Fix minor compilation errors

4 files changed, 106 insertions, 83 deletions

diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
index a807f75..f2d1a5d 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
@@ -106,12 +106,11 @@ object RSAComb extends App {
   /* Command-line options */
   val config = RSAConfig.parse(args.toList)
 
-  val ontology = RSAOntology(
+  val rsa = RSAOntology(
     config('ontology).get[File],
     config('data).get[List[File]],
     None
   )
-  val rsa = ontology.toRSA()
 
   if (config contains 'query) {
     val query =
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
index 4d0f13d..247b5d5 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
@@ -80,7 +80,7 @@ object RSAUtil {
     * construction of the dependency graph is computed regardless. The
     * input axioms are assumed to be normalized.
     */
-  private def dependencyGraph(
+  def dependencyGraph(
       axioms: List[OWLLogicalAxiom],
       datafiles: List[File]
   ): (Graph[Resource, DiEdge], Map[String, OWLAxiom]) = {
@@ -166,18 +166,23 @@ object RSAOntology {
 
   import uk.ac.ox.cs.rsacomb.implicits.JavaCollections._
 
+  /** Manager instance to interface with OWLAPI */
+  val manager = OWLManager.createOWLOntologyManager()
+  val factory = manager.getOWLDataFactory()
+
   /** Name of the RDFox data store used for CQ answering */
   private val DataStore = "answer_computation"
 
-  /** Simple fresh variable generator */
+  /** Simple fresh variable/class generator */
   private var counter = -1;
   def genFreshVariable(): Variable = {
     counter += 1
     Variable.create(f"I$counter%05d")
   }
-
-  /** Manager instance to interface with OWLAPI */
-  val manager = OWLManager.createOWLOntologyManager()
+  def getFreshOWLClass(): OWLClass = {
+    counter += 1
+    factory.getOWLClass(s"X$counter")
+  }
 
   def apply(
       axioms: List[OWLLogicalAxiom],
@@ -254,13 +259,16 @@ class RSAOntology(val axioms: List[OWLLogicalAxiom], val datafiles: File*) {
   /** Simplify conversion between OWLAPI and RDFox concepts */
   import implicits.RDFox._
   import uk.ac.ox.cs.rsacomb.implicits.RSAAxiom._
+
+  /** Simplify conversion between Java and Scala collections */
   import uk.ac.ox.cs.rsacomb.implicits.JavaCollections._
 
   /** Set of axioms removed during the approximation to RSA */
   private var removed: Seq[OWLAxiom] = Seq.empty
 
   /** Normalized Horn-ALCHOIQ ontology */
-  val ontology = RSAOntology.manager.createOntology(axioms.asJava)
+  val ontology =
+    RSAOntology.manager.createOntology((axioms: List[OWLAxiom]).asJava)
 
