Review main workflow

4 files changed, 61 insertions, 17 deletions

diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/CanonicalModel.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/CanonicalModel.scala
index af6c463..ee808c3 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/CanonicalModel.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/CanonicalModel.scala
@@ -77,7 +77,7 @@ class CanonicalModel(val ontology: RSAOntology) {
     // Compute rules from ontology axioms
     val (facts, rules) = {
       val term = RSAUtil.genFreshVariable()
-      val unsafe = ontology.unsafeRoles
+      val unsafe = ontology.unsafe
       ontology.axioms
         .map(a =>
           CanonicalModelConverter.convert(a, term, unsafe, Constant(a), Empty)
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 82da9df..8e5169d 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
@@ -10,6 +10,10 @@ import tech.oxfordsemantic.jrdfox.logic.sparql.statement.SelectQuery
 import util.{Logger, RDFoxUtil, RSA}
 import sparql.ConjunctiveQuery
 
+import uk.ac.ox.cs.rsacomb.ontology.Ontology
+import uk.ac.ox.cs.rsacomb.converter.Normalizer
+import uk.ac.ox.cs.rsacomb.approximation.LowerBound
+
 case class RSAOption[+T](opt: T) {
   def get[T]: T = opt.asInstanceOf[T]
 }
@@ -103,24 +107,18 @@ object RSAConfig {
 /** Main entry point to the program */
 object RSAComb extends App {
 
-  /*
-   * TODO: Aiming for this workflow:
-   *
-   *    implicit val manager = new Manager(...)
-   *    val original = manager.importFromFile("ontology.owl")
-   *    val axioms = original.getAxioms.filter(isLogicalAxiom).normalize(normalizer)
-   *    val ontology = new Ontology(axioms, data)
-   *    val rsa = ontology.toRSA(approximator)
-   */
-
   /* Command-line options */
   val config = RSAConfig.parse(args.toList)
 
-  val rsa = RSAOntology(
+  /* Load original ontology and normalize it */
+  val ontology = Ontology(
     config('ontology).get[File],
-    config('data).get[List[File]],
-    None
-  )
+    config('data).get[List[File]]
+  ).normalize(new Normalizer)
+
+  /* Approximate the ontology to RSA */
+  val toRSA = new LowerBound
+  val rsa = ontology approximate 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 630d2a0..73c4411 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
@@ -209,9 +209,9 @@ class RSAOntology(axioms: List[OWLLogicalAxiom], datafiles: List[File])
       .map(implicits.RDFox.owlapiToRdfoxLiteral)
 
   /** Retrieve concepts/roles in the ontology */
-  private val concepts: List[OWLClass] =
+  val concepts: List[OWLClass] =
     ontology.getClassesInSignature().asScala.toList
-  private val roles: List[OWLObjectPropertyExpression] =
+  val roles: List[OWLObjectPropertyExpression] =
     axioms
       .flatMap(_.objectPropertyExpressionsInSignature)
       .distinct
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/ontologies/Ontology.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/ontologies/Ontology.scala
index 9d947bc..723bcaa 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/ontologies/Ontology.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/ontologies/Ontology.scala
@@ -17,12 +17,14 @@
 package uk.ac.ox.cs.rsacomb.ontology
 
 import java.io.File
+import java.util.stream.Collectors
 
 import scala.collection.mutable.Map
 import scala.collection.JavaConverters._
 import scalax.collection.Graph
 import scalax.collection.GraphPredef._, scalax.collection.GraphEdge._
 
+import org.semanticweb.owlapi.model.parameters.Imports
 import org.semanticweb.owlapi.apibinding.OWLManager
 import org.semanticweb.owlapi.model.{OWLOntology, OWLAxiom, OWLLogicalAxiom}
 import org.semanticweb.owlapi.model.{OWLObjectPropertyExpression}
@@ -39,6 +41,9 @@ import uk.ac.ox.cs.rsacomb.RSAUtil
 
 object Ontology {
 
+  /** Simplify conversion between Java and Scala collections */
+  import uk.ac.ox.cs.rsacomb.implicits.JavaCollections._
+
   /** Type wrapper representing a dependency graph for the ontology.
     *
     * The graph is returned along with a map associating each node (IRI
@@ -155,6 +160,47 @@ object Ontology {
 
     (graph, nodemap)
   }
+
+  def apply(axioms: List[OWLLogicalAxiom], datafiles: List[File]): Ontology =
+    new Ontology(axioms, datafiles)
+
+  def apply(ontology: OWLOntology, datafiles: List[File]): Ontology = {
+
+    /** TBox axioms */
+    var tbox: List[OWLLogicalAxiom] =
+      ontology
+        .tboxAxioms(Imports.INCLUDED)
+        .collect(Collectors.toList())
+        .collect { case a: OWLLogicalAxiom => a }
+
+    /** RBox axioms */
+    var rbox: List[OWLLogicalAxiom] =
+      ontology
+        .rboxAxioms(Imports.INCLUDED)
+        .collect(Collectors.toList())
+        .collect { case a: OWLLogicalAxiom => a }
+
+    /** ABox axioms
+      *
+      * @note this represents only the set of assertions contained in the
+      * ontology file. Data files specified in `datafiles` are directly
+      * imported in RDFox due to performance issues when trying to import
+      * large data files via OWLAPI.
+      */
+    var abox: List[OWLLogicalAxiom] =
+      ontology
+        .aboxAxioms(Imports.INCLUDED)
+        .collect(Collectors.toList())
+        .collect { case a: OWLLogicalAxiom => a }
+
+    Ontology(abox ::: tbox ::: rbox, datafiles)
+  }
+
+  def apply(ontofile: File, datafiles: List[File]): Ontology = {
+    val ontology = manager.loadOntologyFromOntologyDocument(ontofile)
+    Ontology(ontology, datafiles)
+  }
+
 }
 
 /** A wrapper for a generic OWL2 ontology