implemented scholix Flat mapping
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package eu.dnetlib.dhp.sx.graph.scholix;
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import java.util.List;
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public class ScholixFlat {
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private String identifier;
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private String relationType;
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private String sourceId;
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private String sourceType;
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private String sourceSubType;
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private List<String> sourcePid;
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private List<String> sourcePidType;
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private List<String> sourcePublisher;
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private String targetId;
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private String targetType;
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private String targetSubType;
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private List<String> targetPid;
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private List<String> targetPidType;
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private List<String> targetPublisher;
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private List<String> linkProviders;
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private String publicationDate;
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private String blob;
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public String getIdentifier() {
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return identifier;
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}
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public void setIdentifier(String identifier) {
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this.identifier = identifier;
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}
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public String getRelationType() {
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return relationType;
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}
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public void setRelationType(String relationType) {
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this.relationType = relationType;
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}
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public String getSourceId() {
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return sourceId;
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}
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public void setSourceId(String sourceId) {
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this.sourceId = sourceId;
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}
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public String getSourceType() {
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return sourceType;
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}
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public void setSourceType(String sourceType) {
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this.sourceType = sourceType;
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}
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public String getSourceSubType() {
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return sourceSubType;
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}
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public void setSourceSubType(String sourceSubType) {
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this.sourceSubType = sourceSubType;
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}
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public List<String> getSourcePid() {
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return sourcePid;
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}
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public void setSourcePid(List<String> sourcePid) {
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this.sourcePid = sourcePid;
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}
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public List<String> getSourcePidType() {
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return sourcePidType;
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}
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public void setSourcePidType(List<String> sourcePidType) {
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this.sourcePidType = sourcePidType;
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}
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public List<String> getSourcePublisher() {
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return sourcePublisher;
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}
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public void setSourcePublisher(List<String> sourcePublisher) {
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this.sourcePublisher = sourcePublisher;
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}
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public String getTargetId() {
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return targetId;
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}
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public void setTargetId(String targetId) {
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this.targetId = targetId;
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}
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public String getTargetType() {
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return targetType;
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}
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public void setTargetType(String targetType) {
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this.targetType = targetType;
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}
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public String getTargetSubType() {
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return targetSubType;
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}
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public void setTargetSubType(String targetSubType) {
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this.targetSubType = targetSubType;
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}
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public List<String> getTargetPid() {
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return targetPid;
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}
