From c952c8d236bf0e2201df5500b6fa6a9c164ad157 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 6 Jul 2021 09:53:14 +0200 Subject: [PATCH] generate first side of scholix mapping --- .../dhp/sx/graph/SparkCreateScholix.scala | 66 ++++++ .../dhp/sx/graph/scholix/ScholixUtils.scala | 194 +++++++++++++++++- .../sx/graph/scholix/ScholixGraphTest.scala | 85 ++++++++ .../eu/dnetlib/dhp/sx/graph/oaf_to_summary | 10 + .../dhp/sx/graph/relation_transform.json | 26 +++ pom.xml | 2 +- 6 files changed, 374 insertions(+), 9 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/relation_transform.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala new file mode 100644 index 0000000000..6b4eacaf66 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala @@ -0,0 +1,66 @@ +package eu.dnetlib.dhp.sx.graph + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.Relation +import eu.dnetlib.dhp.schema.sx.scholix.Scholix +import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +object SparkCreateScholix { + + def main(args: Array[String]): Unit = { + val log: Logger = LoggerFactory.getLogger(getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/create_scholix_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + val relationPath = parser.get("relationPath") + log.info(s"relationPath -> $relationPath") + val summaryPath = parser.get("summaryPath") + log.info(s"summaryPath -> $summaryPath") + val targetPath = parser.get("targetPath") + log.info(s"targetPath -> $targetPath") + + + implicit val relEncoder:Encoder[Relation] = Encoders.kryo[Relation] + implicit val summaryEncoder :Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary] + implicit val scholixEncoder :Encoder[Scholix] = Encoders.kryo[Scholix] + + + val relationDS:Dataset[(String, Relation)] = spark.read.load(relationPath).as[Relation] + .map(r => (r.getSource, r))(Encoders.tuple(Encoders.STRING, relEncoder)) + + val summaryDS:Dataset[(String, ScholixSummary)] = spark.read.load(summaryPath).as[ScholixSummary] + .map(r => (r.getId, r))(Encoders.tuple(Encoders.STRING, summaryEncoder)) + + + +// relationDS.joinWith(summaryDS, relationDS("_1").equalTo(summaryDS("_1")), "left") +// .map {input:((String,Relation), (String, ScholixSummary)) => +// val rel:Relation = input._1._2 +// val source:ScholixSummary = input._2._2 +// +// +// val s = new Scholix +// +// +// } + + + + + + + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala index c0e28ee36b..f7d8a22c48 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala @@ -1,25 +1,203 @@ package eu.dnetlib.dhp.sx.graph.scholix -import eu.dnetlib.dhp.schema.oaf.{Dataset, Result} -import eu.dnetlib.dhp.schema.sx.summary.{CollectedFromType, SchemeValue, ScholixSummary, TypedIdentifier, Typology} + +import eu.dnetlib.dhp.schema.oaf.{Dataset, Relation, Result, StructuredProperty} +import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixCollectedFrom, ScholixEntityId, ScholixIdentifier, ScholixRelationship, ScholixResource} +import eu.dnetlib.dhp.schema.sx.summary.{CollectedFromType, SchemeValue, ScholixSummary, Typology} +import org.json4s +import org.json4s.DefaultFormats +import org.json4s.jackson.JsonMethods.parse import scala.collection.JavaConverters._ +import scala.io.Source import scala.language.postfixOps object ScholixUtils { + val DNET_IDENTIFIER_SCHEMA: String = "DNET Identifier" + + val DATE_RELATION_KEY:String = "RelationDate" + case class RelationVocabulary(original:String, inverse:String){} + + val relations:Map[String, RelationVocabulary] = { + val input =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/relations.json")).mkString + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + + lazy val json: json4s.JValue = parse(input) + + json.extract[Map[String, RelationVocabulary]] + } + + + def extractRelationDate(relation: Relation):String = { + + if (relation.getProperties== null || !relation.getProperties.isEmpty) + null + else { + val date =relation.getProperties.asScala.find(p => DATE_RELATION_KEY.equalsIgnoreCase(p.getKey)).map(p => p.getValue) + if (date.isDefined) + date.get + else + null + } + } + + def extractRelationDate(summary: ScholixSummary):String = { + + if(summary.getDate== null && !summary.getDate.isEmpty) + null + else { + summary.getDate.get(0) + } + + + } + + + def extractCollectedFrom(summary:ScholixSummary): List[ScholixEntityId] = { + if (summary.getDatasources!