Add setup code to compute the RSA filtering program

Not all rules of the filtering program have been implemented, but the
code for the generation and reification of the rules seems to work.

6 files changed, 261 insertions, 48 deletions

diff --git a/src/main/scala/rsacomb/Main.scala b/src/main/scala/rsacomb/Main.scala
index 9cd6680..d2bc2a8 100644
--- a/src/main/scala/rsacomb/Main.scala
+++ b/src/main/scala/rsacomb/Main.scala
@@ -48,18 +48,20 @@ object RSAComb {
      */
 
     val ontology = RSA.loadOntology(ontoPath)
-    ontology.isRSA
+    if (ontology.isRSA) {
 
-    /* Build canonical model */
-    //val tboxCanon = rsa.canonicalModel()
+      /* Build canonical model */
+      //val tboxCanon = rsa.canonicalModel()
 
-    /* Load query */
-    //val query = ...
+      /* Load query */
+      val query = RSA.test_query
 
-    /* Compute the filtering program from the given query */
-    //val tboxFilter = rsa.filteringProgram(query)
+      /* Compute the filtering program from the given query */
+      val filter = ontology.getFilteringProgram(query)
 
-    /* ... */
+      /* ... */
+
+    }
 
     /* DEBUG ONLY */
     println("Ok!")
diff --git a/src/main/scala/rsacomb/RDFoxClassExprConverter.scala b/src/main/scala/rsacomb/RDFoxClassExprConverter.scala
index b9d3ea2..467b3f1 100644
--- a/src/main/scala/rsacomb/RDFoxClassExprConverter.scala
+++ b/src/main/scala/rsacomb/RDFoxClassExprConverter.scala
@@ -61,7 +61,8 @@ class RDFoxClassExprConverter(
 
   // OWLClass
   override def visit(expr: OWLClass): RDFoxRuleShards = {
-    val atom = List(Atom.rdf(term, IRI.RDF_TYPE, expr.getIRI()))
+    val iri: IRI = if (expr.isTopEntity()) IRI.THING else expr.getIRI()
+    val atom = List(Atom.rdf(term, IRI.RDF_TYPE, iri))
     RDFoxRuleShards(atom, List())
   }
 
@@ -97,6 +98,7 @@ class RDFoxClassExprConverter(
     // TODO: variables needs to be handled at visitor level. Hardcoding
     // the name of the varibles might lead to errors for complex cases.
     val y = Variable.create("y")
+    // Here we are assuming a role name
     val prop = expr.getProperty()
     // Computes the result of rule skolemization. Depending on the used
     // technique it might involve the introduction of additional atoms,
diff --git a/src/main/scala/rsacomb/RDFoxUtil.scala b/src/main/scala/rsacomb/RDFoxUtil.scala
index 4cefd83..9699fb4 100644
--- a/src/main/scala/rsacomb/RDFoxUtil.scala
+++ b/src/main/scala/rsacomb/RDFoxUtil.scala
@@ -15,6 +15,10 @@ object RDFoxUtil {
     IRI.create(iri.getIRIString())
   }
 
+  implicit def owlapi2rdfox(iri: String): IRI = {
+    IRI.create(iri)
+  }
+
   def openConnection(
       dataStore: String
   ): (ServerConnection, DataStoreConnection) = {
@@ -37,7 +41,7 @@ object RDFoxUtil {
     (server, data)
   }
 
-  def query(
+  def submitQuery(
       data: DataStoreConnection,
       prefixes: Prefixes,
       query: String
diff --git a/src/main/scala/rsacomb/RSA.scala b/src/main/scala/rsacomb/RSA.scala
index 79617c7..c0d4e51 100644
--- a/src/main/scala/rsacomb/RSA.scala
+++ b/src/main/scala/rsacomb/RSA.scala
@@ -8,6 +8,18 @@ import tech.oxfordsemantic.jrdfox.Prefixes
 import tech.oxfordsemantic.jrdfox.logic.IRI
 import org.semanticweb.owlapi.apibinding.OWLManager
 import org.semanticweb.owlapi.model.OWLOntology
+import rsacomb.RSAOntology
+
+// Debug only
+import tech.oxfordsemantic.jrdfox.logic.{
+  Formula,
+  Atom,
+  Variable,
+  Query,
+  QueryType,
+  Conjunction
+}
+import scala.collection.JavaConverters._
 
 object RSA extends RSAOntology {
 
@@ -18,6 +30,18 @@ object RSA extends RSAOntology {
   Prefixes.declarePrefix("rdfs:", "http://www.w3.org/2000/01/rdf-schema#")
   Prefixes.declarePrefix("owl:", "http://www.w3.org/2002/07/owl#")
 