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public void setTargetPid(List<String> targetPid) {
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this.targetPid = targetPid;
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}
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public List<String> getTargetPidType() {
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return targetPidType;
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}
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public void setTargetPidType(List<String> targetPidType) {
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this.targetPidType = targetPidType;
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}
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public List<String> getTargetPublisher() {
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return targetPublisher;
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}
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public void setTargetPublisher(List<String> targetPublisher) {
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this.targetPublisher = targetPublisher;
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}
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public List<String> getLinkProviders() {
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return linkProviders;
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}
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public void setLinkProviders(List<String> linkProviders) {
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this.linkProviders = linkProviders;
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}
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public String getPublicationDate() {
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return publicationDate;
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}
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public void setPublicationDate(String publicationDate) {
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this.publicationDate = publicationDate;
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}
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public String getBlob() {
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return blob;
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}
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public void setBlob(String blob) {
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this.blob = blob;
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}
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}
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@ -1,14 +1,15 @@
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package eu.dnetlib.dhp.sx.graph.scholix
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import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Result, StructuredProperty}
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import eu.dnetlib.dhp.schema.oaf.{Dataset, OtherResearchProduct, Publication, Relation, Result, Software, StructuredProperty}
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import eu.dnetlib.dhp.schema.sx.scholix._
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import eu.dnetlib.dhp.schema.sx.summary.{CollectedFromType, SchemeValue, ScholixSummary, Typology}
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import eu.dnetlib.dhp.schema.sx.summary.{AuthorPid, CollectedFromType, SchemeValue, ScholixSummary, Typology}
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import eu.dnetlib.dhp.utils.DHPUtils
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import org.apache.spark.sql.expressions.Aggregator
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import org.apache.spark.sql.{Encoder, Encoders}
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import org.json4s
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import org.json4s.DefaultFormats
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import org.json4s.jackson.JsonMethods.parse
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import scala.collection.JavaConverters._
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import scala.io.Source
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@ -59,6 +60,36 @@ object ScholixUtils extends Serializable {
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}
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}
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def flattenizeScholix(input: Scholix, json: String): ScholixFlat = {
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val flat: ScholixFlat = new ScholixFlat
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flat.setIdentifier(input.getIdentifier)
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flat.setRelationType(input.getRelationship.getName)
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if (input.getSource != null && input.getSource.getIdentifier != null) {
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flat.setSourceId(input.getSource.getDnetIdentifier)
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flat.setSourcePid(input.getSource.getIdentifier.asScala.map(p => p.getIdentifier).distinct.toList.asJava)
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flat.setSourcePidType(input.getSource.getIdentifier.asScala.map(p => p.getSchema).distinct.toList.asJava)
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flat.setSourceType(input.getSource.getObjectType)
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flat.setSourceSubType(input.getSource.getObjectSubType)
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} else return null
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if (input.getSource.getPublisher != null)
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flat.setSourcePublisher(input.getSource.getPublisher.asScala.map(p => p.getName).toList.asJava)
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if (input.getTarget != null && input.getTarget.getIdentifier != null) {
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flat.setTargetId(input.getTarget.getDnetIdentifier)
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flat.setTargetPid(input.getTarget.getIdentifier.asScala.map(p => p.getIdentifier).distinct.toList.asJava)
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flat.setTargetPidType(input.getTarget.getIdentifier.asScala.map(p => p.getSchema).distinct.toList.asJava)
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flat.setTargetType(input.getTarget.getObjectType)
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flat.setTargetSubType(input.getTarget.getObjectSubType)
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} else return null
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if (input.getTarget.getPublisher != null)
