Update code to RDFox v4.0

11 files changed, 247 insertions, 172 deletions

diff --git a/src/main/scala/rsacomb/CanonicalModel.scala b/src/main/scala/rsacomb/CanonicalModel.scala
index cc89a85..fcc404a 100644
--- a/src/main/scala/rsacomb/CanonicalModel.scala
+++ b/src/main/scala/rsacomb/CanonicalModel.scala
@@ -9,14 +9,14 @@ import org.semanticweb.owlapi.model.{
   OWLObjectPropertyExpression,
   OWLObjectSomeValuesFrom
 }
-import tech.oxfordsemantic.jrdfox.logic.{
-  IRI,
+import tech.oxfordsemantic.jrdfox.logic.Datatype
+import tech.oxfordsemantic.jrdfox.logic.expression.{IRI, Term, Variable}
+import tech.oxfordsemantic.jrdfox.logic.datalog.{
   BodyFormula,
-  Atom,
-  Rule,
-  Term,
-  Variable
+  TupleTableAtom,
+  Rule
 }
+
 import scala.collection.JavaConverters._
 import rsacomb.RSA._
 
@@ -36,28 +36,35 @@ object ProgramGenerator {
       val varY = Variable.create("Y")
       List(
         Rule.create(
-          Atom.rdf(varX, IRI.create(pred), varY),
-          Atom.rdf(varX, IRI.create(pred ++ RSASuffix.Forward.getSuffix), varY)
+          TupleTableAtom.rdf(varX, IRI.create(pred), varY),
+          TupleTableAtom
+            .rdf(varX, IRI.create(pred ++ RSASuffix.Forward.getSuffix), varY)
         ),
         Rule.create(
-          Atom.rdf(varX, IRI.create(pred), varY),
-          Atom.rdf(varX, IRI.create(pred ++ RSASuffix.Backward.getSuffix), varY)
+          TupleTableAtom.rdf(varX, IRI.create(pred), varY),
+          TupleTableAtom
+            .rdf(varX, IRI.create(pred ++ RSASuffix.Backward.getSuffix), varY)
         ),
         Rule.create(
-          Atom.rdf(
+          TupleTableAtom.rdf(
             varY,
             IRI.create(pred ++ RSASuffix.Backward.getSuffix ++ "_inv"),
             varX
           ),
-          Atom.rdf(varX, IRI.create(pred ++ RSASuffix.Forward.getSuffix), varY)
+          TupleTableAtom
+            .rdf(varX, IRI.create(pred ++ RSASuffix.Forward.getSuffix), varY)
         ),
         Rule.create(
-          Atom.rdf(
+          TupleTableAtom.rdf(
             varY,
             IRI.create(pred ++ RSASuffix.Forward.getSuffix ++ "_inv"),
             varX
           ),
-          Atom.rdf(varX, IRI.create(pred ++ RSASuffix.Backward.getSuffix), varY)
+          TupleTableAtom.rdf(
+            varX,
+            IRI.create(pred ++ RSASuffix.Backward.getSuffix),
+            varY
+          )
         )
       )
     }
@@ -67,8 +74,8 @@ object ProgramGenerator {
       .toList
   }
 
-  def NIs(individuals: List[IRI]): List[Atom] =
-    individuals.map(Atom.rdf(_, IRI.RDF_TYPE, RSA.internal("NI")))
+  def NIs(individuals: List[IRI]): List[TupleTableAtom] =
+    individuals.map(TupleTableAtom.rdf(_, IRI.RDF_TYPE, RSA.internal("NI")))
 
