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Merge remote-tracking branch 'origin/beta' into zenodo_dump_collection

This commit is contained in:
sandro.labruzzo 2024-12-04 13:41:25 +01:00
parent 32e2a8b340 4034da7579
commit 5f134c4045
7 changed files with 82 additions and 70 deletions
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2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
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@ -1,3 +1,4 @@
package eu.dnetlib.dhp.sx.bio.pubmed;
/**
@ -14,6 +15,7 @@ public class PMAffiliation {
public PMAffiliation() {
}
public PMAffiliation(String name, PMIdentifier identifier) {
this.name = name;
this.identifier = identifier;

1
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java
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@ -97,5 +97,4 @@ public class PMAuthor implements Serializable {
this.affiliation = affiliation;
}
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java
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@ -1,3 +1,4 @@
package eu.dnetlib.dhp.sx.bio.pubmed;
public class PMIdentifier {
@ -5,7 +6,6 @@ public class PMIdentifier {
private String pid;
private String type;
public PMIdentifier(String pid, String type) {
this.pid = cleanPid(pid);
this.type = type;

1
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
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@ -673,7 +673,6 @@ case object Crossref2Oaf {
val doi = input.getString(0)
val rorId = input.getString(1)
val pubId = IdentifierFactory.idFromPid("50", "doi", DoiCleaningRule.clean(doi), true)
val affId = GenerateRorActionSetJob.calculateOpenaireId(rorId)

11
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala
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@ -82,21 +82,22 @@ class PMParser2 {
a.setLastName((author \ "LastName").text)
a.setForeName((author \ "ForeName").text)
val id = (author \ "Identifier").text
val idType =(author \ "Identifier" \ "@Source").text
val idType = (author \ "Identifier" \ "@Source").text
if(id != null && id.nonEmpty && idType != null && idType.nonEmpty) {
if (id != null && id.nonEmpty && idType != null && idType.nonEmpty) {
a.setIdentifier(new PMIdentifier(id, idType))
}
val affiliation = (author \ "AffiliationInfo" \ "Affiliation").text
val affiliationId = (author \ "AffiliationInfo" \ "Identifier").text
val affiliationIdType = (author \ "AffiliationInfo" \ "Identifier" \ "@Source").text
if(affiliation != null && affiliation.nonEmpty) {
if (affiliation != null && affiliation.nonEmpty) {
val aff = new PMAffiliation()
aff.setName(affiliation)
if(affiliationId != null && affiliationId.nonEmpty && affiliationIdType != null && affiliationIdType.nonEmpty) {
if (
affiliationId != null && affiliationId.nonEmpty && affiliationIdType != null && affiliationIdType.nonEmpty
) {
aff.setIdentifier(new PMIdentifier(affiliationId, affiliationIdType))
}
a.setAffiliation(aff)

20
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
View File

@ -294,11 +294,23 @@ object PubMedToOaf {
author.setName(a.getForeName)
author.setSurname(a.getLastName)
author.setFullname(a.getFullName)
if(a.getIdentifier != null) {
author.setPid(List(OafMapperUtils.structuredProperty(a.getIdentifier.getPid,
OafMapperUtils.qualifier(a.getIdentifier.getType,a.getIdentifier.getType,ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES), dataInfo)).asJava)
if (a.getIdentifier != null) {
author.setPid(
List(
OafMapperUtils.structuredProperty(
a.getIdentifier.getPid,
OafMapperUtils.qualifier(
a.getIdentifier.getType,
a.getIdentifier.getType,
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES
),
dataInfo
)
).asJava
)
}
if (a.getAffiliation!= null)
if (a.getAffiliation != null)
author.setRawAffiliationString(List(a.getAffiliation.getName).asJava)
author.setRank(index + 1)
author

1
dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
View File

@ -63,7 +63,6 @@ class BioScholixTest extends AbstractVocabularyTest {
"0000000333457333",
"0000000335964515",
"0000000302921949",
"http://orcid.org/0000-0001-8567-3543",
"http://orcid.org/0000-0001-7868-8528",
"0000-0001-9189-1440",