+  val varX = Variable.create("X")
+  val varY = Variable.create("Y")
+  val varZ = Variable.create("Z")
+  val testAnswerVars = List[Variable](varX, varY, varZ).asJava;
+  val testFormula: Formula =
+    Conjunction.create(
+      Atom.rdf(varX, IRI.TOP_OBJECT_PROPERTY, varY),
+      Atom.rdf(varY, IRI.TOP_OBJECT_PROPERTY, varZ)
+    )
+  val test_query =
+    Query.create(QueryType.SELECT, false, testAnswerVars, testFormula)
+
   def internal(name: String): IRI =
     IRI.create(
       Prefixes.getPrefixIRIsByPrefixName.get("internal:").getIRI + name
diff --git a/src/main/scala/rsacomb/RSAAxiom.scala b/src/main/scala/rsacomb/RSAAxiom.scala
index 9e9a016..50dc37e 100644
--- a/src/main/scala/rsacomb/RSAAxiom.scala
+++ b/src/main/scala/rsacomb/RSAAxiom.scala
@@ -1,10 +1,23 @@
 package rsacomb
 
 /* Java imports */
-import org.semanticweb.owlapi.model.{OWLAxiom,OWLSubClassOfAxiom, OWLEquivalentClassesAxiom}
-import org.semanticweb.owlapi.model.{OWLObjectPropertyExpression,OWLClass,OWLClassExpression,OWLObjectSomeValuesFrom,OWLObjectMaxCardinality}
+import org.semanticweb.owlapi.model.{
+  OWLAxiom,
+  OWLSubClassOfAxiom,
+  OWLEquivalentClassesAxiom
+}
+import org.semanticweb.owlapi.model.{
+  OWLObjectPropertyExpression,
+  OWLClass,
+  OWLClassExpression,
+  OWLObjectSomeValuesFrom,
+  OWLObjectMaxCardinality
+}
 import org.semanticweb.owlapi.model.ClassExpressionType
-import org.semanticweb.owlapi.model.{OWLAxiomVisitorEx,OWLClassExpressionVisitorEx}
+import org.semanticweb.owlapi.model.{
+  OWLAxiomVisitorEx,
+  OWLClassExpressionVisitorEx
+}
 
 /* Wrapper trait for the implicit class `RSAAxiom`.
  */
@@ -16,10 +29,10 @@ trait RSAAxiom {
    */
   private sealed trait RSAAxiomType
   private object RSAAxiomType {
-    case object T3    extends RSAAxiomType // ∃R.A ⊑ B
+    case object T3 extends RSAAxiomType // ∃R.A ⊑ B
     case object T3top extends RSAAxiomType // ∃R.⊤ ⊑ B
-    case object T4    extends RSAAxiomType // A ⊑ ≤1R.B
-    case object T5    extends RSAAxiomType // A ⊑ ∃R.B
+    case object T4 extends RSAAxiomType // A ⊑ ≤1R.B
+    case object T5 extends RSAAxiomType // A ⊑ ∃R.B
   }
 