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flat.setTargetPublisher(input.getTarget.getPublisher.asScala.map(p => p.getName).distinct.toList.asJava)
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flat.setPublicationDate(input.getPublicationDate)
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if (input.getLinkprovider != null)
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flat.setLinkProviders(input.getLinkprovider.asScala.map(l => l.getName).distinct.toList.asJava)
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flat.setBlob(json);
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flat
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}
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def inverseRelationShip(rel: ScholixRelationship): ScholixRelationship = {
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new ScholixRelationship(rel.getInverse, rel.getSchema, rel.getName)
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@ -232,7 +263,14 @@ object ScholixUtils extends Serializable {
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if (summaryObject.getAuthor != null && !summaryObject.getAuthor.isEmpty) {
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val l: List[ScholixEntityId] =
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summaryObject.getAuthor.asScala.map(a => new ScholixEntityId(a, null)).toList
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summaryObject.getAuthor.asScala.map(a => {
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if (a.getORCID != null)
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new ScholixEntityId(
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a.getFullname,
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List(new ScholixIdentifier(a.getORCID, "ORCID", s"https://orcid.org/${a.getORCID}")).asJava
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)
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else new ScholixEntityId(a.getFullname, null)
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}).toList
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if (l.nonEmpty)
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r.setCreator(l.asJava)
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}
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if (persistentIdentifiers.isEmpty)
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return null
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s.setLocalIdentifier(persistentIdentifiers.asJava)
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if (r.isInstanceOf[Publication])
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s.setTypology(Typology.publication)
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else
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s.setTypology(Typology.dataset)
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r match {
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case _: Publication => s.setTypology(Typology.publication)
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case _: Dataset => s.setTypology(Typology.dataset)
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case _: Software => s.setTypology(Typology.software)
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case _: OtherResearchProduct => s.setTypology(Typology.otherresearchproduct)
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case _ =>
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}
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s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)
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}
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if (r.getAuthor != null && !r.getAuthor.isEmpty) {
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val authors: List[String] = r.getAuthor.asScala.map(a => a.getFullname).toList
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val authors: List[AuthorPid] = r.getAuthor.asScala
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.map(a => {
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var ORCID: String = null
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if (a.getPid != null) {
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val result = a.getPid.asScala.find(p =>
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p.getQualifier != null && p.getQualifier.getClassid != null && p.getQualifier.getClassid.toLowerCase
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.contains("orcid")
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)
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if (result.isDefined)
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ORCID = result.get.getValue
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}
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new AuthorPid(a.getFullname, ORCID)
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})
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.toList
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if (authors.nonEmpty)
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s.setAuthor(authors.asJava)
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}
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package eu.dnetlib.dhp.sx.graph.scholix;
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import static org.junit.jupiter.api.Assertions.*;
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import java.io.*;
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import java.util.zip.GZIPInputStream;
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import org.junit.jupiter.api.Test;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.sx.scholix.Scholix;
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public class ScholixFlatTest {
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@Test
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public void flattenScholixTest() throws IOException {
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final ObjectMapper mapper = new ObjectMapper();
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InputStream gzipStream = new GZIPInputStream(getClass().getResourceAsStream("scholix_records.gz"));
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Reader decoder = new InputStreamReader(gzipStream, "UTF-8");
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BufferedReader buffered = new BufferedReader(decoder);
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String line;
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FileWriter myWriter = new FileWriter("/Users/sandro/Downloads/records");
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while ((line = buffered.readLine()) != null) {
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final Scholix s = mapper.readValue(line, Scholix.class);
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final ScholixFlat flat = ScholixUtils.flattenizeScholix(s, line);
