updated resolution wf:
- generate a new version of the graph - changed merge from union to join
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fdb75b180e
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35e20b0647
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@ -14,7 +14,7 @@ import org.slf4j.{Logger, LoggerFactory}
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object SparkResolveEntities {
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val mapper = new ObjectMapper()
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val entities = List(EntityType.dataset,EntityType.publication, EntityType.software, EntityType.otherresearchproduct)
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val entities = List(EntityType.dataset, EntityType.publication, EntityType.software, EntityType.otherresearchproduct)
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def main(args: Array[String]): Unit = {
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val log: Logger = LoggerFactory.getLogger(getClass)
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@ -36,25 +36,19 @@ object SparkResolveEntities {
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val unresolvedPath = parser.get("unresolvedPath")
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log.info(s"unresolvedPath -> $unresolvedPath")
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val targetPath = parser.get("targetPath")
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log.info(s"targetPath -> $targetPath")
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val fs = FileSystem.get(spark.sparkContext.hadoopConfiguration)
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fs.mkdirs(new Path(workingPath))
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resolveEntities(spark, workingPath, unresolvedPath)
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generateResolvedEntities(spark, workingPath, graphBasePath)
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// TO BE conservative we keep the original entities in the working dir
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// and save the resolved entities on the graphBasePath
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//In future these lines of code should be removed
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entities.foreach {
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e =>
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fs.rename(new Path(s"$graphBasePath/$e"), new Path(s"$workingPath/${e}_old"))
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fs.rename(new Path(s"$workingPath/resolvedGraph/$e"), new Path(s"$graphBasePath/$e"))
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}
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}
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generateResolvedEntities(spark, workingPath, graphBasePath, targetPath)
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}
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def resolveEntities(spark: SparkSession, workingPath: String, unresolvedPath: String) = {
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def resolveEntities(spark: SparkSession, workingPath: String, unresolvedPath: String) = {
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implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
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import spark.implicits._
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@ -71,37 +65,43 @@ def resolveEntities(spark: SparkSession, workingPath: String, unresolvedPath: St
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}
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def deserializeObject(input:String, entity:EntityType ) :Result = {
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def deserializeObject(input: String, entity: EntityType): Result = {
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entity match {
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case EntityType.publication => mapper.readValue(input, classOf[Publication])
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case EntityType.dataset => mapper.readValue(input, classOf[OafDataset])
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case EntityType.software=> mapper.readValue(input, classOf[Software])
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case EntityType.otherresearchproduct=> mapper.readValue(input, classOf[OtherResearchProduct])
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}
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entity match {
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case EntityType.publication => mapper.readValue(input, classOf[Publication])
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case EntityType.dataset => mapper.readValue(input, classOf[OafDataset])
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case EntityType.software => mapper.readValue(input, classOf[Software])
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case EntityType.otherresearchproduct => mapper.readValue(input, classOf[OtherResearchProduct])
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}
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}
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def generateResolvedEntities(spark:SparkSession, workingPath: String, graphBasePath:String) = {
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def generateResolvedEntities(spark: SparkSession, workingPath: String, graphBasePath: String, targetPath:String) = {
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implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
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import spark.implicits._
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val re:Dataset[Result] = spark.read.load(s"$workingPath/resolvedEntities").as[Result]
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val re: Dataset[(String, Result)] = spark.read.load(s"$workingPath/resolvedEntities").as[Result].map(r => (r.getId, r))
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entities.foreach {
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e =>
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e => {
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val currentEntityDataset: Dataset[(String, Result)] = spark.read.text(s"$graphBasePath/$e").as[String].map(s => deserializeObject(s, e)).map(r => (r.getId, r))
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currentEntityDataset.joinWith(re, currentEntityDataset("_1").equalTo(re("_1")), "left").map(k => {
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val a = k._1
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val b = k._2
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if (b == null)
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a._2
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else {
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a._2.mergeFrom(b._2)
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a._2
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}
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}).map(r => mapper.writeValueAsString(r))(Encoders.STRING)
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.write.mode(SaveMode.Overwrite).option("compression", "gzip").text(s"$targetPath/$e")
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}
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spark.read.text(s"$graphBasePath/$e").as[String]
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.map(s => deserializeObject(s, e))
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.union(re)
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.groupByKey(_.getId)
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.reduceGroups {
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(x, y) =>
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x.mergeFrom(y)
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x
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}.map(_._2)
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.filter(r => r.getClass.getSimpleName.toLowerCase != "result")
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.map(r => mapper.writeValueAsString(r))(Encoders.STRING)
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.write.mode(SaveMode.Overwrite).option("compression", "gzip").text(s"$workingPath/resolvedGraph/$e")
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}
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}
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}
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@ -35,6 +35,9 @@ object SparkResolveRelation {
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val workingPath = parser.get("workingPath")
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log.info(s"workingPath -> $workingPath")
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val targetPath = parser.get("targetPath")
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log.info(s"targetPath -> $targetPath")
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implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
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import spark.implicits._
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@ -80,20 +83,13 @@ object SparkResolveRelation {
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.mode(SaveMode.Overwrite)
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.save(s"$workingPath/relation_resolved")
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// TO BE conservative we keep the original relation in the working dir
