diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala new file mode 100644 index 000000000..60df58e45 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala @@ -0,0 +1,96 @@ +package eu.dnetlib.dhp.oa.graph.resolution + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.common.EntityType +import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Result, Software, Dataset => OafDataset} +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.sql._ +import org.slf4j.{Logger, LoggerFactory} + +object SparkResolveEntities { + + val mapper = new ObjectMapper() + val entities = List(EntityType.dataset,EntityType.publication, EntityType.software, EntityType.otherresearchproduct) + + 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/oa/graph/resolution/resolve_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + + val graphBasePath = parser.get("graphBasePath") + log.info(s"graphBasePath -> $graphBasePath") + val workingPath = parser.get("workingPath") + log.info(s"workingPath -> $workingPath") + val unresolvedPath = parser.get("unresolvedPath") + log.info(s"unresolvedPath -> $unresolvedPath") + + + resolveEntities(spark, workingPath, unresolvedPath) + + + generateResolvedEntities(spark, workingPath, graphBasePath) + + } + + +def resolveEntities(spark: SparkSession, workingPath: String, unresolvedPath: String) = { + implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) + import spark.implicits._ + + val rPid: Dataset[(String, String)] = spark.read.load(s"$workingPath/relationResolvedPid").as[(String, String)] + val up: Dataset[(String, Result)] = spark.read.text(unresolvedPath).as[String].map(s => mapper.readValue(s, classOf[Result])).map(r => (r.getId, r))(Encoders.tuple(Encoders.STRING, resEncoder)) + + rPid.joinWith(up, rPid("_2").equalTo(up("_1")), "inner").map { + r => + val result = r._2._2 + val dnetId = r._1._1 + result.setId(dnetId) + result + }.write.mode(SaveMode.Overwrite).save(s"$workingPath/resolvedEntities") + } + + + def deserializeObject(input:String, entity:EntityType ) :Result = { + + entity match { + case EntityType.publication => mapper.readValue(input, classOf[Publication]) + case EntityType.dataset => mapper.readValue(input, classOf[OafDataset]) + case EntityType.software=> mapper.readValue(input, classOf[Software]) + case EntityType.otherresearchproduct=> mapper.readValue(input, classOf[OtherResearchProduct]) + } + } + + def generateResolvedEntities(spark:SparkSession, workingPath: String, graphBasePath:String) = { + + implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) + import spark.implicits._ + + val re:Dataset[Result] = spark.read.load(s"$workingPath/resolvedEntities").as[Result] + entities.foreach { + e => + + spark.read.text(s"$graphBasePath/$e").as[String] + .map(s => deserializeObject(s, e)) + .union(re) + .groupByKey(_.getId) + .reduceGroups { + (x, y) => + x.mergeFrom(y) + x + }.map(_._2) + .filter(r => r.getClass.getSimpleName.toLowerCase != "result") + .map(r => mapper.writeValueAsString(r))(Encoders.STRING) + .write.mode(SaveMode.Overwrite).option("compression", "gzip").text(s"$workingPath/resolvedGraph/$e") + } + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala index db93bc43f..9e44e017c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala @@ -128,7 +128,7 @@ object SparkResolveRelation { source != null } - private def extractPidResolvedTableFromJsonRDD(spark: SparkSession, graphPath: String, workingPath: String) = { + def extractPidResolvedTableFromJsonRDD(spark: SparkSession, graphPath: String, workingPath: String) = { import spark.implicits._ val d: RDD[(String, String)] = spark.sparkContext.textFile(s"$graphPath/*") diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/resolve_entities_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/resolve_entities_params.json new file mode 100644 index 000000000..f38cc1291 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/resolve_entities_params.json @@ -0,0 +1,6 @@ +[ + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the source Path", "paramRequired": true}, + {"paramName":"u", "paramLongName":"unresolvedPath", "paramDescription": "the source Path", "paramRequired": true}, + {"paramName":"g", "paramLongName":"graphBasePath", "paramDescription": "the path of the raw graph", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala new file mode 100644 index 000000000..9a142d3c0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala @@ -0,0 +1,190 @@ +package eu.dnetlib.dhp.oa.graph.resolution + + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.schema.common.EntityType +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils +import eu.dnetlib.dhp.schema.oaf.{Result, StructuredProperty} +import org.apache.commons.io.FileUtils +import org.apache.spark.SparkConf +import org.apache.spark.sql._ +import org.junit.jupiter.api.Assertions._ +import org.junit.jupiter.api.TestInstance.Lifecycle +import org.junit.jupiter.api.