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assertNotNull(s);
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assertNotNull(flat);
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assertEquals(s.getIdentifier(), flat.getIdentifier());
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assertEquals(s.getRelationship().getName(), flat.getRelationType());
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assertEquals(s.getSource().getObjectType(), flat.getSourceType());
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assertEquals(s.getSource().getObjectSubType(), flat.getSourceSubType());
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myWriter.write(mapper.writeValueAsString(flat));
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myWriter.write("\n");
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}
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myWriter.close();
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}
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}
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@ -1,194 +1,190 @@
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package eu.dnetlib.dhp.sx.provision;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.sx.scholix.Scholix;
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import eu.dnetlib.dhp.schema.sx.scholix.ScholixResource;
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import java.util.ArrayList;
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import java.util.List;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.sx.scholix.Scholix;
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import eu.dnetlib.dhp.schema.sx.scholix.ScholixResource;
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public class ScholixFlat {
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private static ObjectMapper MAPPER = new ObjectMapper();
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private List<String> linkProvider= new ArrayList<>();
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private static ObjectMapper MAPPER = new ObjectMapper();
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private List<String> linkProvider = new ArrayList<>();
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private String publicationDate;
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private String publicationDate;
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private List<String> sourceLinkPublisher = new ArrayList<>();
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private List<String> targetLinkPublisher = new ArrayList<>();
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private List<String> sourceLinkPublisher = new ArrayList<>();
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private List<String> targetLinkPublisher = new ArrayList<>();
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private String sourceDnetIdentifier ;
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private String targetDnetIdentifier ;
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private List<String> sourcePids = new ArrayList<>();
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private List<String> sourcePidTypes = new ArrayList<>();
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private List<String> targetPids = new ArrayList<>();
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private List<String> targetPidTypes = new ArrayList<>();
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private String sourceDnetIdentifier;
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private String targetDnetIdentifier;
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private List<String> sourcePids = new ArrayList<>();
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private List<String> sourcePidTypes = new ArrayList<>();
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private List<String> targetPids = new ArrayList<>();
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private List<String> targetPidTypes = new ArrayList<>();
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private String json;
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private String json;
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public void addLinkProvider(final String providerName) {
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addStringToList(providerName, this.linkProvider);
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}
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public void addSourceLinkPublisher(final String linkPublisher) {
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addStringToList(linkPublisher, sourceLinkPublisher);
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public void addLinkProvider(final String providerName) {
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addStringToList(providerName, this.linkProvider);
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}
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}
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public void addSourceLinkPublisher(final String linkPublisher) {
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addStringToList(linkPublisher, sourceLinkPublisher);
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public void addTargetLinkPublisher(final String linkPublisher) {
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addStringToList(linkPublisher, targetLinkPublisher);
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}
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public void addTargetLinkPublisher(final String linkPublisher) {
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addStringToList(linkPublisher, targetLinkPublisher);
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}
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}
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public void addSourcePid(final String pid) {
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addStringToList(pid, sourcePids);
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}
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public void addSourcePid(final String pid) {
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addStringToList(pid, sourcePids);
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}
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public void addSourcePidType(final String pidType) {
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addStringToList(pidType, sourcePidTypes);
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}
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public void addSourcePidType(final String pidType) {
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addStringToList(pidType, sourcePidTypes);
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}
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public void addTargetPidType(final String pidType) {
