Multiple fixes

4 files changed, 80 insertions, 54 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 74084af..a807f75 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
@@ -108,10 +108,10 @@ object RSAComb extends App {
 
   val ontology = RSAOntology(
     config('ontology).get[File],
-    config('data).get[List[File]]: _*
+    config('data).get[List[File]],
+    None
   )
   val rsa = ontology.toRSA()
-  ontology.statistics()
 
   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 e048c28..4d0f13d 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
@@ -50,13 +50,13 @@ import scala.collection.JavaConverters._
 import scala.collection.mutable.{Set, Map}
 import scalax.collection.Graph
 import scalax.collection.GraphPredef._, scalax.collection.GraphEdge._
-import scalax.collection.GraphTraversal._
 
 /* Debug only */
 import org.semanticweb.owlapi.dlsyntax.renderer.DLSyntaxObjectRenderer
 import tech.oxfordsemantic.jrdfox.logic._
 import org.semanticweb.owlapi.model.OWLObjectInverseOf
 
+import uk.ac.ox.cs.rsacomb.approximation.Approximation
 import uk.ac.ox.cs.rsacomb.converter._
 import uk.ac.ox.cs.rsacomb.filtering.{FilteringProgram, FilterType}
 import uk.ac.ox.cs.rsacomb.suffix._
@@ -66,10 +66,10 @@ import uk.ac.ox.cs.rsacomb.util.Logger
 
 object RSAUtil {
 
-  implicit def axiomsToOntology(axioms: Seq[OWLAxiom]) = {
-    val manager = OWLManager.createOWLOntologyManager()
-    manager.createOntology(axioms.asJava)
-  }
+  // implicit def axiomsToOntology(axioms: Seq[OWLAxiom]) = {
+  //   val manager = OWLManager.createOWLOntologyManager()
+  //   manager.createOntology(axioms.asJava)
+  // }
 
   /** Compute the RSA dependency graph for a set of axioms
     *
@@ -81,10 +81,10 @@ object RSAUtil {
     * input axioms are assumed to be normalized.
     */
   private def dependencyGraph(
-      axioms: Seq[OWLAxiom],
-      datafiles: Seq[File]
+      axioms: List[OWLLogicalAxiom],
+      datafiles: List[File]
   ): (Graph[Resource, DiEdge], Map[String, OWLAxiom]) = {
-    val unsafe = this.unsafeRoles
+    val unsafe = RSAOntology(axioms, datafiles).unsafeRoles
     var nodemap = Map.empty[String, OWLAxiom]
 
     object RSAConverter extends RDFoxConverter {
@@ -164,6 +164,8 @@ object RSAUtil {
 
 object RSAOntology {
 
+  import uk.ac.ox.cs.rsacomb.implicits.JavaCollections._
+
   /** Name of the RDFox data store used for CQ answering */
   private val DataStore = "answer_computation"
 
@@ -178,9 +180,14 @@ object RSAOntology {
   val manager = OWLManager.createOWLOntologyManager()
 
   def apply(
+      axioms: List[OWLLogicalAxiom],
+      datafiles: List[File]
+  ): RSAOntology = new RSAOntology(axioms, datafiles: _*)
+
+  def apply(
       ontofile: File,
-      datafiles: Seq[File],
-      approx: Option[Approximation] = None
+      datafiles: List[File],
+      approx: Option[Approximation]
   ): RSAOntology = {
     val ontology = manager.loadOntologyFromOntologyDocument(ontofile)
     RSAOntology(ontology, datafiles, approx)
@@ -188,14 +195,14 @@ object RSAOntology {
 
   def apply(
       ontology: OWLOntology,
-      datafiles: Seq[File],
-      approx: Option[Approximation] = None
+      datafiles: List[File],
+      approx: Option[Approximation]
   ): RSAOntology = {
     val normalizer = new Normalizer()
 