= null && !summary.getDatasources.isEmpty) { + val l: List[ScholixEntityId] = summary.getDatasources.asScala.map{ + d => new ScholixEntityId(d.getDatasourceName, List(new ScholixIdentifier(d.getDatasourceId, "DNET Identifier", null)).asJava) + }(collection.breakOut) + l + } else List() + } + + def extractCollectedFrom(relation: Relation) : List[ScholixEntityId] = { + if (relation.getCollectedfrom != null && !relation.getCollectedfrom.isEmpty) { + + + val l: List[ScholixEntityId] = relation.getCollectedfrom.asScala.map { + c => + + new ScholixEntityId(c.getValue, List(new ScholixIdentifier(c.getKey, DNET_IDENTIFIER_SCHEMA,null)).asJava) + }(collection breakOut) + l + } else List() + } + + + def generateScholixResourceFromSummary(summaryObject: ScholixSummary): ScholixResource = { + val r = new ScholixResource + r.setIdentifier(summaryObject.getLocalIdentifier) + r.setDnetIdentifier(summaryObject.getId) + + r.setObjectType(summaryObject.getTypology.toString) + r.setObjectSubType(summaryObject.getSubType) + + if (summaryObject.getTitle!= null && !summaryObject.getTitle.isEmpty) + r.setTitle(summaryObject.getTitle.get(0)) + + if (summaryObject.getAuthor!= null && !summaryObject.getAuthor.isEmpty){ + val l:List[ScholixEntityId] = summaryObject.getAuthor.asScala.map(a => new ScholixEntityId(a,null)).toList + if (l.nonEmpty) + r.setCreator(l.asJava) + } + + if (summaryObject.getDate!= null && !summaryObject.getDate.isEmpty) + r.setPublicationDate(summaryObject.getDate.get(0)) + if (summaryObject.getPublisher!= null && !summaryObject.getPublisher.isEmpty) + { + val plist:List[ScholixEntityId] =summaryObject.getPublisher.asScala.map(p => new ScholixEntityId(p, null)).toList + + if (plist.nonEmpty) + r.setPublisher(plist.asJava) + } + + + if (summaryObject.getDatasources!= null && !summaryObject.getDatasources.isEmpty) { + + val l:List[ScholixCollectedFrom] = summaryObject.getDatasources.asScala.map(c => new ScholixCollectedFrom( + new ScholixEntityId(c.getDatasourceName, List(new ScholixIdentifier(c.getDatasourceId, DNET_IDENTIFIER_SCHEMA, null)).asJava) + , "collected", "complete" + + )).toList + + if (l.nonEmpty) + r.setCollectedFrom(l.asJava) + + } + r + } + + + + + + def scholixFromSource(relation:Relation, source:ScholixSummary):Scholix = { + + if (relation== null || source== null) + return null + + val s = new Scholix + + var l: List[ScholixEntityId] = extractCollectedFrom(relation) + if (l.isEmpty) + l = extractCollectedFrom(source) + if (l.isEmpty) + return null + + s.setLinkprovider(l.asJava) + + var d = extractRelationDate(relation) + if (d == null) + d = extractRelationDate(source) + + s.setPublicationDate(d) + + + if (source.getPublisher!= null && !source.getPublisher.isEmpty) { + val l: List[ScholixEntityId] = source.getPublisher.asScala + .map{ + p => + new ScholixEntityId(p, null) + }(collection.breakOut) + + if (l.nonEmpty) + s.setPublisher(l.asJava) + } + + val semanticRelation = relations.getOrElse(relation.getRelClass.toLowerCase, null) + if (semanticRelation== null) + return null + s.setRelationship(new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse)) + s.setSource(generateScholixResourceFromSummary(source)) + + s + } + + + def findURLforPID(pidValue:List[StructuredProperty], urls:List[String]):List[(StructuredProperty, String)] = { + pidValue.map{ + p => + val pv = p.getValue + + val r = urls.find(u => u.toLowerCase.contains(pv.toLowerCase)) + (p, r.orNull) + } + } + + + def extractTypedIdentifierFromInstance(r:Result):List[ScholixIdentifier] = { + if (r.getInstance() == null || r.getInstance().isEmpty) + return List() + r.getInstance().asScala.filter(i => i.getUrl!= null && !i.getUrl.isEmpty) + + .flatMap(i => findURLforPID(i.getPid.asScala.toList, i.getUrl.asScala.toList)) + .map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2)).distinct.toList + } + def resultToSummary(r:Result):ScholixSummary = { val s = new ScholixSummary s.setId(r.getId) if (r.getPid == null || r.getPid.isEmpty) return null - val pids:List[TypedIdentifier] = r.getPid.asScala.map(p => new TypedIdentifier(p.getValue, p.getQualifier.getClassid))(collection breakOut) + val pids:List[ScholixIdentifier] = extractTypedIdentifierFromInstance(r) + if (pids.isEmpty) + return null s.setLocalIdentifier(pids.asJava) - - s.getLocalIdentifier.isEmpty - if (r.isInstanceOf[Dataset]) s.setTypology(Typology.dataset) else @@ -43,7 +221,7 @@ object ScholixUtils { if (r.getInstance() != null) { val dt:List[String] = r.getInstance().asScala.filter(i => i.getDateofacceptance != null).map(i => i.getDateofacceptance.getValue)(collection.breakOut) if (dt.nonEmpty) - s.setDate(dt.asJava) + s.setDate(dt.distinct.asJava) } if (r.getDescription!= null && !r.getDescription.isEmpty) { val d = r.getDescription.asScala.find(f => f.getValue!=null) @@ -63,7 +241,7 @@ object ScholixUtils { if (r.getCollectedfrom!