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addStringToList(pidType, targetPidTypes);
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}
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public void addTargetPidType(final String pidType) {
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addStringToList(pidType, targetPidTypes);
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}
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public void addTargetPid(final String pid) {
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addStringToList(pid, targetPids);
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}
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public void addStringToList(final String s, final List<String> l) {
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if (l != null && !l.contains(s))
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l.add(s);
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}
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public void addTargetPid(final String pid) {
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addStringToList(pid, targetPids);
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}
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public String getSourceDnetIdentifier() {
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return sourceDnetIdentifier;
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}
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public void addStringToList(final String s, final List<String>l ) {
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if (l!= null && !l.contains(s))
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l.add(s);
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}
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public void setSourceDnetIdentifier(String sourceDnetIdentifier) {
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this.sourceDnetIdentifier = sourceDnetIdentifier;
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}
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public String getSourceDnetIdentifier() {
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return sourceDnetIdentifier;
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}
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public String getTargetDnetIdentifier() {
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return targetDnetIdentifier;
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}
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public void setSourceDnetIdentifier(String sourceDnetIdentifier) {
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this.sourceDnetIdentifier = sourceDnetIdentifier;
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}
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public void setTargetDnetIdentifier(String targetDnetIdentifier) {
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this.targetDnetIdentifier = targetDnetIdentifier;
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}
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public String getTargetDnetIdentifier() {
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return targetDnetIdentifier;
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}
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public List<String> getSourcePids() {
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return sourcePids;
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}
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public void setTargetDnetIdentifier(String targetDnetIdentifier) {
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this.targetDnetIdentifier = targetDnetIdentifier;
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}
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public void setSourcePids(List<String> sourcePids) {
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this.sourcePids = sourcePids;
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}
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public List<String> getSourcePids() {
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return sourcePids;
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}
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public List<String> getSourcePidTypes() {
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return sourcePidTypes;
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}
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public void setSourcePids(List<String> sourcePids) {
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this.sourcePids = sourcePids;
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}
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public void setSourcePidTypes(List<String> sourcePidTypes) {
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this.sourcePidTypes = sourcePidTypes;
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}
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public List<String> getSourcePidTypes() {
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return sourcePidTypes;
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}
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public List<String> getTargetPids() {
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return targetPids;
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}
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public void setSourcePidTypes(List<String> sourcePidTypes) {
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this.sourcePidTypes = sourcePidTypes;
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}
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public void setTargetPids(List<String> targetPids) {
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this.targetPids = targetPids;
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}
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public List<String> getTargetPids() {
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return targetPids;
|
||||
}
|
||||
public List<String> getTargetPidTypes() {
|
||||
return targetPidTypes;
|
||||
}
|
||||
|
||||
public void setTargetPids(List<String> targetPids) {
|
||||
this.targetPids = targetPids;
|
||||
}
|
||||
public void setTargetPidTypes(List<String> targetPidTypes) {
|
||||
this.targetPidTypes = targetPidTypes;
|
||||
}
|
||||
|
||||
public List<String> getTargetPidTypes() {
|
||||
return targetPidTypes;
|
||||
}
|
||||
public List<String> getSourceLinkPublisher() {
|
||||
return sourceLinkPublisher;
|
||||
}
|
||||
|
||||
public void setTargetPidTypes(List<String> targetPidTypes) {
|
||||
this.targetPidTypes = targetPidTypes;
|
||||
}
|
||||
public void setSourceLinkPublisher(List<String> sourceLinkPublisher) {
|
||||
this.sourceLinkPublisher = sourceLinkPublisher;
|
||||
}
|
||||
|
||||
public List<String> getSourceLinkPublisher() {
|
||||