 }
 
@@ -91,18 +98,18 @@ class ProgramGenerator(
     val v0 = IRI.create("v0_" ++ axiom.hashCode.toString)
     val varX = Variable.create("X")
     // Predicates
-    val atomA: Atom = {
+    val atomA: TupleTableAtom = {
       val cls = axiom.getSubClass.asInstanceOf[OWLClass].getIRI
-      Atom.rdf(varX, IRI.RDF_TYPE, cls)
+      TupleTableAtom.rdf(varX, IRI.RDF_TYPE, cls)
     }
-    def notIn(t: Term): Atom = {
-      Atom.rdf(
+    def notIn(t: Term): TupleTableAtom = {
+      TupleTableAtom.rdf(
         t,
         RSA.internal("notIn"),
         RSA.internal(unfold.hashCode.toString)
       )
     }
-    val roleRf: Atom = {
+    val roleRf: TupleTableAtom = {
       val visitor =
         new RDFoxPropertyExprConverter(varX, v0, RSASuffix.Forward)
       axiom.getSuperClass
@@ -111,13 +118,13 @@ class ProgramGenerator(
         .accept(visitor)
         .head
     }
-    val atomB: Atom = {
+    val atomB: TupleTableAtom = {
       val cls = axiom.getSuperClass
         .asInstanceOf[OWLObjectSomeValuesFrom]
         .getFiller
         .asInstanceOf[OWLClass]
         .getIRI
-      Atom.rdf(v0, IRI.RDF_TYPE, cls)
+      TupleTableAtom.rdf(v0, IRI.RDF_TYPE, cls)
     }
     // TODO: To be consistent with the specifics of the visitor we are
     // returning facts as `Rule`s with true body. While this is correct
@@ -142,21 +149,21 @@ class ProgramGenerator(
       val v1 = IRI.create("v1_" ++ axiom.hashCode.toString)
       val v2 = IRI.create("v2_" ++ axiom.hashCode.toString)
       // Predicates
-      def atomA(t: Term): Atom = {
+      def atomA(t: Term): TupleTableAtom = {
         val cls = axiom.getSubClass.asInstanceOf[OWLClass].getIRI
-        Atom.rdf(t, IRI.RDF_TYPE, cls)
+        TupleTableAtom.rdf(t, IRI.RDF_TYPE, cls)
       }
-      def roleRf(t1: Term, t2: Term): Atom = {
+      def roleRf(t1: Term, t2: Term): TupleTableAtom = {
         val visitor = new RDFoxPropertyExprConverter(t1, t2, RSASuffix.Forward)
         roleR.accept(visitor).head
       }
-      def atomB(t: Term): Atom = {
+      def atomB(t: Term): TupleTableAtom = {
         val cls = axiom.getSuperClass
           .asInstanceOf[OWLObjectSomeValuesFrom]
           .getFiller
           .asInstanceOf[OWLClass]
           .getIRI
-        Atom.rdf(t, IRI.RDF_TYPE, cls)
+        TupleTableAtom.rdf(t, IRI.RDF_TYPE, cls)
       }
       //Rules
       List(
@@ -179,22 +186,22 @@ class ProgramGenerator(
     // Fresh Variables
     val v1 = IRI.create("v1_" ++ axiom.hashCode.toString)
     // Predicates
-    def atomA(t: Term): Atom = {
+    def atomA(t: Term): TupleTableAtom = {
       val cls = axiom.getSubClass.asInstanceOf[OWLClass].getIRI
-      Atom.rdf(t, IRI.RDF_TYPE, cls)
+      TupleTableAtom.rdf(t, IRI.RDF_TYPE, cls)
     }
-    def roleRf(t: Term): Atom = {
+    def roleRf(t: Term): TupleTableAtom = {
       val visitor =
         new RDFoxPropertyExprConverter(t, v1, RSASuffix.Forward)
       roleR.accept(visitor).head
     }
-    val atomB: Atom = {
+    val atomB: TupleTableAtom = {
       val cls = axiom.getSuperClass
         .asInstanceOf[OWLObjectSomeValuesFrom]
         .getFiller
         .asInstanceOf[OWLClass]
         .getIRI
-      Atom.rdf(v1, IRI.RDF_TYPE, cls)
+      TupleTableAtom.rdf(v1, IRI.RDF_TYPE, cls)
     }
     cycle.flatMap { x =>
       List(
diff --git a/src/main/scala/rsacomb/FilteringProgram.scala b/src/main/scala/rsacomb/FilteringProgram.scala
index 9c19b7f..dc5e95e 100644
--- a/src/main/scala/rsacomb/FilteringProgram.scala
+++ b/src/main/scala/rsacomb/FilteringProgram.scala
@@ -1,93 +1,130 @@
 package rsacomb
 
-import tech.oxfordsemantic.jrdfox.logic._
+import tech.oxfordsemantic.jrdfox.logic.Datatype
+import tech.oxfordsemantic.jrdfox.logic.expression.{
+  Term,
+  IRI,
+  Variable,
+  Literal,
+  FunctionCall
+}
+import tech.oxfordsemantic.jrdfox.logic.datalog.{
+  Rule,
+  TupleTableAtom,
+  BindAtom,
+  TupleTableName,
+  BodyFormula,
+  Negation
+}
+import tech.oxfordsemantic.jrdfox.logic.sparql.statement.{SelectQuery}
+import tech.oxfordsemantic.jrdfox.logic.sparql.pattern.{
+  GroupGraphPattern,
+  ConjunctionPattern,
+  TriplePattern,
+  QueryPattern
+}
+
 import scala.collection.JavaConverters._
 
-class FilteringProgram(query: Query, constants: List[Term]) extends RDFTriple {
+class FilteringProgram(query: SelectQuery, constants: List[Term])
+    extends RDFTriple {
 
   /* Makes mplicit conversion OWLAPI IRI <-> RDFox IRI available */
   import RDFoxUtil._
 
-  val answer: List[Term] = query.getAnswerVariables.asScala.toList
+  val answer: List[Term] = query.getSelection.asScala.map(_.getVariable).toList
   val bounded: List[Term] = this.getBoundedVariables
 
-  val facts: List[Atom] = constants.map(named)
+  val facts: List[TupleTableAtom] = constants.map(named)
   val rules: List[Rule] = this.generateFilteringProgram().map(reifyRule)
 
