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using constants from ModelConstants

This commit is contained in:
Claudio Atzori 2021-05-18 11:10:07 +02:00
parent d9a0bbda7b
commit eeb8bcf075
1 changed files with 29 additions and 28 deletions
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55
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala
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@ -6,6 +6,7 @@ import java.time.LocalDateTime
import java.time.format.DateTimeFormatter import java.time.format.DateTimeFormatter
import eu.dnetlib.dhp.common.PacePerson import eu.dnetlib.dhp.common.PacePerson
import eu.dnetlib.dhp.schema.action.AtomicAction import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty} import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication} import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication}
import eu.dnetlib.dhp.utils.DHPUtils import eu.dnetlib.dhp.utils.DHPUtils
@ -43,18 +44,18 @@ object DLIToOAF {
val relationTypeMapping: Map[String, (String, String)] = Map( val relationTypeMapping: Map[String, (String, String)] = Map(
"IsReferencedBy" -> ("isRelatedTo", "relationship"), "IsReferencedBy" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"References" -> ("isRelatedTo", "relationship"), "References" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"IsRelatedTo" -> ("isRelatedTo", "relationship"), "IsRelatedTo" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"IsSupplementedBy" -> ("isSupplementedBy", "supplement"), "IsSupplementedBy" -> (ModelConstants.IS_SUPPLEMENTED_BY, ModelConstants.SUPPLEMENT),
"Documents"-> ("isRelatedTo", "relationship"), "Documents"-> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"Cites" -> ("cites", "citation"), "Cites" -> (ModelConstants.CITES, ModelConstants.CITATION),
"Unknown" -> ("isRelatedTo", "relationship"), "Unknown" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"IsSourceOf" -> ("isRelatedTo", "relationship"), "IsSourceOf" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"IsCitedBy" -> ("IsCitedBy", "citation"), "IsCitedBy" -> (ModelConstants.IS_CITED_BY, ModelConstants.CITATION),
"Reviews" -> ("reviews", "review"), "Reviews" -> (ModelConstants.REVIEWS, ModelConstants.REVIEW),
"Describes" -> ("isRelatedTo", "relationship"), "Describes" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"HasAssociationWith" -> ("isRelatedTo", "relationship") "HasAssociationWith" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP)
) )
val expectecdPidType = List("uniprot", "ena", "chembl", "ncbi-n", "ncbi-p", "genbank", "pdb", "url") val expectecdPidType = List("uniprot", "ena", "chembl", "ncbi-n", "ncbi-p", "genbank", "pdb", "url")
@ -83,11 +84,11 @@ object DLIToOAF {
val rel_inverse: Map[String, String] = Map( val rel_inverse: Map[String, String] = Map(
"isRelatedTo" -> "isRelatedTo", ModelConstants.IS_RELATED_TO -> ModelConstants.IS_RELATED_TO,
"isSupplementedBy" -> "isSupplementTo", ModelConstants.IS_SUPPLEMENTED_BY -> ModelConstants.IS_SUPPLEMENT_TO,
"cites" -> "IsCitedBy", ModelConstants.CITES -> ModelConstants.IS_CITED_BY,
"IsCitedBy" -> "cites", ModelConstants.IS_CITED_BY -> ModelConstants.CITES,
"reviews" -> "IsReviewedBy" ModelConstants.REVIEWS -> ModelConstants.IS_REVIEWED_BY
) )
@ -158,7 +159,7 @@ object DLIToOAF {
result.setUrl(e.url) result.setUrl(e.url)
result.setRefidentifier(e.pid) result.setRefidentifier(e.pid)
result.setDataInfo(generateDataInfo()) result.setDataInfo(generateDataInfo())
result.setQualifier(createQualifier(e.classId, "dnet:externalReference_typologies")) result.setQualifier(createQualifier(e.classId, ModelConstants.DNET_EXTERNAL_REFERENCE_TYPE))
result result
}) })
publication.setExternalReference(eRefs.asJava) publication.setExternalReference(eRefs.asJava)
@ -237,7 +238,7 @@ object DLIToOAF {
if (inputPublication.getAuthor == null || inputPublication.getAuthor.isEmpty) if (inputPublication.getAuthor == null || inputPublication.getAuthor.isEmpty)
return null return null
result.setAuthor(inputPublication.getAuthor.asScala.map(convertAuthor).asJava) result.setAuthor(inputPublication.getAuthor.asScala.map(convertAuthor).asJava)
result.setResulttype(createQualifier(inputPublication.getResulttype.getClassid, inputPublication.getResulttype.getClassname, "dnet:result_typologies", "dnet:result_typologies")) result.setResulttype(createQualifier(inputPublication.getResulttype.getClassid, inputPublication.getResulttype.getClassname, ModelConstants.DNET_RESULT_TYPOLOGIES, ModelConstants.DNET_RESULT_TYPOLOGIES))