   /** OWLAPI internal reasoner instantiated over the approximated ontology */
   private val reasoner =
@@ -340,61 +348,61 @@ class RSAOntology(val axioms: List[OWLLogicalAxiom], val datafiles: File*) {
     * @param graph the graph used to compute the axioms to remove.
     * @param nodemap map from graph nodes to ontology axioms.
     */
-  def toRSA(): RSAOntology = Logger.timed(
-    {
-
-      /* Compute the dependency graph for the ontology */
-      val (graph, nodemap) = this.dependencyGraph()
-
-      /* Define node colors for the graph visit */
-      sealed trait NodeColor
-      case object Unvisited extends NodeColor
-      case object Visited extends NodeColor
-      case object ToDelete extends NodeColor
-
-      /* Keep track of node colors during graph visit */
-      var color = Map.from[Resource, NodeColor](
-        graph.nodes.toOuter.map(k => (k, Unvisited))
-      )
-
-      for {
-        component <- graph.componentTraverser().map(_ to Graph)
-        edge <- component
-          .outerEdgeTraverser(component.nodes.head)
-          .withKind(BreadthFirst)
-      } yield {
-        val source = edge._1
-        val target = edge._2
-        color(source) match {
-          case Unvisited | Visited => {
-            color(target) match {
-              case Unvisited =>
-                color(source) = Visited;
-                color(target) = Visited
-              case Visited =>
-                color(source) = ToDelete
-              case ToDelete =>
-                color(source) = Visited
-            }
-          }
-          case ToDelete =>
-        }
-      }
-
-      val toDelete = color.iterator.collect { case (resource: IRI, ToDelete) =>
-        nodemap(resource.getIRI)
-      }.toSeq
-
-      /* Remove axioms from approximated ontology */
-      ontology.removeAxioms(toDelete: _*)
-      this.removed = toDelete
-
-      /* Return RSA ontology */
-      RSAOntology(ontology, datafiles: _*)
-    },
-    "Horn-ALCHOIQ to RSA approximation:",
-    Logger.DEBUG
-  )
+  // def toRSA(): RSAOntology = Logger.timed(
+  //   {
+
+  //     /* Compute the dependency graph for the ontology */
+  //     val (graph, nodemap) = this.dependencyGraph()
+
+  //     /* Define node colors for the graph visit */
+  //     sealed trait NodeColor
+  //     case object Unvisited extends NodeColor
+  //     case object Visited extends NodeColor
+  //     case object ToDelete extends NodeColor
+
+  //     /* Keep track of node colors during graph visit */
+  //     var color = Map.from[Resource, NodeColor](
+  //       graph.nodes.toOuter.map(k => (k, Unvisited))
+  //     )
+
+  //     for {
+  //       component <- graph.componentTraverser().map(_ to Graph)
+  //       edge <- component
+  //         .outerEdgeTraverser(component.nodes.head)
+  //         .withKind(BreadthFirst)
+  //     } yield {
+  //       val source = edge._1
+  //       val target = edge._2
+  //       color(source) match {
+  //         case Unvisited | Visited => {
+  //           color(target) match {
+  //             case Unvisited =>
+  //               color(source) = Visited;
+  //               color(target) = Visited
+  //             case Visited =>
+  //               color(source) = ToDelete
+  //             case ToDelete =>
+  //               color(source) = Visited
+  //           }
+  //         }
+  //         case ToDelete =>
+  //       }
+  //     }
+
+  //     val toDelete = color.iterator.collect { case (resource: IRI, ToDelete) =>
+  //       nodemap(resource.getIRI)
+  //     }.toSeq
+
+  //     /* Remove axioms from approximated ontology */
+  //     ontology.removeAxioms(toDelete: _*)
+  //     this.removed = toDelete
+
+  //     /* Return RSA ontology */
+  //     RSAOntology(ontology, datafiles: _*)
+  //   },
+  //   "Horn-ALCHOIQ to RSA approximation:",
+  //   Logger.DEBUG
+  // )
   // val edges1 = Seq('A ~> 'B, 'B ~> 'C, 'C ~> 'D, 'D ~> 'H, 'H ~>
   // 'G, 'G ~> 'F, 'E ~> 'A, 'E ~> 'F, 'B ~> 'E, 'F ~> 'G, 'B ~> 'F,
   // 'C ~> 'G, 'D ~> 'C, 'H ~> 'D)
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/approximation/lowerbound.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/approximation/lowerbound.scala
index 3437bcd..8a86d19 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/approximation/lowerbound.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/approximation/lowerbound.scala
@@ -2,13 +2,18 @@ package uk.ac.ox.cs.rsacomb.approximation
 
 import java.io.File
 
-import org.semanticweb.owlapi.model._
+import org.semanticweb.owlapi.apibinding.OWLManager
+import org.semanticweb.owlapi.model.{IRI => _, _}
+
+import tech.oxfordsemantic.jrdfox.logic.expression.{Resource, IRI}
 
 import scala.collection.mutable.{Set, Map}
 import scalax.collection.Graph
 import scalax.collection.GraphPredef._, scalax.collection.GraphEdge._
 import scalax.collection.GraphTraversal._
 
+import uk.ac.ox.cs.rsacomb.RSAOntology
+import uk.ac.ox.cs.rsacomb.RSAUtil
 import uk.ac.ox.cs.rsacomb.converter.Normalizer
 
 /** Approximation algorithm that mantains soundness for CQ answering.
@@ -28,6 +33,16 @@ import uk.ac.ox.cs.rsacomb.converter.Normalizer
   */
 class LowerBound extends Approximation {
 
+  /** Simplify conversion between Java and Scala collections */
+  import uk.ac.ox.cs.rsacomb.implicits.JavaCollections._
+
+  /** Simplify conversion between OWLAPI and RDFox concepts */
+  import uk.ac.ox.cs.rsacomb.implicits.RDFox._
+
+  /** Manager instance to interface with OWLAPI */
+  val manager = OWLManager.createOWLOntologyManager()
+  val factory = manager.getOWLDataFactory()
+
   val normalizer = new Normalizer()
 
   /** Main entry point for the approximation algorithm */
@@ -36,14 +51,14 @@ class LowerBound extends Approximation {
       datafiles: List[File]
   ): List[OWLLogicalAxiom] = {
     /* Normalize axioms */
-    val axioms1 = axioms flatMap normalizer.normalize(_)
+    val axioms1 = ontology flatMap normalizer.normalize
     /* Delete any axiom outside of ALCHOIQ */
-    val axioms2 = axioms1 filterNot inHornLACHOIQ
+    val axioms2 = axioms1 filterNot inALCHOIQ
     /* Shift any axiom with disjunction on the rhs */
     val axioms3 = for {
       a1 <- axioms1
       a2 <- shift(a1)
-      a3 <- normalize(a2)
+      a3 <- normalizer.normalize(a2)
     } yield a3
     /* Approximate to RSA */
     toRSA(axioms3, datafiles)
@@ -113,8 +128,12 @@ class LowerBound extends Approximation {
         val sup = a.getSuperClass.getNNF
         sup match {
           case sup: OWLObjectUnionOf => {
-            val body = sub.asConjunctSet.map((atom) => (atom, freshOWLClass()))
-            val head = sup.asDisjunctSet.map((atom) => (atom, freshOWLClass()))
+            val body = sub.asConjunctSet.map((atom) =>
+              (atom, RSAOntology.getFreshOWLClass())
+            )
+            val head = sup.asDisjunctSet.map((atom) =>
+              (atom, RSAOntology.getFreshOWLClass())
+            )
 