-  private def named(t: Term): Atom =
-    Atom.rdf(t, IRI.RDF_TYPE, RSA.internal("NAMED"))
+  private def named(t: Term): TupleTableAtom =
+    TupleTableAtom.rdf(
+      t,
+      IRI.RDF_TYPE,
+      RSA.internal("NAMED")
+    )
 
   private def getBoundedVariables: List[Term] = {
-    def extract(f: Formula): Set[Term] = {
-      f match {
-        case b: BodyFormula =>
-          b.getArguments()
-            .asScala
-            .filter(_.isInstanceOf[Variable])
-            .filterNot(answer.contains(_))
-            .toSet
-        case c: Conjunction =>
-          c.getConjuncts().asScala.flatMap(extract).toSet
-        case d: Disjunction =>
-          d.getDisjuncts().asScala.flatMap(extract).toSet
-        /* Ignoring Minus, Optional, Query, Values cases for now */
+    def extract(body: GroupGraphPattern): Set[Term] = {
+      body match {
+        case b: ConjunctionPattern => {
+          b.getConjuncts.asScala.toSet.flatMap { conj: QueryPattern =>
+            conj match {
+              case c: TriplePattern =>
+                Set(c.getSubject, c.getPredicate, c.getObject).filter(
+                  _.isInstanceOf[Variable]
+                )
+              case _ => Set()
+            }
+          }
+        }
         case _ => Set()
       }
     }
-    extract(query.getQueryFormula()).toList
+    extract(query.getQueryBody.getWherePattern).toList
   }
 
   /* NOTE: we are restricting to queries that contain conjunctions of
    * atoms for the time being. This might need to be reviewed in the
    * future.
    */
-  private def queryToBody(body: Formula): List[Atom] =
+  private def queryToBody(body: GroupGraphPattern): List[TupleTableAtom] =
     body match {
-      case a: Atom => List(a);
-      case a: Conjunction =>
-        a.getConjuncts.asScala.toList.flatMap(queryToBody);
+      case b: ConjunctionPattern => {
+        val conjuncts = b.getConjuncts.asScala.toList
+        conjuncts flatMap { conj =>
+          conj match {
+            case c: TriplePattern =>
+              List(
+                TupleTableAtom.rdf(c.getSubject, c.getPredicate, c.getObject)
+              )
+            case _ => List()
+          }
+        }
+      }
       case _ => List()
     }
 
   private def generateFilteringProgram(): List[Rule] = {
     // Query formula as a rule body
-    val body = queryToBody(query.getQueryFormula)
+    val body = queryToBody(query.getQueryBody.getWherePattern)
     // Auxiliar predicates/helpers
-    def not(atom: Atom): BodyFormula = Negation.create(atom)
+    def not(atom: TupleTableAtom): BodyFormula = Negation.create(atom)
     val predQM =
-      Atom.create(
+      TupleTableAtom.create(
         TupleTableName.create(RSA.internal("QM").getIRI),
         (answer ++ bounded): _*
       )
     def predID(t1: Term, t2: Term) =
-      Atom.create(
+      TupleTableAtom.create(
         TupleTableName.create(RSA.internal("ID").getIRI),
         (answer ++ bounded).appended(t1).appended(t2): _*
       )
-    def predNI(t1: Term): Atom =
-      Atom.rdf(t1, IRI.RDF_TYPE, RSA.internal("NI"))
+    def predNI(t1: Term): TupleTableAtom =
+      TupleTableAtom.rdf(t1, IRI.RDF_TYPE, RSA.internal("NI"))
     def predTQ(sx: String, t1: Term, t2: Term) =
-      Atom.create(
+      TupleTableAtom.create(
         TupleTableName.create(RSA.internal(s"TQ_$sx").getIRI),
         (answer ++ bounded).appended(t1).appended(t2): _*
       )
     def predAQ(sx: String, t1: Term, t2: Term) =
-      Atom.create(
+      TupleTableAtom.create(
         TupleTableName.create(RSA.internal(s"AQ_$sx").getIRI),
         (answer ++ bounded).appended(t1).appended(t2): _*
       )
     val predFK =
-      Atom.create(
+      TupleTableAtom.create(
         TupleTableName.create(RSA.internal("FK").getIRI),
         (answer ++ bounded): _*
       )
     val predSP =
-      Atom.create(
+      TupleTableAtom.create(
         TupleTableName.create(RSA.internal("SP").getIRI),
         (answer ++ bounded): _*
       )
     val predANS =
-      Atom.create(
+      TupleTableAtom.create(
         TupleTableName.create(RSA.internal("ANS").getIRI),
         answer: _*
       )
@@ -116,60 +153,78 @@ class FilteringProgram(query: Query, constants: List[Term]) extends RDFTriple {
     /* Rules 4x */
     val r4a = for {
       role1 <- body.filter(_.isRoleAssertion)
-      if bounded contains (role1 getArgument 2)
+      if bounded contains (role1.getArguments.get(2))
       role2 <- body.filter(_.isRoleAssertion)
-      if bounded contains (role2 getArgument 2)
+      if bounded contains (role2.getArguments.get(2))
     } yield Rule.create(
       predFK,
       role1 suffix "_f",
       role2 suffix "_f",
       predID(
-        RSA.internal(bounded.indexOf(role1 getArgument 2)),
-        RSA.internal(bounded.indexOf(role2 getArgument 2))
+        RSA.internal(bounded.indexOf(role1.getArguments.get(2))),
+        RSA.internal(bounded.indexOf(role2.getArguments.get(2)))
       ),
-      not(Atom.rdf(role1 getArgument 0, IRI.SAME_AS, role2 getArgument 0))
+      not(
+        TupleTableAtom.rdf(
+          role1.getArguments.get(0),
+          IRI.SAME_AS,
+          role2.getArguments.get(0)
+        )
+      )
     )
     val r4b = for {
       role1 <- body.filter(_.isRoleAssertion)
-      if bounded contains (role1 getArgument 2)
+      if bounded contains (role1.getArguments.get(2))
       role2 <- body.filter(_.isRoleAssertion)
-      if bounded contains (role2 getArgument 0)
+      if bounded contains (role2.getArguments.get(0))
     } yield Rule.create(
       predFK,
       role1 suffix "_f",
       role2 suffix "_b",
       predID(
-        RSA.internal(bounded.indexOf(role1 getArgument 2)),
-        RSA.internal(bounded.indexOf(role2 getArgument 0))
+        RSA.internal(bounded.indexOf(role1.getArguments.get(2))),
+        RSA.internal(bounded.indexOf(role2.getArguments.get(0)))
       ),
-      not(Atom.rdf(role1 getArgument 0, IRI.SAME_AS, role2 getArgument 2))
+      not(
+        TupleTableAtom.rdf(
+          role1.getArguments.get(0),
+          IRI.SAME_AS,
+          role2.getArguments.get(2)
+        )
+      )
     )
     val r4c = for {
       role1 <- body.filter(_.isRoleAssertion)
-      if bounded contains (role1 getArgument 0)
+      if bounded contains (role1.getArguments.get(0))
       role2 <- body.filter(_.isRoleAssertion)
-      if bounded contains (role2 getArgument 0)
+      if bounded contains (role2.getArguments.get(0))
     } yield Rule.create(
       predFK,
       role1 suffix "_b",
       role2 suffix "_b",
       predID(
-        RSA.internal(bounded.indexOf(role1 getArgument 0)),
-        RSA.internal(bounded.indexOf(role2 getArgument 0))
+        RSA.internal(bounded.indexOf(role1.getArguments.get(0))),
+        RSA.internal(bounded.indexOf(role2.getArguments.get(0)))
       ),
-      not(Atom.rdf(role1 getArgument 2, IRI.SAME_AS, role2 getArgument 2))
+      not(
+        TupleTableAtom.rdf(
+          role1.getArguments.get(2),
+          IRI.SAME_AS,
+          role2.getArguments.get(2)
+        )
+      )
     )
 
