3 files changed, 121 insertions, 218 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 db52793..678a5fa 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
@@ -46,9 +46,7 @@ object RSAComb extends App {
     sys.exit;
   }
 
-  /* Create RSA object from generic OWLOntology
-   *
-   * TODO: It might be required to check if the ontology in input is
+  /* TODO: It might be required to check if the ontology in input is
    * Horn-ALCHOIQ. At the moment we are assuming this is always the
    * case.
    */
@@ -56,183 +54,13 @@ object RSAComb extends App {
   val ontology = RSAOntology(ontoPath)
   if (ontology.isRSA) {
 
-    /* Load query */
-    val query = """
-        PREFIX  :  <http://example.com/rsa_example.owl#>
-
-        SELECT ?X
-        WHERE {
-          ?X a  :D ;
-             :R ?Y .
-          ?Y :S ?Z .
-          ?Z a  :D .
-        }
-    """
+    /** Read SPARQL query from file */
+    val source = io.Source.fromFile(queryPath.getAbsoluteFile)
+    val query = source.getLines mkString "\n"
+    source.close()
 
     /* Compute answers to query */
-    ConjunctiveQuery(query) match {
-      case Some(query) => {
-
-        import implicits.JavaCollections._
-
-        // Open connection to RDFox
-        val (server, data) = RDFoxHelpers.openConnection("AnswerComputation")
-
-        {
-          println("\nQuery")
-          println(query)
-        }
-
-        val canon = ontology.canonicalModel
-        data.addRules(canon.rules)
-        val filter = ontology.filteringProgram(query)
-        data.addRules(filter.rules)
-
-        {
-          println("\nCanonical Model rules:")
-          canon.rules.foreach(println)
-          println("\nFiltering rules")
-          filter.rules.foreach(println)
-        }
-
-        // Retrieve answers
-        println("\nAnswers:")
-        val ans =
-          RDFoxHelpers.queryInternalPredicate(data, "Ans", filter.answer.length)
-        println(ans)
-
-        /* DEBUG: adding additional checks
-         */
-        {
-          import suffix.{Forward, Backward}
-
-          val arity = filter.answer.length + filter.bounded.length
-
-          println("\nIndividuals:")
-          ontology.individuals.foreach(println)
-
-          println("\nThings:")
-          val things = RDFoxHelpers.submitQuery(
-            data,
-            """
-             PREFIX  owl:  <http://www.w3.org/2002/07/owl#>
-
-             SELECT ?X {
-               ?X a owl:Thing
-             }
-             """
-          )
-          println(things)
-
-          println("\nNAMEDs:")
-          val named = RDFoxHelpers.submitQuery(
-            data,
-            """
-             SELECT ?X {
-               ?X a rsa:Named
-             }
-             """,
-            RSA.Prefixes
-          )
-          println(named)
-
-          println("\nNIs:")
-          val nis = RDFoxHelpers.submitQuery(
-            data,
-            """
-             SELECT ?X {
-               ?X a rsa:NI
-             }
-             """,
-            RSA.Prefixes
-          )
-          println(nis)
-
-          // ID instances
-          println("\nIDs:")
-          val ids = RDFoxHelpers.queryInternalPredicate(
-            data,
-            "ID",
-            arity + 2
-          )
-          println(ids)
-
-          println("\nCongruent:")
-          val equivs = RDFoxHelpers.submitQuery(
-            data,
-            """
-              SELECT ?X ?Y {
-                ?X rsa:congruent ?Y
-              }
-            """,
-            RSA.Prefixes
-          )
-          println(equivs)
-
-          // Unfiltered answers
-          println("\nPossible answers:")
-          val qms = RDFoxHelpers.queryInternalPredicate(
-            data,
-            "QM",
-            arity
-          )
-          println(qms)
-
-          // Cycle detected
-          println("\nCycle detection:")
-          val aqf = RDFoxHelpers.queryInternalPredicate(
-            data,
-            "AQ" :: Forward,
-            arity + 2
-          )
-          val aqb = RDFoxHelpers.queryInternalPredicate(
-            data,
-            "AQ" :: Backward,
-            arity + 2
-          )
-          println(aqf)
-          println(aqb)
-
-          // Forks detected
-          println("\nForks:")
-          val fk = RDFoxHelpers.queryInternalPredicate(
-            data,
-            "FK",
-            arity
-          )
-          println(fk)
-
-          // Spurious answers
-          println("\nSpurious answers")
-          val sp = RDFoxHelpers.queryInternalPredicate(
-            data,
-            "SP",
-            arity
-          )
-          println(sp)
-        }
-
-        // Close connection to RDFox
-        RDFoxHelpers.closeConnection(server, data)
-      }
-      case None => {}
-    }
+    val answers = ConjunctiveQuery(query).map(ontology ask _)
+    answers map (_.toString) foreach println
   }
 }
-
-/* Notes:
- *
- * To establish a connection with a local RDFox instance, do the
- * following:
- *
- * ```
- * val serverConnection : ServerConnection = ConnectionFactory.newServerConnection("rdfox:local", "", "")
- * serverConnection.createDataStore("test","seq",new HashMap())
- * val dataStoreConnection : DataStoreConnection = serverConnection.newDataStoreConnection("test")
- * dataStoreConnection.importData(
- *    UpdateType.ADDITION,
- *    Prefixes.s_emptyPrefixes,
- *    new File("./path/to/file")
- * )
- * ```
- */
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 9640ccc..56fbac3 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
@@ -1,6 +1,7 @@
 package uk.ac.ox.cs.rsacomb
 