{AfterAll, BeforeAll, Test, TestInstance} + +import java.nio.file.{Files, Path} +import scala.collection.JavaConverters._ +import scala.io.Source + +@TestInstance(Lifecycle.PER_CLASS) +class ResolveEntitiesTest extends Serializable { + + var workingDir:Path = null + + val FAKE_TITLE = "FAKETITLE" + val FAKE_SUBJECT = "FAKESUBJECT" + + var sparkSession:Option[SparkSession] = None + + + @BeforeAll + def setUp() :Unit = { + workingDir = Files.createTempDirectory(getClass.getSimpleName) + + val conf = new SparkConf() + sparkSession = Some(SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master("local[*]").getOrCreate()) + populateDatasets(sparkSession.get) + generateUpdates(sparkSession.get) + + } + + + @AfterAll + def tearDown():Unit = { + FileUtils.deleteDirectory(workingDir.toFile) + sparkSession.get.stop() + + + } + + + + + def generateUpdates(spark:SparkSession):Unit = { + val template = Source.fromInputStream(this.getClass.getResourceAsStream("updates")).mkString + + + val pids:List[String] = template.lines.map{id => + val r = new Result + r.setId(id.toLowerCase.trim) + r.setSubject(List(OafMapperUtils.structuredProperty(FAKE_SUBJECT, OafMapperUtils.qualifier("fos","fosCS", "fossSchema", "fossiFIgo"), null)).asJava) + r.setTitle(List(OafMapperUtils.structuredProperty(FAKE_TITLE, OafMapperUtils.qualifier("fos","fosCS", "fossSchema", "fossiFIgo"), null)).asJava) + r + }.map{r => + val mapper = new ObjectMapper() + + mapper.writeValueAsString(r)}.toList + + + val sc =spark.sparkContext + + println(sc.parallelize(pids).count()) + + spark.createDataset(sc.parallelize(pids))(Encoders.STRING).write.mode(SaveMode.Overwrite).option("compression", "gzip").text(s"$workingDir/updates") + + + + + + import spark.implicits._ + implicit val resEncoder: Encoder[Result] = Encoders.bean(classOf[Result]) + val ds = spark.read.text(s"$workingDir/updates").as[String].map{s => val mapper = new ObjectMapper() + mapper.readValue(s, classOf[Result])}.collect() + + + + + assertEquals(4, ds.length) + ds.foreach{r => assertNotNull(r.getSubject)} + ds.foreach{r => assertEquals(1,r.getSubject.size())} + ds.foreach{r => assertNotNull(r.getTitle)} + ds.foreach{r => assertEquals(1,r.getTitle.size())} + + + + ds.flatMap(r => r.getTitle.asScala.map(t => t.getValue)).foreach(t => assertEquals(FAKE_TITLE,t)) + ds.flatMap(r => r.getSubject.asScala.map(t => t.getValue)).foreach(t => assertEquals(FAKE_SUBJECT,t)) + + println("generated Updates") + } + + + def populateDatasets(spark:SparkSession):Unit = { + import spark.implicits._ + val entities =SparkResolveEntities.entities + + entities.foreach{ + e => + val template = Source.fromInputStream(this.getClass.getResourceAsStream(s"$e")).mkString + spark.createDataset(spark.sparkContext.parallelize(template.lines.toList)).as[String].write.option("compression", "gzip").text(s"$workingDir/graph/$e") + println(s"Created Dataset $e") + } + SparkResolveRelation.extractPidResolvedTableFromJsonRDD(spark, s"$workingDir/graph", s"$workingDir/work") + + } + + + @Test + def testResolution():Unit = { + val spark:SparkSession = sparkSession.get + implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) + SparkResolveEntities.resolveEntities(spark,s"$workingDir/work", s"$workingDir/updates" ) + + val ds = spark.read.load(s"$workingDir/work/resolvedEntities").as[Result] + + assertEquals(3, ds.count()) + + ds.collect().foreach{ + r => + assertTrue(r.getId.startsWith("50")) + } + } + + + + + private def structuredPContainsValue(l:java.util.List[StructuredProperty], exptectedValue:String):Boolean = { + l.asScala.exists(p =>p.getValue!= null && p.getValue.equalsIgnoreCase(exptectedValue)) + } + + @Test + def testUpdate():Unit = { + val spark:SparkSession = sparkSession.get + import spark.implicits._ + implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) + val m = new ObjectMapper() + SparkResolveEntities.resolveEntities(spark,s"$workingDir/work", s"$workingDir/updates" ) + SparkResolveEntities.generateResolvedEntities(spark,s"$workingDir/work",s"$workingDir/graph" ) + + + + + val pubDS:Dataset[Result] = spark.read.text(s"$workingDir/work/resolvedGraph/publication").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.publication)) + val t = pubDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count() + + + + val datDS:Dataset[Result] = spark.read.text(s"$workingDir/work/resolvedGraph/dataset").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.dataset)) + val td = datDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count() + + + val softDS:Dataset[Result] = spark.read.text(s"$workingDir/work/resolvedGraph/software").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.software)) + val ts = softDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count() + + + val orpDS:Dataset[Result] = spark.read.text(s"$workingDir/work/resolvedGraph/otherresearchproduct").