     /* Rules 5x */
     val r5a = for {
       role1 <- body.filter(_.isRoleAssertion)
-      role1arg0 = role1 getArgument 0
-      role1arg2 = role1 getArgument 2
+      role1arg0 = role1.getArguments.get(0)
+      role1arg2 = role1.getArguments.get(2)
       if bounded contains role1arg0
       if bounded contains role1arg2
       role2 <- body.filter(_.isRoleAssertion)
-      role2arg0 = role2 getArgument 0
-      role2arg2 = role2 getArgument 2
+      role2arg0 = role2.getArguments.get(0)
+      role2arg2 = role2.getArguments.get(2)
       if bounded contains role2arg0
       if bounded contains role2arg2
     } yield Rule.create(
@@ -183,18 +238,18 @@ class FilteringProgram(query: Query, constants: List[Term]) extends RDFTriple {
         RSA.internal(bounded indexOf role1arg2),
         RSA.internal(bounded indexOf role2arg2)
       ),
-      Atom.rdf(role1arg0, IRI.SAME_AS, role2arg0),
+      TupleTableAtom.rdf(role1arg0, IRI.SAME_AS, role2arg0),
       not(predNI(role1arg0))
     )
     val r5b = for {
       role1 <- body.filter(_.isRoleAssertion)
-      role1arg0 = role1 getArgument 0
-      role1arg2 = role1 getArgument 2
+      role1arg0 = role1.getArguments.get(0)
+      role1arg2 = role1.getArguments.get(2)
       if bounded contains role1arg0
       if bounded contains role1arg2
       role2 <- body.filter(_.isRoleAssertion)
-      role2arg0 = role2 getArgument 0
-      role2arg2 = role2 getArgument 2
+      role2arg0 = role2.getArguments.get(0)
+      role2arg2 = role2.getArguments.get(2)
       if bounded contains role2arg0
       if bounded contains role2arg2
     } yield Rule.create(
@@ -208,18 +263,18 @@ class FilteringProgram(query: Query, constants: List[Term]) extends RDFTriple {
         RSA.internal(bounded indexOf role1arg2),
         RSA.internal(bounded indexOf role2arg0)
       ),
-      Atom.rdf(role1arg0, IRI.SAME_AS, role2arg2),
+      TupleTableAtom.rdf(role1arg0, IRI.SAME_AS, role2arg2),
       not(predNI(role1arg0))
     )
     val r5c = for {
       role1 <- body.filter(_.isRoleAssertion)
-      role1arg0 = role1 getArgument 0
-      role1arg2 = role1 getArgument 2
+      role1arg0 = role1.getArguments.get(0)
+      role1arg2 = role1.getArguments.get(2)
       if bounded contains role1arg0
       if bounded contains role1arg2
       role2 <- body.filter(_.isRoleAssertion)
-      role2arg0 = role2 getArgument 0
-      role2arg2 = role2 getArgument 2
+      role2arg0 = role2.getArguments.get(0)
+      role2arg2 = role2.getArguments.get(2)
       if bounded contains role2arg0
       if bounded contains role2arg2
     } yield Rule.create(
@@ -233,15 +288,15 @@ class FilteringProgram(query: Query, constants: List[Term]) extends RDFTriple {
         RSA.internal(bounded indexOf role1arg0),
         RSA.internal(bounded indexOf role2arg0)
       ),
-      Atom.rdf(role1arg2, IRI.SAME_AS, role2arg2),
+      TupleTableAtom.rdf(role1arg2, IRI.SAME_AS, role2arg2),
       not(predNI(role1arg2))
     )
 