if (inputPublication.getSubject != null) if (inputPublication.getSubject != null)
result.setSubject(inputPublication.getSubject.asScala.map(convertSubject).asJava) result.setSubject(inputPublication.getSubject.asScala.map(convertSubject).asJava)
@ -258,7 +259,7 @@ object DLIToOAF {
result.setDateofacceptance(asField(inputPublication.getRelevantdate.get(0).getValue)) result.setDateofacceptance(asField(inputPublication.getRelevantdate.get(0).getValue))
result.setPublisher(inputPublication.getPublisher) result.setPublisher(inputPublication.getPublisher)
result.setSource(inputPublication.getSource) result.setSource(inputPublication.getSource)
result.setBestaccessright(createQualifier("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes")) result.setBestaccessright(createQualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES))
val dois = result.getPid.asScala.filter(p => "doi".equalsIgnoreCase(p.getQualifier.getClassname)).map(p => p.getValue) val dois = result.getPid.asScala.filter(p => "doi".equalsIgnoreCase(p.getQualifier.getClassname)).map(p => p.getValue)
if (dois.isEmpty) if (dois.isEmpty)
@ -316,7 +317,7 @@ object DLIToOAF {
if (d.getAuthor == null || d.getAuthor.isEmpty) if (d.getAuthor == null || d.getAuthor.isEmpty)
return null return null
result.setAuthor(d.getAuthor.asScala.map(convertAuthor).asJava) result.setAuthor(d.getAuthor.asScala.map(convertAuthor).asJava)
result.setResulttype(createQualifier(d.getResulttype.getClassid, d.getResulttype.getClassname, "dnet:result_typologies", "dnet:result_typologies")) result.setResulttype(createQualifier(d.getResulttype.getClassid, d.getResulttype.getClassname, ModelConstants.DNET_RESULT_TYPOLOGIES, ModelConstants.DNET_RESULT_TYPOLOGIES))
if (d.getSubject != null) if (d.getSubject != null)
result.setSubject(d.getSubject.asScala.map(convertSubject).asJava) result.setSubject(d.getSubject.asScala.map(convertSubject).asJava)
@ -337,7 +338,7 @@ object DLIToOAF {
result.setDateofacceptance(asField(d.getRelevantdate.get(0).getValue)) result.setDateofacceptance(asField(d.getRelevantdate.get(0).getValue))
result.setPublisher(d.getPublisher) result.setPublisher(d.getPublisher)
result.setSource(d.getSource) result.setSource(d.getSource)
result.setBestaccessright(createQualifier("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes")) result.setBestaccessright(createQualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES))
val instance_urls = if (fpids.head.length < 5) s"https://www.rcsb.org/structure/${fpids.head}" else s"https://dx.doi.org/${fpids.head}" val instance_urls = if (fpids.head.length < 5) s"https://www.rcsb.org/structure/${fpids.head}" else s"https://dx.doi.org/${fpids.head}"
@ -364,13 +365,13 @@ object DLIToOAF {
val i = new Instance val i = new Instance
i.setUrl(List(url).asJava) i.setUrl(List(url).asJava)
if (dataset) if (dataset)
i.setInstancetype(createQualifier("0021", "Dataset", "dnet:publication_resource", "dnet:publication_resource")) i.setInstancetype(createQualifier("0021", "Dataset", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
else else
i.setInstancetype(createQualifier("0000", "Unknown", "dnet:publication_resource", "dnet:publication_resource")) i.setInstancetype(createQualifier("0000", "Unknown", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
if (originalInstance != null && originalInstance.getHostedby != null) if (originalInstance != null && originalInstance.getHostedby != null)
i.setHostedby(originalInstance.getHostedby) i.setHostedby(originalInstance.getHostedby)
i.setAccessright(createQualifier("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes")) i.setAccessright(createQualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES))
i.setDateofacceptance(doa) i.setDateofacceptance(doa)
i i
@ -380,7 +381,7 @@ object DLIToOAF {
def patchRelevantDate(d: StructuredProperty): StructuredProperty = { def patchRelevantDate(d: StructuredProperty): StructuredProperty = {
d.setQualifier(createQualifier("UNKNOWN", "dnet:dataCite_date")) d.setQualifier(createQualifier("UNKNOWN", ModelConstants.DNET_DATA_CITE_DATE))
d d
} }
@ -392,7 +393,7 @@ object DLIToOAF {
def convertSubject(s: StructuredProperty): StructuredProperty = { def convertSubject(s: StructuredProperty): StructuredProperty = {
s.setQualifier(createQualifier("keyword", "dnet:subject_classification_typologies")) s.setQualifier(createQualifier("keyword", ModelConstants.DNET_SUBJECT_TYPOLOGIES))
s s