 /* Java imports */
+import java.{util => ju}
 import java.util.HashMap
 import java.util.stream.{Collectors, Stream}
 import java.io.File
@@ -48,8 +49,8 @@ import org.semanticweb.owlapi.model.OWLObjectInverseOf
 
 import uk.ac.ox.cs.rsacomb.converter.{RDFoxAxiomConverter, SkolemStrategy}
 import uk.ac.ox.cs.rsacomb.implicits.RSAAxiom
-import uk.ac.ox.cs.rsacomb.suffix.{Empty, Forward, Backward, Inverse}
-import uk.ac.ox.cs.rsacomb.sparql.ConjunctiveQuery
+import uk.ac.ox.cs.rsacomb.suffix._
+import uk.ac.ox.cs.rsacomb.sparql._
 import uk.ac.ox.cs.rsacomb.util.{RDFoxHelpers, RSA}
 
 object RSAOntology {
@@ -256,8 +257,8 @@ class RSAOntology(val ontology: OWLOntology) extends RSAAxiom {
   ): Graph[Resource, UnDiEdge] = {
     val query = "SELECT ?X ?Y WHERE { ?X rsa:E ?Y }"
     val answers = RDFoxHelpers.submitQuery(data, query, RSA.Prefixes).get
-    var edges: List[UnDiEdge[Resource]] = answers.map {
-      case n1 :: n2 :: _ => UnDiEdge(n1, n2)
+    var edges: Seq[UnDiEdge[Resource]] = answers.map {
+      case Seq(n1, n2) => UnDiEdge(n1, n2)
     }
     Graph(edges: _*)
   }
@@ -291,6 +292,52 @@ class RSAOntology(val ontology: OWLOntology) extends RSAAxiom {
       .filterNot(_.getInverseProperty.isOWLTopObjectProperty())
   }
 
+  /** Returns the answers to a query
+    *
+    *  @param query query to execute
+    *  @return a collection of answers
+    */
+  def ask(query: ConjunctiveQuery): ConjunctiveQueryAnswers = {
+    import implicits.JavaCollections._
+    val (server, data) = RDFoxHelpers.openConnection("AnswerComputation")
+    data.addRules(this.canonicalModel.rules)
+    data.addRules(this.filteringProgram(query).rules)
+    new ConjunctiveQueryAnswers(
+      query.boolean,
+      queryInternalPredicate(data, "Ans", query.answer.size)
+    )
+  }
+
+  /** Returns instances of a reified predicate
+    *
+    * Predicated with arity higher than 2 are internally reified to be
+    * compatible with RDFox engine. This helper queries for predicate
+    * instances and returns a set of un-reified answers.
+    *
+    * @param data open datastore connection to RDFox
+    * @param pred name of the predicate
+    * @param arity arity of the predicate
+    * @param opts additional options to RDFox
+    * @return a collection of instances of the given predicate
+    */
+  private def queryInternalPredicate(
+      data: DataStoreConnection,
+      pred: String,
+      arity: Int,
+      opts: ju.Map[String, String] = new ju.HashMap[String, String]()
+  ): Seq[Seq[Resource]] = {
+    val query =
+      if (arity > 0) {
+        (0 until arity).mkString("SELECT ?X", " ?X", "\n") +
+          (0 until arity)
+            .map(i => s"?S rsa:${pred :: Nth(i)} ?X$i .")
+            .mkString("WHERE {\n", "\n", "\n}")
+      } else {
+        s"ASK { ?X a rsa:$pred }"
+      }
+    RDFoxHelpers.submitQuery(data, query, RSA.Prefixes).get
+  }
+
   def self(axiom: OWLSubClassOfAxiom): Set[Term] = {
     // Assuming just one role in the signature of a T5 axiom
     val role = axiom.objectPropertyExpressionsInSignature(0)
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxHelpers.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxHelpers.scala
index 5b85436..43e5d28 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxHelpers.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxHelpers.scala
@@ -1,6 +1,5 @@
 package uk.ac.ox.cs.rsacomb.util
 
-import java.util.{Map => JMap, HashMap => JHashMap}
 import java.io.StringReader
 import tech.oxfordsemantic.jrdfox.Prefixes
 import tech.oxfordsemantic.jrdfox.client.{
@@ -12,32 +11,52 @@ import tech.oxfordsemantic.jrdfox.formats.SPARQLParser
 import tech.oxfordsemantic.jrdfox.logic.expression.Resource
 import tech.oxfordsemantic.jrdfox.logic.sparql.statement.SelectQuery
 
-import uk.ac.ox.cs.rsacomb.suffix.Nth
-
+/** A collection of helper methods for RDFox */
 object RDFoxHelpers {
 