     /** TBox axioms */
     var tbox: List[OWLLogicalAxiom] =
-      original
+      ontology
         .tboxAxioms(Imports.INCLUDED)
         .collect(Collectors.toList())
         .collect { case a: OWLLogicalAxiom => a }
@@ -203,7 +210,7 @@ object RSAOntology {
 
     /** RBox axioms */
     var rbox: List[OWLLogicalAxiom] =
-      original
+      ontology
         .rboxAxioms(Imports.INCLUDED)
         .collect(Collectors.toList())
         .collect { case a: OWLLogicalAxiom => a }
@@ -217,7 +224,7 @@ object RSAOntology {
       * large data files via OWLAPI.
       */
     var abox: List[OWLLogicalAxiom] =
-      original
+      ontology
         .aboxAxioms(Imports.INCLUDED)
         .collect(Collectors.toList())
         .collect { case a: OWLLogicalAxiom => a }
@@ -231,9 +238,10 @@ object RSAOntology {
         case Some(a) => a.approximate(axioms, datafiles)
         case None    => axioms
       },
-      datafiles
+      datafiles: _*
     )
   }
+
 }
 
 /** Wrapper class for an ontology in RSA
@@ -241,7 +249,7 @@ object RSAOntology {
   * @param ontology the input OWL2 ontology.
   * @param datafiles additinal data (treated as part of the ABox)
   */
-class RSAOntology(val axioms: Seq[OWLAxiom], val datafiles: File*) {
+class RSAOntology(val axioms: List[OWLLogicalAxiom], val datafiles: File*) {
 
   /** Simplify conversion between OWLAPI and RDFox concepts */
   import implicits.RDFox._
@@ -697,28 +705,28 @@ class RSAOntology(val axioms: Seq[OWLAxiom], val datafiles: File*) {
     this.self(axiom) | this.cycle(axiom)
 
   /** Log normalization/approximation statistics */
-  def statistics(level: Logger.Level = Logger.DEBUG): Unit = {
-    Logger.print(
-      s"Logical axioms in original input ontology: ${original.getLogicalAxiomCount(true)}",
-      level
-    )
-    Logger.print(
-      s"Logical axioms discarded in Horn-ALCHOIQ approximation: ${normalizer.discarded}",
-      level
-    )
-    Logger.print(
-      s"Logical axioms shifted in Horn-ALCHOIQ approximation: ${normalizer.shifted}",
-      level
-    )
-    Logger.print(
-      s"Logical axioms in Horn-ALCHOIQ ontology: ${ontology
-        .getLogicalAxiomCount(true)} (${axioms.length}/${axioms.length}/${axioms.length})",
-      level
-    )
-    Logger.print(
-      s"Logical axioms discarded in RSA approximation: ${removed.length}",
-      level
-    )
-  }
+  // def statistics(level: Logger.Level = Logger.DEBUG): Unit = {
+  //   Logger.print(
+  //     s"Logical axioms in original input ontology: ${original.getLogicalAxiomCount(true)}",
+  //     level
+  //   )
+  //   Logger.print(
+  //     s"Logical axioms discarded in Horn-ALCHOIQ approximation: ${normalizer.discarded}",
+  //     level
+  //   )
+  //   Logger.print(
+  //     s"Logical axioms shifted in Horn-ALCHOIQ approximation: ${normalizer.shifted}",
+  //     level
+  //   )
+  //   Logger.print(
+  //     s"Logical axioms in Horn-ALCHOIQ ontology: ${ontology
+  //       .getLogicalAxiomCount(true)} (${axioms.length}/${axioms.length}/${axioms.length})",
+  //     level
+  //   )
+  //   Logger.print(
+  //     s"Logical axioms discarded in RSA approximation: ${removed.length}",
+  //     level
+  //   )
+  // }
 