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// and save the relation resolved on the graphBasePath
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//In future this two line of code should be removed
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fs.rename(new Path(s"$graphBasePath/relation"), new Path(s"$workingPath/relation"))
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spark.read.load(s"$workingPath/relation_resolved").as[Relation]
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.filter(r => !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved"))
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.map(r => mapper.writeValueAsString(r))
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.write
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.text(s"$graphBasePath/relation")
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.text(s"$targetPath/relation")
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}
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def extractInstanceCF(input: String): List[(String, String)] = {
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@ -8,6 +8,10 @@
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<name>unresolvedPath</name>
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<description>the path of the unresolved Entities</description>
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</property>
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<property>
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<name>targetPath</name>
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<description>the target path after resolution</description>
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</property>
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</parameters>
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<start to="ResolveRelations"/>
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@ -36,6 +40,7 @@
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<arg>--master</arg><arg>yarn</arg>
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<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
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<arg>--workingPath</arg><arg>${workingDir}</arg>
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<arg>--targetPath</arg><arg>${targetPath}</arg>
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</spark>
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<ok to="ResolveEntities"/>
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<error to="Kill"/>
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@ -62,6 +67,7 @@
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<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
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<arg>--unresolvedPath</arg><arg>${unresolvedPath}</arg>
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<arg>--workingPath</arg><arg>${workingDir}</arg>
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<arg>--targetPath</arg><arg>${targetPath}</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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@ -2,5 +2,6 @@
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{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
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{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the source Path", "paramRequired": true},
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{"paramName":"u", "paramLongName":"unresolvedPath", "paramDescription": "the source Path", "paramRequired": true},
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{"paramName":"g", "paramLongName":"graphBasePath", "paramDescription": "the path of the raw graph", "paramRequired": true}
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{"paramName":"g", "paramLongName":"graphBasePath", "paramDescription": "the path of the raw graph", "paramRequired": true},
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{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the target path", "paramRequired": true}
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]
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@ -1,5 +1,6 @@
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[
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{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
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{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the source Path", "paramRequired": true},
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{"paramName":"g", "paramLongName":"graphBasePath", "paramDescription": "the path of the raw graph", "paramRequired": true}
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{"paramName":"g", "paramLongName":"graphBasePath", "paramDescription": "the path of the raw graph", "paramRequired": true},
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{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the target path", "paramRequired": true}
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]
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@ -4,7 +4,7 @@ package eu.dnetlib.dhp.oa.graph.resolution
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.schema.common.EntityType
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
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import eu.dnetlib.dhp.schema.oaf.{Result, StructuredProperty}
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import eu.dnetlib.dhp.schema.oaf.{Publication, Result, StructuredProperty}
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import org.apache.commons.io.FileUtils
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import org.apache.spark.SparkConf
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import org.apache.spark.sql._
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@ -154,19 +154,39 @@ class ResolveEntitiesTest extends Serializable {
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val t = pubDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count()
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var ct = pubDS.count()
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var et = pubDS.filter(p => p.getTitle!= null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty)).count()
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assertEquals(ct, et)
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val datDS:Dataset[Result] = spark.read.text(s"$workingDir/work/resolvedGraph/dataset").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.dataset))
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val td = datDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count()
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ct = datDS.count()
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et = datDS.filter(p => p.getTitle!= null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty)).count()
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assertEquals(ct, et)
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val softDS:Dataset[Result] = spark.read.text(s"$workingDir/work/resolvedGraph/software").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.software))
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val ts = softDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count()
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ct = softDS.count()
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et = softDS.filter(p => p.getTitle!= null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty)).count()
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assertEquals(ct, et)
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val orpDS:Dataset[Result] = spark.read.text(s"$workingDir/work/resolvedGraph/otherresearchproduct").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.otherresearchproduct))
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val to = orpDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count()
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ct = orpDS.count()
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et = orpDS.filter(p => p.getTitle!= null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty)).count()
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assertEquals(ct, et)
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assertEquals(0, t)
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assertEquals(2, td)
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assertEquals(1, ts)
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@ -178,6 +198,32 @@ class ResolveEntitiesTest extends Serializable {
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@Test
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def testMerge():Unit = {
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val r = new Result
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r.setSubject(List(OafMapperUtils.structuredProperty(FAKE_SUBJECT, OafMapperUtils.qualifier("fos","fosCS", "fossSchema", "fossiFIgo"), null)).asJava)
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val mapper = new ObjectMapper()
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val p = mapper.readValue(Source.fromInputStream(this.getClass.getResourceAsStream(s"publication")).mkString.lines.next(), classOf[Publication])
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r.mergeFrom(p)
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println(mapper.writeValueAsString(r))
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}
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