+  /** Type alias for a collection of answers to a
+    * [[tech.oxfordsemantic.jrdfox.logic.sparql.statement.Query]].
+    */
+  private type QueryAnswers = Seq[Seq[Resource]]
+  private def QueryAnswers() = List.empty[Seq[Resource]]
+
+  /** Type alias for <option => value> RDFox options. */
+  private type RDFoxOpts = java.util.Map[String, String]
+  private def RDFoxOpts() = new java.util.HashMap[String, String]()
+
+  /** Setup a new local connection with RDFox.
+    *
+    * @param dataStore data store identifier
+    * @param opts additional options to RDFox
+    * @return a tuple with the newly opened server and data store
+    * connections.
+    *
+    * @see [[uk.ac.ox.cs.rsacomb.util.RDFoxHelpers.closeConnection
+    * RDFoxHelpers.closeConnection]] for
+    * details on how to close an open connection.
+    */
   def openConnection(
       dataStore: String,
-      opts: JMap[String, String] = new JHashMap[String, String]()
+      opts: RDFoxOpts = RDFoxOpts()
   ): (ServerConnection, DataStoreConnection) = {
-    /* Create local server connection
-     */
     val serverUrl = "rdfox:local"
     val role = ""
     val password = ""
     val server =
       ConnectionFactory.newServerConnection(serverUrl, role, password)
-
-    /* Create datastore connection
-     */
-    // parameters.put("owl-in-rdf-support", "relaxed")
-    // parameters.put("equality", "noUNA")
     server.createDataStore(dataStore, "par-complex-nn", opts)
     val data = server.newDataStoreConnection(dataStore)
-
     (server, data)
   }
 
+  /** Parse a SELECT query from a string in SPARQL format.
+    *
+    * @param query the string containing the SPARQL query
+    * @param prefixes additional prefixes for the query. It defaults to
+    * an empty set.
+    * @return a [[tech.oxfordsemantic.jrdfox.logic.sparql.statement.SelectQuery SelectQuery]]
+    * if the input string is a SELECT query, none otherwise.
+    */
   def parseSelectQuery(
       query: String,
       prefixes: Prefixes = new Prefixes()
@@ -52,13 +71,22 @@ object RDFoxHelpers {
     }
   }
 
+  /** Execute a query over a given datastore connection.
+    *
+    * @param data RDFox datastore connection.
+    * @param query a
+    * [[tech.oxfordsemantic.jrdfox.logic.sparql.statement.SelectQuery SelectQuery]]
+    * to be executed.
+    * @param opts additional options to RDFox.
+    * @returns a collection of answers to the query.
+    */
   def submitSelectQuery(
       data: DataStoreConnection,
       query: SelectQuery,
-      opts: JMap[String, String] = new JHashMap[String, String]()
-  ): List[List[Resource]] = {
+      opts: RDFoxOpts = RDFoxOpts()
+  ): QueryAnswers = {
     val cursor = data.createCursor(query, opts)
-    var answers: List[List[Resource]] = List()
+    var answers = QueryAnswers()
     var mul = cursor.open()
     while (mul > 0) {
       val answer =
@@ -70,32 +98,32 @@ object RDFoxHelpers {
     answers
   }
 
+  /** Execute a query over a given datastore connection.
+    *
+    * @param data RDFox datastore connection.
+    * @param query a string representing a SPARQL query.
+    * @param prefixes additional prefixes for the query. It defaults to
+    * an empty set.
+    * @param opts additional options to RDFox.
+    * @returns a collection of answers to the query if the input query
+    * is a SELECT query, none otherwise.
+    */
   def submitQuery(
       data: DataStoreConnection,
       query: String,
       prefixes: Prefixes = new Prefixes(),
-      opts: JMap[String, String] = new JHashMap[String, String]()
-  ): Option[List[List[Resource]]] =
+      opts: RDFoxOpts = RDFoxOpts()
+  ): Option[QueryAnswers] =
     parseSelectQuery(query, prefixes).map(submitSelectQuery(data, _, opts))
 
-  def queryInternalPredicate(
-      data: DataStoreConnection,
-      pred: String,
-      arity: Int,
-      opts: JMap[String, String] = new JHashMap[String, String]()
-  ): List[List[Resource]] = {
-    var query = "SELECT"
-    for (i <- 0 until arity) {
-      query ++= s" ?X$i"
-    }
-    query ++= " WHERE {"
-    for (i <- 0 until arity) {
-      query ++= s" ?S rsa:${pred :: Nth(i)} ?X$i ."
-    }
-    query ++= " }"
-    submitQuery(data, query, RSA.Prefixes, opts).get
-  }
-
+  /** Close an open connection to RDFox.
+    *
+    * @param server server connection
+    * @param data data store connections
+    *
+    * @see [[uk.ac.ox.cs.rsacomb.util.RDFoxHelpers.openConnection RDFoxHelpers.openConnection]]
+    * for details on how to create a new connection with RDFox.
+    */
   def closeConnection(
       server: ServerConnection,
       data: DataStoreConnection