 } // class RSAOntology
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/approximation/approximation.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/approximation/approximation.scala
index 073d0d9..1b49413 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/approximation/approximation.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/approximation/approximation.scala
@@ -1,7 +1,7 @@
 package uk.ac.ox.cs.rsacomb.approximation
 
 import java.io.File
-import org.semanticweb.owlapi.model.OWLAxiom
+import org.semanticweb.owlapi.model.OWLLogicalAxiom
 
 /** Ontology approximation technique. */
 trait Approximation {
@@ -11,6 +11,9 @@ trait Approximation {
     * @param ontology input ontology
     * @return a new approximated ontology
     */
-  def approximate(ontology: Seq[OWLAxiom], datafiles: Seq[File]): Seq[OWLAxiom]
+  def approximate(
+      ontology: List[OWLLogicalAxiom],
+      datafiles: List[File]
+  ): List[OWLLogicalAxiom]
 
 }
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 8036250..3437bcd 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
@@ -1,5 +1,16 @@
 package uk.ac.ox.cs.rsacomb.approximation
 
+import java.io.File
+
+import org.semanticweb.owlapi.model._
+
+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.converter.Normalizer
+
 /** Approximation algorithm that mantains soundness for CQ answering.
   *
   * The input OWL 2 ontology is assumed to be normalized and the output
@@ -21,11 +32,11 @@ class LowerBound extends Approximation {
 
   /** Main entry point for the approximation algorithm */
   def approximate(
-      ontology: Seq[OWLAxiom],
-      datafiles: Seq[File]
-  ): Seq[OWLAxiom] = {
+      ontology: List[OWLLogicalAxiom],
+      datafiles: List[File]
+  ): List[OWLLogicalAxiom] = {
     /* Normalize axioms */
-    val axioms1 = axioms flatMap normalizer.normalize
+    val axioms1 = axioms flatMap normalizer.normalize(_)
     /* Delete any axiom outside of ALCHOIQ */
     val axioms2 = axioms1 filterNot inHornLACHOIQ
     /* Shift any axiom with disjunction on the rhs */
@@ -95,7 +106,7 @@ class LowerBound extends Approximation {
     *   where nA, nB1, nB2, nB3 are fresh predicates "corresponding" to
     *   the negation of A, B1, B2, B3 respectively.
     */
-  def shift(axiom: OWLLogicalAxiom): Seq[OWLLogicalAxiom] =
+  def shift(axiom: OWLLogicalAxiom): List[OWLLogicalAxiom] =
     axiom match {
       case a: OWLSubClassOfAxiom => {
         val sub = a.getSubClass.getNNF
@@ -135,12 +146,12 @@ class LowerBound extends Approximation {
                 na
               )
 
-            Seq(r1) ++ r2s ++ r3s
+            List(r1) ++ r2s ++ r3s
           }
-          case _ => Seq(axiom)
+          case _ => List(axiom)
         }
       }
-      case _ => Seq(axiom)
+      case _ => List(axiom)
     }
 
   /** Approximate a Horn-ALCHOIQ ontology to RSA
@@ -151,7 +162,10 @@ class LowerBound extends Approximation {
     * @param axioms the set of axioms to approximate.
     * @return the approximated set of axioms.
     */
-  def toRSA(axioms: Seq[OWLAxiom], datafiles: Seq[File]): Seq[OWLAxiom] = {
+  def toRSA(
+      axioms: List[OWLLogicalAxiom],
+      datafiles: List[File]
+  ): List[OWLLogicalAxiom] = {
     /* Compute the dependency graph for the ontology */
     val (graph, nodemap) = RSAUtil.dependencyGraph(axioms, datafiles)
 
@@ -192,11 +206,12 @@ class LowerBound extends Approximation {
 
     val toDelete = color.iterator.collect { case (resource: IRI, ToDelete) =>
       nodemap(resource.getIRI)
-    }.toSeq
+    }.toList
 
     /* Remove axioms from approximated ontology */
     axioms diff toDelete
   }
+
   // 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)