   /* Implements additional features on top of `OWLAxiom` from
@@ -32,20 +45,22 @@ trait RSAAxiom {
      * In order to reason about role unsafety in Horn-ALCHOIQ
      * ontologies we need to detect and filter axioms by their
      * "type".
-     * 
+     *
      * This is a simple implementation following the Visitor
      * pattern imposed by the OWLAPI.
      */
     private class RSAAxiomTypeDetector(t: RSAAxiomType)
-      extends OWLAxiomVisitorEx[Boolean]
-    {
-      override
-      def visit(axiom: OWLSubClassOfAxiom): Boolean = {
+        extends OWLAxiomVisitorEx[Boolean] {
+      override def visit(axiom: OWLSubClassOfAxiom): Boolean = {
         val sub = axiom.getSubClass().getClassExpressionType()
         val sup = axiom.getSuperClass().getClassExpressionType()
         t match {
           case RSAAxiomType.T3top => // ∃R.⊤ ⊑ B
-            axiom.isT5 && axiom.getSubClass().asInstanceOf[OWLObjectSomeValuesFrom].getFiller.isOWLThing
+            axiom.isT3 && axiom
+              .getSubClass()
+              .asInstanceOf[OWLObjectSomeValuesFrom]
+              .getFiller
+              .isOWLThing
           case RSAAxiomType.T3 => // ∃R.A ⊑ B
             sub == ClassExpressionType.OBJECT_SOME_VALUES_FROM && sup == ClassExpressionType.OWL_CLASS
           case RSAAxiomType.T4 => // A ⊑ ≤1R.B
@@ -55,13 +70,12 @@ trait RSAAxiom {
         }
       }
 
-      override
-      def visit(axiom: OWLEquivalentClassesAxiom): Boolean = {
+      override def visit(axiom: OWLEquivalentClassesAxiom): Boolean = {
         // TODO
         false
       }
 
-      def doDefault(axiom : OWLAxiom): Boolean = false
+      def doDefault(axiom: OWLAxiom): Boolean = false
     }
 
     private def isOfType(t: RSAAxiomType): Boolean = {
@@ -74,13 +88,13 @@ trait RSAAxiom {
     def isT3: Boolean = isOfType(RSAAxiomType.T3)
     def isT4: Boolean = isOfType(RSAAxiomType.T4)
     def isT5: Boolean = isOfType(RSAAxiomType.T5)
-    
+
     /* Extracting ObjectPropertyExpressions from axioms
      *
      * This extracts all ObjectPropertyExpressions from a given
      * axiom. While the implementation is generic we use it on axioms
      * of specific types (see above).
-     * 
+     *
      * NOTE: it is not possible to use the `objectPropertyInSignature`
      * method of `OWLAxiom` because it returns all "role names" involved
      * in the signature of an axiom. In particular we won't get the inverse
@@ -88,55 +102,61 @@ trait RSAAxiom {
      * itself instead).
      */
     private class RSAAxiomRoleExtractor()
-      extends OWLAxiomVisitorEx[List[OWLObjectPropertyExpression]]
-    {
+        extends OWLAxiomVisitorEx[List[OWLObjectPropertyExpression]] {
 
       private class RSAExprRoleExtractor()
-        extends OWLClassExpressionVisitorEx[List[OWLObjectPropertyExpression]]
-      {
-        override
-        def visit(expr: OWLObjectSomeValuesFrom): List[OWLObjectPropertyExpression] =
+          extends OWLClassExpressionVisitorEx[
+            List[OWLObjectPropertyExpression]
+          ] {
+        override def visit(
+            expr: OWLObjectSomeValuesFrom
+        ): List[OWLObjectPropertyExpression] =
           List(expr.getProperty)
 
-        override
-        def visit(expr: OWLObjectMaxCardinality): List[OWLObjectPropertyExpression] =
+        override def visit(
+            expr: OWLObjectMaxCardinality
+        ): List[OWLObjectPropertyExpression] =
           List(expr.getProperty)
 
         /* NOTE: this instance of `visit` for `OWLClass` shouldn't be necessary. However
          * if missing, the code throws a `NullPointerException`. It seems like, for some
-         * reason, `OWLClass` is not really a subinterface of `OWLClassExpression`, as 
+         * reason, `OWLClass` is not really a subinterface of `OWLClassExpression`, as
          * stated in the JavaDocs.
          */
-        override
-        def visit(expr: OWLClass): List[OWLObjectPropertyExpression] =
+        override def visit(expr: OWLClass): List[OWLObjectPropertyExpression] =
           List()
 
-        def doDefault(expr: OWLClassExpression): List[OWLObjectPropertyExpression] =
+        def doDefault(
+            expr: OWLClassExpression
+        ): List[OWLObjectPropertyExpression] =
           List()
       }
 