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.otherresearchproduct)) + val to = orpDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count() + + + assertEquals(0, t) + assertEquals(2, td) + assertEquals(1, ts) + assertEquals(0, to) + + } + + + + + + + + + + + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/resolution/dataset b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/resolution/dataset new file mode 100644 index 000000000..05c875148 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/resolution/dataset @@ -0,0 +1,3 @@ +{"author":[{"affiliation":[],"fullname":"Greenough, 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simulacija; usklađivanje oblika; opruge i mase"}],"title":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Simulacija elastičnih objekata"},{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Soft bodies simulation"}],"tool":[]} +{"author":[{"affiliation":[],"fullname":"Sobočanec, Sandra","name":"Sandra","pid":[],"rank":1,"surname":"Sobočanec"}],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::345c9d171ef3c5d706d08041d506428c","value":"Croatian Scientific Bibliography - CROSBI"}],"contactgroup":[],"contactperson":[],"context":[],"contributor":[],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2006-01-01"},"dateofcollection":"2021-10-25T05:50:25+0000","dateoftransformation":"2021-10-26T05:22:35.748Z","description":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Propolis je tijekom stoljeća, a u posljednje vrijeme i u suvremenoj medicinskoj praksi ispitivan i korišten kao protuvirusno, protubakterijsko i protugljivično sredstvo. Biološki učinci propolisa vezani su uz antibiotska, protuupalna i antioksidacijska svojstva. Jedan od sastojaka propolisa su flavonoidi, čija je karakteristika visoki antioksidacijski potencijal zbog kojeg im se pripisuje sposobnost prevencije različitih bolesti kao što su različite vrste tumora, osteoporoza, kardiovaskularne i neurodegenerativne bolesti. U našim ispitivanjima koristili smo nativni propolis u dvije doze (100 mg kg-1, 300 mg kg-1), kojem smo istražili sastav, udio i vrstu flavonoida odgovornih za njegov oksidacijski/antioksidacijski učinak. Krizin je bio prisutan u najvećoj koncentraciji, dok je izoramnetin bio prisutan u najmanjoj. Antioksidacijski potencijal nativnog propolisa u in vitro uvjetima je bio relativno nizak. Međutim, propolis značajno povisuje antioksidacijski učinak in vivo uvjetima u jetri, plućima i mozgu miševa. Učinak nativnog propolisa pokazao ovisio je o dozi i to tako da je u manjoj dozi djelovao antioksidacijski (zaštitno), a u većoj dozi prooksidacijski (štetno). Oksidacijski status nakon obradaa nativnim propolisom nije pokazao tkivnu, ali je pokazao doznu ovisnost. Antioksidacijski status pokazao je tkivnu i doznu ovisnost ; u mozgu nije pokazao promjenu, dok je najveća promjena zabilježena u plućima i u manjoj mjeri u jetri. Promjena aktivnosti antioksidacijskih enzima u jetri nije korelirala s količinom njihove mRNA, dok je u plućima promjena u aktivnosti istih uglavnom bila proporcionalna promjeni u mRNA. Nije zapažena značajna promjena u ekpresiji proteina za sve ispitivane antioksidacijske enzime, niti obzirom na dozu, niti obzirom na ispitivano tkivo. Analizom DNA čipova utvrđeno je da propolis u dozi od 100 mg kg-1 u jetri ima zaštitni učinak, dok je u dozi od 300 mg kg-1 taj učinak prooksidacijski. U plućima je propolis u obje doze imao zaštitni učinak, dok u mozgu nije imao učinka na ispitivane gene. U hiperbaričkim uvjetima propolis je smanjio oksidacijski stres u sva tri ispitivana tkiva u dozi od 100 mg kg-1. U plućima je taj učinak propolis ostvario povećanjem aktivnosti antioksidacijskih enzima (MnSOD, KAT). Antioksidacijski učinak propolisa porijeklom iz Hrvatske do sada nije istraživan u in vivo sistemima. Isto tako po prvi puta se ispituje nativni propolis (tehnologijska inovacija) za razliku od do sada ispitivanih vodenih ili alkoholnih ekstrakata. Rezultati ove studije također pokazuju da sposobnost zaštitnog odgovora u plućima na oksidacijski stres koji postoji u novorođenih, ali se gubi u odraslih jedinki, može biti obnovljena uporabom nativnog propolisa tijekom hiperoksije. Ta spoznaja može pomoći u zaštiti od hiperoksije u populaciji odraslih tijekom terapije kisikom."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|57a035e5b1ae::15786c1f0f2930ea867a234fbcb8ef08","instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[],"collectedfrom":{"key":"10|openaire____::345c9d171ef3c5d706d08041d506428c","value":"Croatian Scientific Bibliography - CROSBI"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2006-01-01"},"hostedby":{"key":"10|openaire____::345c9d171ef3c5d706d08041d506428c","value":"Croatian Scientific Bibliography - CROSBI"},"instancetype":{"classid":"doctoral thesis","classname":"doctoral 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