Prepare: added concept of neighbours lib and trying to compute concepts without success

prepare/build.gradle

@@ -16,6 +16,7 @@ dependencies {
 	implementation 'org.slf4j:slf4j-simple:1.7.36'
 	implementation 'net.sourceforge.argparse4j:argparse4j:0.9.0'
 	implementation 'org.json:json:20220320'
+	implementation files("lib/conceptualKNN.v1.6.jar")
 }
 
 sourceSets {

prepare/src/main/guessNNprepare/Utils.scala

@@ -1,5 +1,7 @@
 package guessNNprepare
 
+import org.apache.jena.rdf.model.{InfModel, ModelFactory}
+import org.apache.jena.reasoner.ReasonerRegistry
 import org.json.JSONArray
 
 import java.util.stream.StreamSupport
@@ -8,6 +10,16 @@ import scala.util.{Failure, Success, Try}
 
 object Utils {
 
+	def loadMondialDataset(): Try[InfModel] = {
+		Option(ClassLoader.getSystemResourceAsStream("mondial_2022_04_04.n3"))
+			.map(stream => {
+				val kg: InfModel = ModelFactory.createInfModel(ReasonerRegistry.getTransitiveReasoner, ModelFactory.createDefaultModel)
+				kg.read(stream, null, "TTL")
+				Success(kg)
+			})
+			.getOrElse(Failure(new RuntimeException("Impossible to open mondial dataset (should not happen)")))
+	}
+
 	def JSONArrayElementsAs[T](array: JSONArray): Seq[T] = {
 		StreamSupport.stream(array.spliterator(), false).toScala(LazyList)
 			.map(obj => obj.asInstanceOf[T])

prepare/src/main/guessNNprepare/mains/ComputeConcepts.scala

@@ -1,11 +1,17 @@
 package guessNNprepare.mains
 
+import conceptualKNN.utils.Table
+import conceptualKNN.{ConceptualKNNModel, Partition}
 import guessNNprepare.{NamedEntity, Utils}
 import net.sourceforge.argparse4j.impl.Arguments
 import net.sourceforge.argparse4j.inf.{ArgumentParser, Namespace}
+import org.apache.jena.sparql.core.Var
+import org.apache.jena.sparql.engine.binding.BindingFactory
 import org.json.{JSONArray, JSONObject, JSONTokener}
 
 import java.nio.file.{Files, Path, Paths}
+import java.util.concurrent.atomic.AtomicBoolean
+import scala.jdk.CollectionConverters.SeqHasAsJava
 import scala.util.Try
 
 object ComputeConcepts extends MainCommand {
@@ -15,15 +21,37 @@ object ComputeConcepts extends MainCommand {
 		parser.description(description)
 
 		parser.addArgument("guessable_entities").`type`(Arguments.fileType().verifyCanRead()).help("JSON file containing all guessable entities")
+		parser.addArgument("target").help("URI of the entity that should be guessed")
 	}
 
 	override def execute(ARGS: Namespace): Unit = {
 		// CLI args
 		val entitiesFilePath = Paths.get(ARGS.getString("guessable_entities"))
+		val guessTarget = ARGS.getString("target")
 
 		println(s"Loading entities from ${entitiesFilePath}")
 		val entities: List[NamedEntity] = loadEntitiesOrFail(entitiesFilePath)
 		println(s"Loaded ${entities.length} entities")
+		if (!entities.exists(e => e.rdfResource.getURI == guessTarget)) {
+			System.err.println("Error: target entities is not part of the guessable entities")
+			System.exit(1)
+		}
+		println("Loading data graph...")
+		val dataGraph = Utils.loadMondialDataset().get
+		println(s"Loaded ${dataGraph.listStatements().toList.size()} triples")
+
+		val entityVar = Var.alloc("e")
+		val entityTable = new Table(List(entityVar).asJava)
+		entities
+			.map(entity => dataGraph.createResource(entity.rdfResource))
+			.map(resource => resource.asNode())
+			.map(node => BindingFactory.binding(entityVar, node))
+			.foreach(binding => entityTable.addBinding(binding))
+
+		val cnnPartition = new Partition(new ConceptualKNNModel(dataGraph), List(guessTarget).asJava, entityTable, 0)
+		println("Starting concept computation")
+		cnnPartition.fullPartitioning(new AtomicBoolean(false))
+		println(s"Computation finished, ${cnnPartition.getNbConcepts} concepts computed")
 
 
 	}

prepare/src/main/guessNNprepare/mains/ExtractEntities.scala

@@ -1,6 +1,6 @@
 package guessNNprepare.mains
 
-import guessNNprepare.NamedEntity
+import guessNNprepare.{NamedEntity, Utils}
 import net.sourceforge.argparse4j.impl.Arguments
 import net.sourceforge.argparse4j.inf.{ArgumentParser, Namespace}
 import org.apache.jena.query.QueryExecutionFactory
@@ -24,14 +24,7 @@ object ExtractEntities extends MainCommand {
 		val jsonFilePath = ARGS.getString("json_file")
 
 		println("Loading knowledge graph...")
-		val kg: InfModel = ModelFactory.createInfModel(ReasonerRegistry.getTransitiveReasoner, ModelFactory.createDefaultModel)
+		val kg = Utils.loadMondialDataset().get
-		val mondialDataset: InputStream = Option(ClassLoader.getSystemResourceAsStream("mondial_2022_04_04.n3"))
-			.getOrElse({
-				System.err.println("Impossible to open dataset")
-				System.exit(1)
-				null
-			})
-		kg.read(mondialDataset, null, "TTL");
 		printf("Loaded %s triples\n", kg.listStatements().toList.size)
 		val guessableEntities = (List[NamedEntity]() ++
 			getMondialNamedEntities(kg, "Country") ++