-      override
-      def visit(axiom: OWLSubClassOfAxiom): List[OWLObjectPropertyExpression] = {
+      override def visit(
+          axiom: OWLSubClassOfAxiom
+      ): List[OWLObjectPropertyExpression] = {
         val visitor = new RSAExprRoleExtractor()
         val sub = axiom.getSubClass.accept(visitor)
         val sup = axiom.getSuperClass.accept(visitor)
         sub ++ sup
       }
 
-      override
-      def visit(axiom: OWLEquivalentClassesAxiom): List[OWLObjectPropertyExpression] = {
+      override def visit(
+          axiom: OWLEquivalentClassesAxiom
+      ): List[OWLObjectPropertyExpression] = {
         // TODO
         List()
       }
 
-      def doDefault(axiom : OWLAxiom): List[OWLObjectPropertyExpression] = List()
+      def doDefault(axiom: OWLAxiom): List[OWLObjectPropertyExpression] = List()
     }
 
     /* Exposed methods */
-    def objectPropertyExpressionsInSignature: List[OWLObjectPropertyExpression] = {
+    def objectPropertyExpressionsInSignature
+        : List[OWLObjectPropertyExpression] = {
       val visitor = new RSAAxiomRoleExtractor()
       axiom.accept(visitor)
     }
   }
 
-} // trait RSAAxiom
\ No newline at end of file
+} // trait RSAAxiom
diff --git a/src/main/scala/rsacomb/RSAOntology.scala b/src/main/scala/rsacomb/RSAOntology.scala
index 3d9210e..9d52612 100644
--- a/src/main/scala/rsacomb/RSAOntology.scala
+++ b/src/main/scala/rsacomb/RSAOntology.scala
@@ -19,6 +19,7 @@ import scalax.collection.GraphEdge.UnDiEdge
 
 /* Debug only */
 import org.semanticweb.owlapi.dlsyntax.renderer.DLSyntaxObjectRenderer
+import tech.oxfordsemantic.jrdfox.logic._
 
 /* Wrapper trait for the implicit class `RSAOntology`.
  */
@@ -163,8 +164,9 @@ trait RSAOntology {
       } yield role1
 
       /* TODO: We should be able to avoid this last conversion to List.
-       * Maybe we should just move everything to Sets instead of Lists, since
-       * they have a more straightforward conversion from Java collections.
+       * Maybe we should just move everything to Sets instead of Lists,
+       * since they have a more straightforward conversion from Java
+       * collections.
        */
       (unsafe1 ++ unsafe2).toList
     }
@@ -184,6 +186,165 @@ trait RSAOntology {
       Graph(edges: _*)
     }
 