return sourceLinkPublisher;
|
||||
}
|
||||
public List<String> getTargetLinkPublisher() {
|
||||
return targetLinkPublisher;
|
||||
}
|
||||
|
||||
public void setSourceLinkPublisher(List<String> sourceLinkPublisher) {
|
||||
this.sourceLinkPublisher = sourceLinkPublisher;
|
||||
}
|
||||
public void setTargetLinkPublisher(List<String> targetLinkPublisher) {
|
||||
this.targetLinkPublisher = targetLinkPublisher;
|
||||
}
|
||||
|
||||
public List<String> getTargetLinkPublisher() {
|
||||
return targetLinkPublisher;
|
||||
}
|
||||
public List<String> getLinkProvider() {
|
||||
return linkProvider;
|
||||
}
|
||||
|
||||
public void setTargetLinkPublisher(List<String> targetLinkPublisher) {
|
||||
this.targetLinkPublisher = targetLinkPublisher;
|
||||
}
|
||||
public void setLinkProvider(List<String> linkProvider) {
|
||||
this.linkProvider = linkProvider;
|
||||
}
|
||||
|
||||
public String getPublicationDate() {
|
||||
return publicationDate;
|
||||
}
|
||||
|
||||
public List<String> getLinkProvider() {
|
||||
return linkProvider;
|
||||
}
|
||||
public void setPublicationDate(String publicationDate) {
|
||||
this.publicationDate = publicationDate;
|
||||
}
|
||||
|
||||
public void setLinkProvider(List<String> linkProvider) {
|
||||
this.linkProvider = linkProvider;
|
||||
}
|
||||
public String getJson() {
|
||||
return json;
|
||||
}
|
||||
|
||||
public String getPublicationDate() {
|
||||
return publicationDate;
|
||||
}
|
||||
public void setJson(String json) {
|
||||
this.json = json;
|
||||
}
|
||||
|
||||
public void setPublicationDate(String publicationDate) {
|
||||
this.publicationDate = publicationDate;
|
||||
}
|
||||
public static ScholixFlat fromScholix(final Scholix scholix) throws JsonProcessingException {
|
||||
if (scholix == null || scholix.getSource() == null || scholix.getTarget() == null)
|
||||
return null;
|
||||
final ScholixFlat flat = new ScholixFlat();
|
||||
if (scholix.getLinkprovider() != null)
|
||||
scholix.getLinkprovider().forEach(l -> flat.addLinkProvider(l.getName()));
|
||||
|
||||
public String getJson() {
|
||||
return json;
|
||||
}
|
||||
flat.setPublicationDate(scholix.getPublicationDate());
|
||||
|
||||
public void setJson(String json) {
|
||||
this.json = json;
|
||||
}
|
||||
final ScholixResource source = scholix.getSource();
|
||||
flat.setSourceDnetIdentifier(source.getDnetIdentifier());
|
||||
if (source.getIdentifier() != null) {
|
||||
source.getIdentifier().forEach(i -> {
|
||||
flat.addSourcePid(i.getIdentifier());
|
||||
flat.addSourcePidType(i.getSchema());
|
||||
});
|
||||
}
|
||||
if (source.getPublisher() != null) {
|
||||
source.getPublisher().forEach(p -> flat.addSourceLinkPublisher(p.getName()));
|
||||
}
|
||||
|
||||
public static ScholixFlat fromScholix(final Scholix scholix) throws JsonProcessingException {
|
||||
if (scholix== null || scholix.getSource()==null || scholix.getTarget()== null)
|
||||
return null;
|
||||
final ScholixFlat flat = new ScholixFlat();
|
||||
if (scholix.getLinkprovider()!= null)
|
||||
scholix.getLinkprovider().forEach(l ->flat.addLinkProvider(l.getName()));
|
||||
|
||||
flat.setPublicationDate(scholix.getPublicationDate());
|
||||
|
||||
final ScholixResource source = scholix.getSource();
|
||||
flat.setSourceDnetIdentifier(source.getDnetIdentifier());
|
||||
if (source.getIdentifier()!= null) {
|
||||
source.getIdentifier().forEach(i -> {
|
||||
flat.addSourcePid(i.getIdentifier());
|
||||
flat.addSourcePidType(i.getSchema());
|
||||
});
|
||||
}
|
||||
if (source.getPublisher()!= null) {
|
||||
source.getPublisher().forEach(p -> flat.addSourceLinkPublisher(p.getName()));
|
||||
}
|
||||
|
||||
|
||||
|
||||
final ScholixResource target = scholix.getSource();
|
||||
flat.setTargetDnetIdentifier(target.getDnetIdentifier());
|
||||
if (target.getIdentifier()!= null) {
|
||||
target.getIdentifier().forEach(i -> {
|
||||
flat.addTargetPid(i.getIdentifier());
|
||||
flat.addTargetPidType(i.getSchema());
|
||||
});
|
||||
}
|
||||
if (target.getPublisher()!= null) {
|
||||
target.getPublisher().forEach(p -> flat.addTargetLinkPublisher(p.getName()));
|
||||
}
|
||||
flat.setJson(MAPPER.writeValueAsString(scholix));
|
||||
return flat;
|
||||
}
|
||||
final ScholixResource target = scholix.getSource();
|
||||
flat.setTargetDnetIdentifier(target.getDnetIdentifier());
|
||||
if (target.getIdentifier() != null) {
|
||||
target.getIdentifier().forEach(i -> {
|
||||
flat.addTargetPid(i.getIdentifier());
|
||||
flat.addTargetPidType(i.getSchema());
|
||||
});
|
||||
}
|
||||
if (target.getPublisher() != null) {
|
||||
target.getPublisher().forEach(p -> flat.addTargetLinkPublisher(p.getName()));
|
||||
}
|
||||
flat.setJson(MAPPER.writeValueAsString(scholix));
|
||||
return flat;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
@ -56,7 +56,7 @@ public class XmlRecordFactoryTest {
|
|||
|
||||
assertNotNull(doc);
|
||||
|
||||
//System.out.println(doc.asXML());
|
||||
// System.out.println(doc.asXML());
|
||||
|
||||
assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid"));
|
||||
assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending"));
|
||||
|
|
|
@ -6,19 +6,17 @@ import org.junit.Before
|
|||
|
||||
import org.junit.jupiter.api.{Test}
|
||||
|
||||
class ScholixFlatTest{
|
||||
|
||||
|
||||
var spark:SparkSession = null
|
||||
class ScholixFlatTest {
|
||||
|
||||
var spark: SparkSession = null
|
||||
|
||||
def initSpark(): Unit = {
|
||||
|
||||
if (spark!= null)
|
||||
if (spark != null)
|
||||
return
|
||||
println("SONO QUI")
|
||||
val conf = new SparkConf
|
||||
conf.setAppName(getClass.getSimpleName )
|
||||
conf.setAppName(getClass.getSimpleName)
|
||||
conf.setMaster("local[*]")
|
||||
conf.set("spark.driver.host", "localhost")
|
||||
conf.set("hive.metastore.local", "true")
|
||||
|
@ -27,26 +25,22 @@ class ScholixFlatTest{
|
|||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(getClass.getSimpleName)
|
||||
.config(conf)
|
||||
.config(conf)
|
||||
.getOrCreate()
|
||||
}
|
||||
|
||||
|
||||
|
||||
def after(): Unit = {
|
||||
spark.stop()
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
def testScholixConversion (): Unit = {
|
||||
def testScholixConversion(): Unit = {
|
||||
initSpark()
|
||||
val p = getClass.getResource("/eu/dnetlib/dhp/sx/provision/scholix_dump.zip").getPath
|
||||
|
||||
val t = spark.read.text(p).count
|
||||
println(s"total =$t")
|
||||
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
2
pom.xml
2
pom.xml
|
@ -807,7 +807,7 @@
|
|||
<mockito-core.version>3.3.3</mockito-core.version>
|
||||
<mongodb.driver.version>3.4.2</mongodb.driver.version>
|
||||
<vtd.version>[2.12,3.0)</vtd.version>
|
||||
<dhp-schemas.version>[3.16.0]</dhp-schemas.version>
|
||||
<dhp-schemas.version>[3.16.1-SNAPSHOT]</dhp-schemas.version>
|
||||
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.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>
|
||||
|
|
Loading…
Reference in New Issue