     /* Rules 6 */
     val r6 = for {
       role <- body.filter(_.isRoleAssertion)
-      arg0 = role getArgument 0
-      arg2 = role getArgument 2
+      arg0 = role.getArguments.get(0)
+      arg2 = role.getArguments.get(2)
       if bounded contains arg0
       if bounded contains arg2
       sx <- List("_f", "_b")
@@ -309,34 +364,37 @@ class FilteringProgram(query: Query, constants: List[Term]) extends RDFTriple {
   }
 
   private sealed trait Reified;
-  private case class ReifiedHead(bind: BindAtom, atoms: List[Atom])
+  private case class ReifiedHead(bind: BindAtom, atoms: List[TupleTableAtom])
       extends Reified
-  private case class ReifiedBody(atoms: List[Atom]) extends Reified
+  private case class ReifiedBody(atoms: List[TupleTableAtom]) extends Reified
   private case class Unaltered(formula: BodyFormula) extends Reified
 
-  private def getBindAtom(atom: Atom): BindAtom = {
+  private def getBindAtom(atom: TupleTableAtom): BindAtom = {
     val newvar = RSA.getFreshVariable()
     val name =
-      Literal.create(atom.getTupleTableName.getIRI, Datatype.XSD_STRING)
+      Literal.create(atom.getTupleTableName.toString(), Datatype.XSD_STRING)
     val args = atom
       .getArguments()
       .asScala
       .toSeq
       .prepended(name) /* Unclear requirement for SKOLEM func calls */
     BindAtom.create(
-      BuiltinFunctionCall
+      FunctionCall
         .create("SKOLEM", args: _*),
       newvar
     )
   }
 
-  private def reifyAtom(atom: Atom, variable: Variable): List[Atom] = {
-    def iri(i: Int) = atom.getTupleTableName().getIRI() ++ s"_$i"
+  private def reifyAtom(
+      atom: TupleTableAtom,
+      variable: Variable
+  ): List[TupleTableAtom] = {
+    def iri(i: Int) = atom.getTupleTableName.getName ++ s"_$i"
     atom
       .getArguments()
       .asScala
       .zipWithIndex
-      .map { case (t, i) => Atom.rdf(variable, iri(i), t) }
+      .map { case (t, i) => TupleTableAtom.rdf(variable, iri(i), t) }
       .toList
   }
 
@@ -345,7 +403,7 @@ class FilteringProgram(query: Query, constants: List[Term]) extends RDFTriple {
       head: Boolean
   ): Reified = {
     formula match {
-      case a: Atom => {
+      case a: TupleTableAtom => {
         if (!a.isRdfTriple) {
           if (head) {
             val b = getBindAtom(a)
@@ -380,7 +438,7 @@ class FilteringProgram(query: Query, constants: List[Term]) extends RDFTriple {
       case ReifiedHead(_, x) => x;
       case ReifiedBody(_)    => List(); /* handle impossible case */
       case Unaltered(x) =>
-        List(x.asInstanceOf[Atom]) /* Can we do better that a cast? */
+        List(x.asInstanceOf[TupleTableAtom]) /* Can we do better that a cast? */
     }
     Rule.create(head.asJava, (skols ++ body).asJava)
   }
@@ -388,6 +446,6 @@ class FilteringProgram(query: Query, constants: List[Term]) extends RDFTriple {
 } // class FilteringProgram
 
 object FilteringProgram {
-  def apply(query: Query, constants: List[Term]): FilteringProgram =
+  def apply(query: SelectQuery, constants: List[Term]): FilteringProgram =
     new FilteringProgram(query, constants)
 } // object FilteringProgram
diff --git a/src/main/scala/rsacomb/RDFTriple.scala b/src/main/scala/rsacomb/RDFTriple.scala
index 11ad6d4..9e593df 100644
--- a/src/main/scala/rsacomb/RDFTriple.scala
+++ b/src/main/scala/rsacomb/RDFTriple.scala
@@ -1,10 +1,11 @@
 package rsacomb
 
-import tech.oxfordsemantic.jrdfox.logic.{Atom, IRI, TupleTableName}
+import tech.oxfordsemantic.jrdfox.logic.datalog.{TupleTableAtom, TupleTableName}
+import tech.oxfordsemantic.jrdfox.logic.expression.{IRI}
 
 trait RDFTriple {
 
-  implicit class RDFTriple(atom: Atom) {
+  implicit class RDFTriple(atom: TupleTableAtom) {
 
