Added fix for pid generation in stableIds

This commit is contained in:
Sandro La Bruzzo 2021-03-17 15:53:24 +01:00
parent b4805b989d
commit 5f98ea74a9
6 changed files with 45 additions and 19 deletions

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@ -60,6 +60,33 @@ public class IdentifierFactory implements Serializable {
return pidFromInstance(pid, collectedFrom).distinct().collect(Collectors.toList()); return pidFromInstance(pid, collectedFrom).distinct().collect(Collectors.toList());
} }
public static <T extends Result> String createDOIBoostIdentifier(T entity) {
if (entity == null)
return null;
StructuredProperty pid = null;
if(entity.getPid() != null ) {
pid = entity.getPid()
.stream()
.filter(Objects::nonNull)
.filter(s -> s.getQualifier()!= null && "doi".equalsIgnoreCase(s.getQualifier().getClassid()))
.filter(IdentifierFactory::pidFilter)
.findAny().orElse(null);
} else {
if (entity.getInstance()!= null) {
pid = entity.getInstance()
.stream()
.filter(i -> i.getPid()!= null)
.flatMap(i -> i.getPid().stream())
.filter(IdentifierFactory::pidFilter)
.findAny().orElse(null);
}
}
if (pid!= null)
return idFromPid(entity, pid, true);
return null;
}
/** /**
* Creates an identifier from the most relevant PID (if available) provided by a known PID authority in the given * Creates an identifier from the most relevant PID (if available) provided by a known PID authority in the given
* entity T. Returns entity.id when none of the PIDs meet the selection criteria is available. * entity T. Returns entity.id when none of the PIDs meet the selection criteria is available.

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@ -206,6 +206,9 @@ case object Crossref2Oaf {
val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null).distinct val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null).distinct
if (links.nonEmpty) if (links.nonEmpty)
instance.setUrl(links.asJava) instance.setUrl(links.asJava)
result.setId(IdentifierFactory.createDOIBoostIdentifier(result))
if (result.getId== null)
return null
result result
} }
@ -240,6 +243,8 @@ case object Crossref2Oaf {
return List() return List()
val cOBJCategory = mappingCrossrefSubType.getOrElse(objectType, mappingCrossrefSubType.getOrElse(objectSubType, "0038 Other literature type")); val cOBJCategory = mappingCrossrefSubType.getOrElse(objectType, mappingCrossrefSubType.getOrElse(objectSubType, "0038 Other literature type"));
mappingResult(result, json, cOBJCategory) mappingResult(result, json, cOBJCategory)
if (result == null)
return List()
val funderList: List[mappingFunder] = (json \ "funder").extractOrElse[List[mappingFunder]](List()) val funderList: List[mappingFunder] = (json \ "funder").extractOrElse[List[mappingFunder]](List())

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@ -197,8 +197,8 @@ case object ConversionUtil {
//IMPORTANT //IMPORTANT
//The old method result.setId(generateIdentifier(result, doi)) //The old method result.setId(generateIdentifier(result, doi))
//will be replaced using IdentifierFactory //will be replaced using IdentifierFactory
pub.setId(generateIdentifier(pub, paper.Doi.toLowerCase))
pub.setId(IdentifierFactory.createIdentifier(pub)) pub.setId(IdentifierFactory.createDOIBoostIdentifier(pub))
val mainTitles = createSP(paper.PaperTitle, "main title", "dnet:dataCite_title") val mainTitles = createSP(paper.PaperTitle, "main title", "dnet:dataCite_title")
val originalTitles = createSP(paper.OriginalTitle, "alternative title", "dnet:dataCite_title") val originalTitles = createSP(paper.OriginalTitle, "alternative title", "dnet:dataCite_title")

