(DATA_INFO) rel.setDataInfo(DATA_INFO)
rel.setRelType("resultResult") rel.setRelType(ModelConstants.RESULT_RESULT)
rel.setSubRelType(subRelType) rel.setSubRelType(subRelType)
rel.setRelClass(relClass) rel.setRelClass(relClass)
@ -263,7 +263,7 @@ object BioDBToOAF {
def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date:String): Relation = { 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)) i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO))
d.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)))
} }
} }

8
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PubMedToOaf.scala
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@ -16,7 +16,7 @@ object PubMedToOaf {
) )
def createResult(cobjQualifier: Qualifier, vocabularies: VocabularyGroup): Result = { 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 { result_typologies.getClassid match {
case "dataset" => new Dataset case "dataset" => new Dataset
case "publication" => new Publication 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 //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)) val ja = article.getPublicationTypes.asScala.find(s => "Journal Article".equalsIgnoreCase(s.getValue))
if (ja.isDefined) { 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) i.setInstancetype(cojbCategory)
} else { } else {
val i_type = article.getPublicationTypes.asScala 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) .find(q => q != null)
if (i_type.isDefined) if (i_type.isDefined)
i.setInstancetype(i_type.get) i.setInstancetype(i_type.get)
@ -112,7 +112,7 @@ object PubMedToOaf {
if (article.getLanguage != null) { if (article.getLanguage != null) {
val term = vocabularies.getSynonymAsQualifier("dnet:languages", article.getLanguage) val term = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_LANGUAGES, article.getLanguage)
if (term != null) if (term != null)
result.setLanguage(term) result.setLanguage(term)
} }

2
pom.xml
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@ -741,7 +741,7 @@
<mockito-core.version>3.3.3</mockito-core.version> <mockito-core.version>3.3.3</mockito-core.version>
<mongodb.driver.version>3.4.2</mongodb.driver.version> <mongodb.driver.version>3.4.2</mongodb.driver.version>
<vtd.version>[2.12,3.0)</vtd.version> <vtd.version>[2.12,3.0)</vtd.version>
<dhp-schemas.version>[2.7.14]</dhp-schemas.version> <dhp-schemas.version>[2.7.15]</dhp-schemas.version>
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version> <dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version> <dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version> <dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>