     /* Is this the best way to determine if an atom is an RDF triple?
      * Note that we can't use `getNumberOfArguments()` because is not
@@ -21,39 +22,39 @@ trait RDFTriple {
      * ```
      */
     def isRdfTriple: Boolean =
-      atom.getTupleTableName.getIRI.equals("internal:triple")
+      atom.getTupleTableName.getName.equals("internal:triple")
 
     def isClassAssertion: Boolean =
-      atom.isRdfTriple && atom.getArgument(1).equals(IRI.RDF_TYPE)
+      atom.isRdfTriple && atom.getArguments.get(1).equals(IRI.RDF_TYPE)
 
     def isRoleAssertion: Boolean =
-      atom.isRdfTriple && !atom.getArgument(1).equals(IRI.RDF_TYPE)
+      atom.isRdfTriple && !atom.getArguments.get(1).equals(IRI.RDF_TYPE)
 
-    def suffix(sx: String): Atom =
+    def suffix(sx: String): TupleTableAtom =
       if (this.isClassAssertion) {
-        val newclass = atom.getArgument(2) match {
+        val newclass = atom.getArguments.get(2) match {
           case iri: IRI => IRI.create(iri.getIRI.appendedAll(sx))
           case other    => other
         }
-        Atom.rdf(
-          atom getArgument 0,
-          atom getArgument 1,
+        TupleTableAtom.rdf(
+          atom.getArguments.get(0),
+          atom.getArguments.get(1),
           newclass
         )
       } else if (this.isRoleAssertion) {
-        val newrole = atom.getArgument(1) match {
+        val newrole = atom.getArguments.get(1) match {
           case iri: IRI => IRI.create(iri.getIRI.appendedAll(sx))
           case other    => other
         }
-        Atom.rdf(
-          atom getArgument 0,
+        TupleTableAtom.rdf(
+          atom.getArguments.get(0),
           newrole,
-          atom getArgument 2
+          atom.getArguments.get(2)
         )
       } else {
         val newname =
-          TupleTableName.create(atom.getTupleTableName.getIRI.appendedAll(sx))
-        Atom.create(newname, atom.getArguments())
+          TupleTableName.create(atom.getTupleTableName.getName.appendedAll(sx))
+        TupleTableAtom.create(newname, atom.getArguments())
       }
   }
 
diff --git a/src/main/scala/rsacomb/RDFoxAxiomConverter.scala b/src/main/scala/rsacomb/RDFoxAxiomConverter.scala
index dab6765..2d04c56 100644
--- a/src/main/scala/rsacomb/RDFoxAxiomConverter.scala
+++ b/src/main/scala/rsacomb/RDFoxAxiomConverter.scala
@@ -8,9 +8,13 @@ import org.semanticweb.owlapi.model.{
 }
 import org.semanticweb.owlapi.model.OWLAxiomVisitorEx
 
-import tech.oxfordsemantic.jrdfox.logic.{Rule, BodyFormula}
-import tech.oxfordsemantic.jrdfox.logic.{Atom, Term, Variable, Literal}
-import tech.oxfordsemantic.jrdfox.logic.{TupleTableName}
+import tech.oxfordsemantic.jrdfox.logic.datalog.{
+  Rule,
+  BodyFormula,
+  TupleTableAtom,
+  TupleTableName
+}
+import tech.oxfordsemantic.jrdfox.logic.expression.{Term, Variable, Literal}
 
 import scala.collection.JavaConverters._
 
@@ -71,7 +75,7 @@ class RDFoxAxiomConverter(
       new RDFoxPropertyExprConverter(term, term1, suffix)
     val superVisitor = new RDFoxPropertyExprConverter(term, term1, suffix)
     val body: List[BodyFormula] = axiom.getSubProperty.accept(subVisitor)
-    val head: List[Atom] = axiom.getSuperProperty.accept(superVisitor)
+    val head: List[TupleTableAtom] = axiom.getSuperProperty.accept(superVisitor)
     List(Rule.create(head.asJava, body.asJava))
   }
 
diff --git a/src/main/scala/rsacomb/RDFoxClassExprConverter.scala b/src/main/scala/rsacomb/RDFoxClassExprConverter.scala
index f07e3c6..de0f623 100644
--- a/src/main/scala/rsacomb/RDFoxClassExprConverter.scala
+++ b/src/main/scala/rsacomb/RDFoxClassExprConverter.scala
@@ -12,17 +12,16 @@ import org.semanticweb.owlapi.model.{
   OWLObjectMaxCardinality
 }
 import org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx
-import tech.oxfordsemantic.jrdfox.logic.{
+import tech.oxfordsemantic.jrdfox.logic.Datatype
+import tech.oxfordsemantic.jrdfox.logic.datalog.{
   BindAtom,
-  BuiltinFunctionCall,
-  TupleTableName
+  TupleTableName,
+  TupleTableAtom
 }
-import tech.oxfordsemantic.jrdfox.logic.{
-  Atom,
+import tech.oxfordsemantic.jrdfox.logic.expression.{
   Term,
   Variable,
-  Literal,
-  Datatype,
+  FunctionCall,
   IRI
 }
 