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@ -1,6 +1,7 @@
package eu.dnetlib.doiboost.orcid package eu.dnetlib.doiboost.orcid
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication} import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication}
import eu.dnetlib.dhp.schema.orcid.OrcidDOI import eu.dnetlib.dhp.schema.orcid.OrcidDOI
import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.DoiBoostMappingUtil
@ -49,7 +50,11 @@ object ORCIDToOAF {
val pub:Publication = new Publication val pub:Publication = new Publication
pub.setPid(List(createSP(doi.toLowerCase, "doi", PID_TYPES)).asJava) pub.setPid(List(createSP(doi.toLowerCase, "doi", PID_TYPES)).asJava)
pub.setDataInfo(generateDataInfo()) pub.setDataInfo(generateDataInfo())
pub.setId(generateIdentifier(pub, doi.toLowerCase))
pub.setId(IdentifierFactory.createDOIBoostIdentifier(pub))
if (pub.getId == null)
return null
try{ try{
val l:List[Author]= input.getAuthors.asScala.map(a=> { val l:List[Author]= input.getAuthors.asScala.map(a=> {

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@ -55,7 +55,6 @@ object UnpayWallToOAF {
val doi = (json \"doi").extract[String] val doi = (json \"doi").extract[String]
val is_oa = (json\ "is_oa").extract[Boolean] val is_oa = (json\ "is_oa").extract[Boolean]
val journal_is_oa= (json\ "journal_is_oa").extract[Boolean] val journal_is_oa= (json\ "journal_is_oa").extract[Boolean]
@ -63,10 +62,6 @@ object UnpayWallToOAF {
val oaLocation:OALocation = (json \ "best_oa_location").extractOrElse[OALocation](null) val oaLocation:OALocation = (json \ "best_oa_location").extractOrElse[OALocation](null)
val colour = get_color(is_oa, oaLocation, journal_is_oa) val colour = get_color(is_oa, oaLocation, journal_is_oa)
pub.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
pub.setCollectedfrom(List(createUnpayWallCollectedFrom()).asJava) pub.setCollectedfrom(List(createUnpayWallCollectedFrom()).asJava)
pub.setDataInfo(generateDataInfo()) pub.setDataInfo(generateDataInfo())
@ -82,12 +77,9 @@ object UnpayWallToOAF {
// i.setAccessright(getOpenAccessQualifier()) // i.setAccessright(getOpenAccessQualifier())
i.setUrl(List(oaLocation.url.get).asJava) i.setUrl(List(oaLocation.url.get).asJava)
// Ticket #6281 added pid to Instance
i.setPid(pub.getPid)
if (oaLocation.license.isDefined) if (oaLocation.license.isDefined)
i.setLicense(asField(oaLocation.license.get)) i.setLicense(asField(oaLocation.license.get))
pub.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
// Ticket #6282 Adding open Access Colour // Ticket #6282 Adding open Access Colour
if (colour.isDefined) { if (colour.isDefined) {
@ -98,6 +90,7 @@ object UnpayWallToOAF {
a.setSchemename(ModelConstants.DNET_ACCESS_MODES) a.setSchemename(ModelConstants.DNET_ACCESS_MODES)
a.setOpenAccessRoute(colour.get) a.setOpenAccessRoute(colour.get)
i.setAccessright(a) i.setAccessright(a)
i.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
} }
pub.setInstance(List(i).asJava) pub.setInstance(List(i).asJava)
@ -105,9 +98,7 @@ object UnpayWallToOAF {
//The old method pub.setId(IdentifierFactory.createIdentifier(pub)) //The old method pub.setId(IdentifierFactory.createIdentifier(pub))
//will be replaced using IdentifierFactory //will be replaced using IdentifierFactory
//pub.setId(generateIdentifier(pub, doi.toLowerCase)) //pub.setId(generateIdentifier(pub, doi.toLowerCase))
val id = IdentifierFactory.createIdentifier(pub) pub.setId(IdentifierFactory.createDOIBoostIdentifier(pub))
logger.info(id);
pub.setId(IdentifierFactory.createIdentifier(pub))
pub pub
} }

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@ -22,13 +22,11 @@ class UnpayWallMappingTest {
for (line <-Ilist.lines) { for (line <-Ilist.lines) {
val p = UnpayWallToOAF.convertToOAF(line) val p = UnpayWallToOAF.convertToOAF(line)
if(p!= null) { if(p!= null) {
assertTrue(p.getPid.size()==1) assertTrue(p.getInstance().size()==1)
logger.info("ID :",p.getId) logger.info(s"ID : ${p.getId}")
} }
assertNotNull(line) assertNotNull(line)
assertTrue(line.nonEmpty) assertTrue(line.nonEmpty)