= null && !r.getCollectedfrom.isEmpty) { val cf:List[CollectedFromType] = r.getCollectedfrom.asScala.map(c => new CollectedFromType(c.getValue, c.getKey, "complete"))(collection breakOut) if (cf.nonEmpty) - s.setDatasources(cf.asJava) + s.setDatasources(cf.distinct.asJava) } s.setRelatedDatasets(0) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala new file mode 100644 index 0000000000..129de20293 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala @@ -0,0 +1,85 @@ +package eu.dnetlib.dhp.sx.graph.scholix + +import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature} +import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result} +import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF +import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.ScholixResolved +import eu.dnetlib.dhp.sx.graph.bio.pubmed.AbstractVocabularyTest +import org.json4s +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse +import org.junit.jupiter.api.Assertions._ +import org.junit.jupiter.api.extension.ExtendWith +import org.junit.jupiter.api.{BeforeEach, Test} +import org.mockito.junit.jupiter.MockitoExtension + +import java.io.{BufferedReader, InputStream, InputStreamReader} +import java.util.zip.GZIPInputStream +import scala.collection.JavaConverters._ +import scala.io.Source +import scala.xml.pull.XMLEventReader + +@ExtendWith(Array(classOf[MockitoExtension])) +class ScholixGraphTest extends AbstractVocabularyTest{ + + + val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT) + mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false) + + @BeforeEach + def setUp() :Unit = { + + super.setUpVocabulary() + } + + + @Test + def testOAFToSummary():Unit= { + val inputRelations = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/oaf_to_summary")).mkString + val items = inputRelations.lines.toList + assertNotNull(items) + items.foreach(i =>assertTrue(i.nonEmpty)) + val result = items.map(r => mapper.readValue(r, classOf[Result])).map(i => ScholixUtils.resultToSummary(i)) + + assertNotNull(result) + + assertEquals(result.size, items.size) + val d = result.find(s => s.getLocalIdentifier.asScala.exists(i => i.getUrl == null || i.getUrl.isEmpty)) + assertFalse(d.isDefined) + + println(mapper.writeValueAsString(result.head)) + + } + + + + + + + @Test + def testScholixRelationshipsClean() = { + val inputRelations = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/relation_transform.json")).mkString + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + + lazy val json: json4s.JValue = parse(inputRelations) + val l:List[String] =json.extract[List[String]] + assertNotNull(l) + assertTrue(l.nonEmpty) + + + val relVocbaulary =ScholixUtils.relations + + l.foreach(r => assertTrue(relVocbaulary.contains(r.toLowerCase))) + + + + + + + } + + + + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary new file mode 100644 index 0000000000..e1fd758b41 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary @@ -0,0 +1,10 @@ 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We first unravel misconceptions as perceived on different continents and subsequently present a revised interpretation of the identity and typification of three European taxa at species level: Ruppia maritima L., Ruppia spiralis L. ex Dumortier, and Ruppia cirrhosa (Petagna) Grande. To do this, historical specimens, illustrations and original descriptions were studied. We supersede a previous choice of the figure of Buccaferrea maritima, foliis minus acutis Micheli (1729) as the lectotype of R. maritima and type species of the genus Ruppia owing to a serious conflict with the protologue. Based on a meticulous interpretation of protologues and figures in a historical context, we reject the recent view of assigning R. cirrhosa and its proposed lectotype (iconotype) as a homotypic synonym of R. maritima. We agree with an earlier lectotypification of R. spiralis, though for another reason than the above-mentioned abused homotypy. Consequently, R. cirrhosa is a synonym of neither R. maritima or R. spiralis, based on material from Petagna in the Herbarium of Naples designated as the holotype of R. cirrhosa. We argue for three species to be considered as fully independent taxa: R. maritima, R. spiralis and R. cirrhosa.","dataInfo":null}],"dateofacceptance":{"value":"2020-01-15","dataInfo":null},"publisher":{"value":"Walter de Gruyter GmbH","dataInfo":null},"embargoenddate":null,"source":[{"value":"Crossref","dataInfo":null}],"fulltext":[],"format":[],"contributor":[],"resourcetype":{"classid":"0001","classname":"0001","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes","openAccessRoute":null},"instancetype":{"classid":"0001","classname":"Article","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown 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