+    def getFilteringProgram(query: Query): List[Rule] = {
+
+      // Import implicit conversion to RDFox IRI
+      import RDFoxUtil._
+
+      sealed trait Reified;
+      case class ReifiedHead(bind: BindAtom, atoms: List[Atom]) extends Reified
+      case class ReifiedBody(atoms: List[Atom]) extends Reified
+      case class Unaltered(formula: BodyFormula) extends Reified
+
+      def getBindAtom(atom: Atom): BindAtom = {
+        // TODO: We need to implement another way to introduce fresh
+        // variables.
+        val varA = Variable.create("A")
+        val args = atom
+          .getArguments()
+          .asScala
+          .toSeq
+        //.prepended(atom.getTupleTableName.getIRI)
+        BindAtom.create(
+          BuiltinFunctionCall
+            .create("SKOLEM", args: _*),
+          varA
+        )
+      }
+
+      def reifyAtom(atom: Atom, variable: Variable): List[Atom] = {
+        def iri(i: Int) = atom.getTupleTableName().getIRI() ++ s"_$i"
+        atom
+          .getArguments()
+          .asScala
+          .zipWithIndex
+          .map { case (t, i) => Atom.rdf(variable, iri(i), t) }
+          .toList
+      }
+
+      // Is this the best way to determine if an atom is an RDF triple?
+      // Note that we can't use `getNumberOfArguments()` because is not
+      // "consistent":
+      // - for an atom created with `rdf(<term1>, <term2>, <term3>)`,
+      // `getNumberOfArguments` returns 3
+      // - for an atom created with `Atom.create(<tupletablename>, <term1>,
+      // <term2>, <term3>)`, `getNumberOfArguments()` returns 3
+      //
+      // This is probably because `Atom.rdf(...) is implemented as:
+      // ```scala
+      //  def rdf(term1: Term, term2: Term, term3: Term): Atom =
+      //    Atom.create(TupleTableName.create("internal:triple"), term1, term2, term3)
+      // ```
+      def isRdfTriple(atom: Atom): Boolean =
+        atom.getTupleTableName.getIRI.equals("internal:triple")
+
+      def reify(
+          formula: BodyFormula,
+          head: Boolean
+      ): Reified = {
+        def default[A <: BodyFormula](x: A) = Unaltered(x)
+        formula match {
+          case a: Atom => {
+            if (!isRdfTriple(a)) {
+              if (head) {
+                val b = getBindAtom(a)
+                ReifiedHead(b, reifyAtom(a, b.getBoundVariable))
+              } else {
+                val varA = Variable.create("A")
+                ReifiedBody(reifyAtom(a, varA))
+              }
+            } else {
+              default(a)
+            }
+          }
+          case a => default(a)
+        }
+      }
+
+      def skolemizeRule(rule: Rule): Rule = {
+        // Rule body
+        val body =
+          rule.getBody.asScala.map(reify(_, false)).flatMap {
+            case ReifiedHead(_, _) => List(); /* handle impossible case */
+            case ReifiedBody(x)    => x;
+            case Unaltered(x)      => List(x)
+          }
+        // Rule head
+        val reified = rule.getHead.asScala.map(reify(_, true))
+        val skols = reified.flatMap {
+          case ReifiedHead(x, _) => Some(x);
+          case ReifiedBody(_)    => None; /* handle impossible case */
+          case Unaltered(_)      => None
+        }
+        val head = reified.flatMap {
+          case ReifiedHead(_, x) => x;
+          case ReifiedBody(_)    => List(); /* handle impossible case */
+          case Unaltered(x) =>
+            List(x.asInstanceOf[Atom]) /* Can we do better that a cast? */
+        }
+        Rule.create(head.asJava, (skols ++ body).asJava)
+      }
+
+      def formulaToRuleBody(body: Formula): List[BodyFormula] = {
+        body match {
+          case a: BodyFormula => List(a);
+          case a: Conjunction =>
+            a.getConjuncts().asScala.toList.flatMap(formulaToRuleBody(_));
+          case _ => List() /* We don't handle this for now */
+        }
+      }
+
+      val body = formulaToRuleBody(query.getQueryFormula)
+      val vars: List[Term] = query.getAnswerVariables.asScala.toList
+      def id(t1: Term, t2: Term) =
+        Atom.create(
+          TupleTableName.create("http://127.0.0.1/ID"),
+          vars.appendedAll(List(t1, t2)).asJava
+        )
+      val qm = Atom.create(TupleTableName.create("QM"), vars.asJava)
+
+      /* Filtering program */
+      val rule1 = Rule.create(qm, body.asJava)
+      val rule3a =
+        for ((v, i) <- vars.zipWithIndex)
+          yield Rule.create(
+            id(
+              IRI.create(s"http://127.0.0.1/$i"),
+              IRI.create(s"http://127.0.0.1/$i")
+            ),
+            List(
+              qm,
+              Negation.create(
+                Atom.rdf(v, IRI.RDF_TYPE, IRI.create("http://127.0.0.1/NI"))
+              )
+            ).asJava
+          )
+      val rule3b = Rule.create(
+        id(Variable.create("V"), Variable.create("U")),
+        id(Variable.create("U"), Variable.create("V"))
+      )
+      val rule3c = Rule.create(
+        id(Variable.create("U"), Variable.create("W")),
+        List[BodyFormula](
+          id(Variable.create("U"), Variable.create("V")),
+          id(Variable.create("V"), Variable.create("W"))
+        ).asJava
+      )
+
+      var rules: List[Rule] =
+        List.empty
+          .prepended(rule3c)
+          .prepended(rule3b)
+          .prependedAll(rule3a)
+          .prepended(rule1)
+
+      // DEBUG
+      println("FILTERING PROGRAM:")
+      rules.map(skolemizeRule(_)).foreach(println(_))
+
+      List()
+    }
+
   } // implicit class RSAOntology
 
 } // trait RSAOntology