             val r1 =
               factory.getOWLSubClassOfAxiom(
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/converter/Normalizer.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/Normalizer.scala
index 5329f26..4b298f4 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/converter/Normalizer.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/Normalizer.scala
@@ -4,6 +4,7 @@ import org.semanticweb.owlapi.apibinding.OWLManager
 import org.semanticweb.owlapi.model._
 
 import uk.ac.ox.cs.rsacomb.util.Logger
+import uk.ac.ox.cs.rsacomb.RSAOntology
 
 object Normalizer {
 
@@ -25,12 +26,6 @@ class Normalizer() {
   /** Simplify conversion between Java and Scala collections */
   import uk.ac.ox.cs.rsacomb.implicits.JavaCollections._
 
-  private var counter = -1
-  def freshOWLClass(): OWLClass = {
-    counter += 1
-    factory.getOWLClass(s"X$counter")
-  }
-
   /** Statistics */
   var discarded = 0
   var shifted = 0
@@ -58,7 +53,7 @@ class Normalizer() {
             *   C c D -> { C c X, X c D }
             */
           case _ if !sub.isOWLClass && !sup.isOWLClass => {
-            val cls = freshOWLClass()
+            val cls = RSAOntology.getFreshOWLClass()
             Seq(
               factory.getOWLSubClassOfAxiom(sub, cls),
               factory.getOWLSubClassOfAxiom(cls, sup)
@@ -79,7 +74,7 @@ class Normalizer() {
                   if (conj.isOWLClass)
                     (acc1 :+ conj, acc2)
                   else {
-                    val cls = freshOWLClass()
+                    val cls = RSAOntology.getFreshOWLClass()
                     (
                       acc1 :+ cls,
                       acc2 :+ factory.getOWLSubClassOfAxiom(conj, cls)
@@ -138,7 +133,7 @@ class Normalizer() {
             */
           case (sub: OWLObjectSomeValuesFrom, _)
               if !sub.getFiller.isOWLClass => {
-            val cls = freshOWLClass()
+            val cls = RSAOntology.getFreshOWLClass()
             Seq(
               factory.getOWLSubClassOfAxiom(sub.getFiller, cls),
               factory.getOWLSubClassOfAxiom(
@@ -153,7 +148,7 @@ class Normalizer() {
             */
           case (_, sup: OWLObjectSomeValuesFrom)
               if !sup.getFiller.isOWLClass => {
-            val cls = freshOWLClass()
+            val cls = RSAOntology.getFreshOWLClass()
             Seq(
               factory.getOWLSubClassOfAxiom(cls, sup.getFiller),
               factory.getOWLSubClassOfAxiom(
@@ -298,7 +293,7 @@ class Normalizer() {
             )
           case (_, sup: OWLObjectMaxCardinality)
               if sup.getCardinality == 1 && !sup.getFiller.isOWLClass => {
-            val cls = freshOWLClass()
+            val cls = RSAOntology.getFreshOWLClass()
             Seq(
               factory.getOWLSubClassOfAxiom(cls, sup.getFiller),
               factory.getOWLSubClassOfAxiom(
@@ -488,7 +483,7 @@ class Normalizer() {
         * C(a) -> { X(a), X c C }
         */
       case a: OWLClassAssertionAxiom if !a.getClassExpression.isOWLClass => {
-        val cls = freshOWLClass()
+        val cls = RSAOntology.getFreshOWLClass()
         Seq(
           factory.getOWLClassAssertionAxiom(cls, a.getIndividual),
           factory.getOWLSubClassOfAxiom(cls, a.getClassExpression)
@@ -532,8 +527,10 @@ class Normalizer() {
       sub: OWLClassExpression,
       sup: OWLObjectUnionOf
   ): Seq[OWLLogicalAxiom] = {
-    val body = sub.asConjunctSet.map((atom) => (atom, freshOWLClass()))
-    val head = sup.asDisjunctSet.map((atom) => (atom, freshOWLClass()))
+    val body =
+      sub.asConjunctSet.map((atom) => (atom, RSAOntology.getFreshOWLClass()))
+    val head =
+      sup.asDisjunctSet.map((atom) => (atom, RSAOntology.getFreshOWLClass()))
 
     /* Update statistics */
     shifted += 1