@@ -64,7 +63,7 @@ class RDFoxClassExprConverter(
   // OWLClass
   override def visit(expr: OWLClass): RDFoxRuleShards = {
     val iri: IRI = if (expr.isTopEntity()) IRI.THING else expr.getIRI()
-    val atom = List(Atom.rdf(term, IRI.RDF_TYPE, iri))
+    val atom = List(TupleTableAtom.rdf(term, IRI.RDF_TYPE, iri))
     RDFoxRuleShards(atom, List())
   }
 
@@ -90,7 +89,7 @@ class RDFoxClassExprConverter(
       .asOWLNamedIndividual
       .getIRI
     val atom = List(
-      Atom.sameAs(term, ind)
+      TupleTableAtom.rdf(term, IRI.SAME_AS, ind)
     )
     RDFoxRuleShards(atom, List())
   }
@@ -110,8 +109,8 @@ class RDFoxClassExprConverter(
         if (unsafe.contains(prop))
           (
             List(
-              Atom.rdf(term, RSA.internal("PE"), c),
-              Atom.rdf(c, IRI.RDF_TYPE, RSA.internal("U"))
+              TupleTableAtom.rdf(term, RSA.internal("PE"), c),
+              TupleTableAtom.rdf(c, IRI.RDF_TYPE, RSA.internal("U"))
             ),
             List(),
             c
@@ -124,7 +123,7 @@ class RDFoxClassExprConverter(
         // a simple builtin function with a "special" name.
         (
           List(),
-          List(BindAtom.create(BuiltinFunctionCall.create("SKOLEM", term), y)),
+          List(BindAtom.create(FunctionCall.create("SKOLEM", term), y)),
           y
         )
     }
@@ -154,7 +153,7 @@ class RDFoxClassExprConverter(
         .map(expr.getProperty.accept(_))
         .flatten
     RDFoxRuleShards(
-      List(Atom.sameAs(vars(0), vars(1))),
+      List(TupleTableAtom.rdf(vars(0), IRI.SAME_AS, vars(1))),
       classResult.res ++ propertyResult
     )
   }
diff --git a/src/main/scala/rsacomb/RDFoxPropertyExprConverter.scala b/src/main/scala/rsacomb/RDFoxPropertyExprConverter.scala
index ba151d0..11d6d86 100644
--- a/src/main/scala/rsacomb/RDFoxPropertyExprConverter.scala
+++ b/src/main/scala/rsacomb/RDFoxPropertyExprConverter.scala
@@ -3,7 +3,8 @@ package rsacomb
 import org.semanticweb.owlapi.model.{OWLPropertyExpression, OWLObjectProperty}
 import org.semanticweb.owlapi.model.OWLPropertyExpressionVisitorEx
 
-import tech.oxfordsemantic.jrdfox.logic.{Atom, Term, IRI, Literal}
+import tech.oxfordsemantic.jrdfox.logic.datalog.TupleTableAtom
+import tech.oxfordsemantic.jrdfox.logic.expression.{Term, IRI, Literal}
 
 import org.semanticweb.owlapi.model.OWLObjectInverseOf
 
@@ -11,23 +12,23 @@ class RDFoxPropertyExprConverter(
     term1: Term,
     term2: Term,
     suffix: RSASuffix
-) extends OWLPropertyExpressionVisitorEx[List[Atom]] {
+) extends OWLPropertyExpressionVisitorEx[List[TupleTableAtom]] {
 
   // Automatically converts OWLAPI types into RDFox equivalent types.
   import RDFoxUtil.owlapi2rdfox;
 
-  override def visit(expr: OWLObjectProperty): List[Atom] = {
+  override def visit(expr: OWLObjectProperty): List[TupleTableAtom] = {
     val pred = IRI.create(expr.getIRI.getIRIString ++ suffix.getSuffix)
-    List(Atom.rdf(term1, pred, term2))
+    List(TupleTableAtom.rdf(term1, pred, term2))
   }
 
-  override def visit(expr: OWLObjectInverseOf): List[Atom] = {
+  override def visit(expr: OWLObjectInverseOf): List[TupleTableAtom] = {
     val pred = IRI.create(
       expr.getInverse.getNamedProperty.getIRI.getIRIString ++ suffix.getSuffix ++ "_inv"
     )
-    List(Atom.rdf(term1, pred, term2))
+    List(TupleTableAtom.rdf(term1, pred, term2))
   }
 
-  def doDefault(expr: OWLPropertyExpression): List[Atom] = List()
+  def doDefault(expr: OWLPropertyExpression): List[TupleTableAtom] = List()
 
 } // class RDFoxPropertyExprConverter
diff --git a/src/main/scala/rsacomb/RDFoxRuleShards.scala b/src/main/scala/rsacomb/RDFoxRuleShards.scala
index 8f72983..b61cc38 100644
--- a/src/main/scala/rsacomb/RDFoxRuleShards.scala
+++ b/src/main/scala/rsacomb/RDFoxRuleShards.scala
@@ -1,6 +1,5 @@
 package rsacomb
 
