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 index 05330d06e..274bdb150 100644 --- 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 @@ -4,9 +4,10 @@ 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 eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf -import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession} +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} object SparkCreateScholix { @@ -31,40 +32,45 @@ object SparkCreateScholix { 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] + implicit val relEncoder: Encoder[Relation] = Encoders.kryo[Relation] + implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary] + implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix] + + import spark.implicits._ - 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)) - - - val res: Array[((String, Relation), (String, ScholixSummary))] =relationDS.joinWith(summaryDS, relationDS("_1").equalTo(summaryDS("_1")), "left").take(10) - - - res.foreach(r =>println(r._1._2)) - -// 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 -// -// -// } - + 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 + (rel.getTarget, ScholixUtils.scholixFromSource(rel, source)) + }(Encoders.tuple(Encoders.STRING, scholixEncoder)) + .write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_from_source") + + val scholixSource: Dataset[(String, Scholix)] = spark.read.load(s"$targetPath/scholix_from_source").as[(String, Scholix)](Encoders.tuple(Encoders.STRING, scholixEncoder)) + + scholixSource.joinWith(summaryDS, scholixSource("_1").equalTo(summaryDS("_1")), "left") + .map { input: ((String, Scholix), (String, ScholixSummary)) => + val s: Scholix = input._1._2 + val target: ScholixSummary = input._2._2 + ScholixUtils.generateCompleteScholix(s, target) + }.write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_one_verse") + val scholix_o_v: Dataset[Scholix] = spark.read.load(s"$targetPath/scholix_one_verse").as[Scholix] + scholix_o_v.flatMap(s => List(s, ScholixUtils.createInverseScholixRelation(s))).groupByKey(_.getIdentifier).reduceGroups { (x, y) => + if (x != null) + x + else + y + }.write.mode(SaveMode.Overwrite).save(s"$targetPath/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 881467e5b..d38ea388a 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 @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.sx.graph.scholix 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 eu.dnetlib.dhp.utils.DHPUtils import org.json4s import org.json4s.DefaultFormats import org.json4s.jackson.JsonMethods.parse @@ -45,13 +46,35 @@ object ScholixUtils { def extractRelationDate(summary: ScholixSummary):String = { - if(summary.getDate== null && !summary.getDate.isEmpty) + if(summary.getDate== null || summary.getDate.isEmpty) null else { summary.getDate.get(0) } + } + + def inverseRelationShip(rel:ScholixRelationship):ScholixRelationship = { + new ScholixRelationship(rel.getInverse, rel.getSchema, rel.getName) + + + } + + + def createInverseScholixRelation(scholix: Scholix):Scholix = { + val s = new Scholix + s.setPublicationDate(scholix.getPublicationDate) + s.setPublisher(scholix.getPublisher) + s.setLinkprovider(scholix.getLinkprovider) + s.setRelationship(inverseRelationShip(scholix.getRelationship)) + s.setSource(scholix.getTarget) + s.setTarget(scholix.getSource) + s.setIdentifier(DHPUtils.md5(s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}")) + s + + + } @@ -78,6 +101,19 @@ object ScholixUtils { } + def generateCompleteScholix(scholix: Scholix, target:ScholixSummary): Scholix = { + val s = new Scholix + s.setPublicationDate(scholix.getPublicationDate) + s.setPublisher(scholix.getPublisher) + s.setLinkprovider(scholix.getLinkprovider) + s.setRelationship(scholix.getRelationship) + s.setSource(scholix.getSource) + s.setTarget(generateScholixResourceFromSummary(target)) + s.setIdentifier(DHPUtils.md5(s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}")) + s + } + + def generateScholixResourceFromSummary(summaryObject: ScholixSummary): ScholixResource = { val r = new ScholixResource r.setIdentifier(summaryObject.getLocalIdentifier) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/create_scholix_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/create_scholix_params.json new file mode 100644 index 000000000..336181e0a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/create_scholix_params.json @@ -0,0 +1,6 @@ +[ + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"r", "paramLongName":"relationPath", "paramDescription": "the relation resolved Path", "paramRequired": true}, + {"paramName":"s", "paramLongName":"summaryPath", "paramDescription": "the summary Path", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the target base path of the scholix", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml index 492b21489..bac3687e2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml @@ -10,7 +10,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -90,6 +90,33 @@ --sourcePath${targetPath}/dedup --targetPath${targetPath}/provision/summaries + + + + + + + yarn + cluster + Generate Scholix Dataset + eu.dnetlib.dhp.sx.graph.SparkCreateScholix + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=6000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --summaryPath${targetPath}/provision/summaries + --targetPath${targetPath}/provision/scholix + --relationPath${targetPath}/resolved/resolvedRelation + + 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 index e1fd758b4..4d581044a 100644 --- 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 @@ -1,10 +1,20 @@ 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These results indicated that these compounds with the twisted naphthalene bridged bis-triphenylamine core could show stable deep-blue electroluminescence properties and introducing the electron-donating group (–OCH 3 ) could enable high luminance and current efficiency for OLEDs.","dataInfo":null}],"dateofacceptance":{"value":"2019-01-29T03:05:29Z","dataInfo":null},"publisher":{"value":"Royal Society of Chemistry 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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. 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