-import tech.oxfordsemantic.jrdfox.logic.{Atom, BodyFormula}
-
-case class RDFoxRuleShards(res : List[Atom], ext : List[BodyFormula])
+import tech.oxfordsemantic.jrdfox.logic.datalog.{TupleTableAtom, BodyFormula}
 
+case class RDFoxRuleShards(res: List[TupleTableAtom], ext: List[BodyFormula])
diff --git a/src/main/scala/rsacomb/RDFoxUtil.scala b/src/main/scala/rsacomb/RDFoxUtil.scala
index 4e0a118..748c72f 100644
--- a/src/main/scala/rsacomb/RDFoxUtil.scala
+++ b/src/main/scala/rsacomb/RDFoxUtil.scala
@@ -2,9 +2,9 @@ package rsacomb
 
 /* Java imports */
 import java.util.HashMap
-import java.io.ByteArrayInputStream
+import java.io.StringReader
 import tech.oxfordsemantic.jrdfox.Prefixes
-import tech.oxfordsemantic.jrdfox.logic.{IRI, Query}
+import tech.oxfordsemantic.jrdfox.logic.sparql.statement.{Query, SelectQuery}
 import tech.oxfordsemantic.jrdfox.client.{
   ConnectionFactory,
   ServerConnection,
@@ -12,7 +12,7 @@ import tech.oxfordsemantic.jrdfox.client.{
 }
 import tech.oxfordsemantic.jrdfox.formats.SPARQLParser
 
-import tech.oxfordsemantic.jrdfox.logic.{IRI => RDFox_IRI}
+import tech.oxfordsemantic.jrdfox.logic.expression.{IRI => RDFox_IRI}
 import org.semanticweb.owlapi.model.{IRI => OWL_IRI}
 
 object RDFoxUtil {
@@ -51,12 +51,19 @@ object RDFoxUtil {
     (server, data)
   }
 
-  def parseQuery(query: String, prefixes: Prefixes = RSA.Prefixes): Query = {
+  def parseQuery(
+      query: String,
+      prefixes: Prefixes = RSA.Prefixes
+  ): Option[SelectQuery] = {
     val parser = new SPARQLParser(
       prefixes,
-      new ByteArrayInputStream(query.getBytes())
+      new StringReader(query)
     )
-    parser.parseSingleQuery()
+    // NOTE: return only conjunctive queries for now (SelectQuery)
+    parser.parseSingleQuery() match {
+      case q: SelectQuery => Some(q)
+      case _              => None
+    }
   }
 
   def submitQuery(
diff --git a/src/main/scala/rsacomb/RSA.scala b/src/main/scala/rsacomb/RSA.scala
index 01982fc..a6f4b88 100644
--- a/src/main/scala/rsacomb/RSA.scala
+++ b/src/main/scala/rsacomb/RSA.scala
@@ -6,20 +6,12 @@ import java.util.Map
 
 import tech.oxfordsemantic.jrdfox.formats.SPARQLParser
 import tech.oxfordsemantic.jrdfox.Prefixes
-import tech.oxfordsemantic.jrdfox.logic.IRI
+import tech.oxfordsemantic.jrdfox.logic.expression.{Variable, 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 {
diff --git a/src/main/scala/rsacomb/RSAOntology.scala b/src/main/scala/rsacomb/RSAOntology.scala
index b81a8f5..ef1885b 100644
--- a/src/main/scala/rsacomb/RSAOntology.scala
+++ b/src/main/scala/rsacomb/RSAOntology.scala
@@ -17,7 +17,14 @@ import org.semanticweb.owlapi.model.{IRI => OWLIRI}
 import uk.ac.manchester.cs.owl.owlapi.OWLObjectPropertyImpl
 
 import tech.oxfordsemantic.jrdfox.client.{UpdateType, DataStoreConnection}
-import tech.oxfordsemantic.jrdfox.logic.{Resource, Rule, Atom, Variable, IRI}
+import tech.oxfordsemantic.jrdfox.logic.datalog.{Rule, TupleTableAtom}
+import tech.oxfordsemantic.jrdfox.logic.expression.{
+  Term,
+  Variable,
+  IRI,
+  Resource
+}
+import tech.oxfordsemantic.jrdfox.logic.sparql.statement.SelectQuery
 
 /* Scala imports */
 import scala.collection.JavaConverters._
@@ -249,7 +256,7 @@ trait RSAOntology {
       Graph(edges: _*)
     }
 
-    def filteringProgram(query: Query): List[Rule] =
+    def filteringProgram(query: SelectQuery): List[Rule] =
       FilteringProgram(query, individuals).rules
 
     // TODO: the following functions needs testing
diff --git a/src/main/scala/rsacomb/SkolemStrategy.scala b/src/main/scala/rsacomb/SkolemStrategy.scala
index 9d45b4c..b05cd17 100644
--- a/src/main/scala/rsacomb/SkolemStrategy.scala
+++ b/src/main/scala/rsacomb/SkolemStrategy.scala
@@ -1,6 +1,6 @@
 package rsacomb
 
-import tech.oxfordsemantic.jrdfox.logic.IRI
+import tech.oxfordsemantic.jrdfox.logic.expression.IRI
 
 sealed trait SkolemStrategy