3 files changed, 70 insertions, 40 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 a1fd20f..b1fd721 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
@@ -49,7 +49,7 @@ object RSAConfig {
       -h | -? | --help
           print this help message
 
-      -q <file> | --query <file>
+      -q <file> | --queries <file>
           path to a file containing a single SPARQL query. If no query
           is provided, only the approximation to RSA will be performed.
 
@@ -97,11 +97,11 @@ object RSAConfig {
         println(help)
         sys.exit(0)
       }
-      case flag @ ("-q" | "--query") :: _query :: tail => {
+      case flag @ ("-q" | "--queries") :: _query :: tail => {
         val query = new File(_query)
         if (!query.isFile)
           exit(s"'$query' is not a valid filename.")
-        parse(tail, config ++ Map('query -> query))
+        parse(tail, config ++ Map('queries -> query))
       }
       case _ontology :: _data => {
         val ontology = new File(_ontology)
@@ -132,36 +132,32 @@ object RSAComb extends App {
     config('data).get[List[File]]
   ).normalize(new Normalizer)
 
+  //ontology.axioms foreach println
+
   /* Approximate the ontology to RSA */
   val toRSA = new Upperbound
   val rsa = ontology approximate toRSA
 
-  if (config contains 'query) {
-    val query =
-      RDFoxUtil.loadQueryFromFile(config('query).get[File].getAbsoluteFile)
-
-    ConjunctiveQuery.parse(query) match {
-      case Some(query) => {
-        // Retrieve answers
-        val answers = rsa ask query
-        Logger.print(s"$answers", Logger.VERBOSE)
-        Logger print s"Number of answers: ${answers.length} (${answers.lengthWithMultiplicity})"
-        // Retrieve unfiltered answers
-        // val unfiltered = rsa.queryDataStore(
-        //   """
-        //     SELECT (count(?K) as ?COUNT)
-        //     WHERE {
-        //         ?K a rsa:QM .
-        //     }
-        //   """,
-        //   RSA.Prefixes
-        // )
-        // unfiltered.foreach((u) =>
-        //   Logger print s"Number of unfiltered answers: ${u.head._2}"
-        // )
-      }
-      case None =>
-        throw new RuntimeException("Submitted query is not conjunctive")
-    }
+  if (config contains 'queries) {
+    val queries =
+      RDFoxUtil.loadQueriesFromFile(config('queries).get[File].getAbsoluteFile)
+
+    val answers = rsa ask queries
+
+    // Logger.print(s"$answers", Logger.VERBOSE)
+    // Logger print s"Number of answers: ${answers.length} (${answers.lengthWithMultiplicity})"
+    // Retrieve unfiltered answers
+    // val unfiltered = rsa.queryDataStore(
+    //   """
+    //     SELECT (count(?K) as ?COUNT)
+    //     WHERE {
+    //         ?K a rsa:QM .
+    //     }
+    //   """,
+    //   RSA.Prefixes
+    // )
+    // unfiltered.foreach((u) =>
+    //   Logger print s"Number of unfiltered answers: ${u.head._2}"
+    // )
   }
 }
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 0c88f7f..8e05f3a 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
@@ -496,6 +496,8 @@ class RSAOntology(axioms: List[OWLLogicalAxiom], datafiles: List[File])
   def unfold(axiom: OWLSubClassOfAxiom): Set[Term] =
     this.self(axiom) | this.cycle(axiom)
 
+  def ask(queries: Seq[ConjunctiveQuery]): Seq[ConjunctiveQueryAnswers] = ???
+
   /** Returns the answers to a query
     *
     *  @param query query to execute
@@ -553,7 +555,7 @@ class RSAOntology(axioms: List[OWLLogicalAxiom], datafiles: List[File])
         val ans = filter.answerQuery
         RDFoxUtil
           .submitQuery(data, ans, RSA.Prefixes)
-          .map(new ConjunctiveQueryAnswers(query.bcq, query.variables, _))
+          .map(new ConjunctiveQueryAnswers(query, query.variables, _))
           .get
       }
 
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxUtil.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxUtil.scala
index 3d67270..620d2dd 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxUtil.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxUtil.scala
@@ -41,6 +41,7 @@ import tech.oxfordsemantic.jrdfox.logic.expression.{
   Term
 }
 import tech.oxfordsemantic.jrdfox.logic.sparql.statement.SelectQuery
+import uk.ac.ox.cs.rsacomb.sparql.ConjunctiveQuery
 import uk.ac.ox.cs.rsacomb.suffix.Nth
 import uk.ac.ox.cs.rsacomb.util.Logger
 
@@ -177,15 +178,6 @@ object RDFoxUtil {
   def materialize(data: DataStoreConnection): Unit =
     Logger.timed(data.updateMaterialization(), "Materialization", Logger.DEBUG)
 
-  /** Load SPARQL query from file. */
-  def loadQueryFromFile(file: File): String = {
-    val source = io.Source.fromFile(file)
-    val query = source.getLines mkString "\n"
-    Logger print s"Loaded query:\n$query"
-    source.close()
-    query
-  }
-
   /** Export data in `text/turtle`.
     *
     * @param data datastore connection from which to export data.
@@ -206,6 +198,46 @@ object RDFoxUtil {
     )
   }
 
+  /** Load SPARQL queries from file.
+    *
+    * The file can list multiple queries, each preceeded with a
+    * single line containing "#^[Query<id>]" where "<id>" is a number.
+    * Empty lines are ignored.
+    *
+    * @note if a query is not recognized as a [[SelectQuery]] by RDFox
+    * it is discarded.
+    *
+    * @param file file containing a list of conjunctive queries.
+    * @param prefixes additional prefixes for the query. It defaults to
+    * an empty set.
+    *
+    * @return a list of [[tech.oxfordsemantic.jrdfox.logic.sparql.statement.SelectQuery SelectQuery]] queries.
+    */
+  def loadQueriesFromFile(
+      file: File,
+      prefixes: Prefixes = new Prefixes()
+  ): List[ConjunctiveQuery] = {
+    val source = io.Source.fromFile(file)
+    val queries = source.getLines
+      .map(_.trim.filter(_ >= ' '))
+      .filterNot(_ == "")
+      .foldRight((List.empty[List[String]], List.empty[String])) {
+        case (line, (acc, query)) => {
+          if ("^#\\^\\[Query\\d+\\]$".r.matches(line))
+            (query :: acc, List.empty)
+          else
+            (acc, line :: query)
+        }
+      }
+      ._1
+      .map(_.mkString(" "))
+      .map(ConjunctiveQuery.parse(_, prefixes))
+      .collect { case Some(q) => q }
+    Logger print s"Loaded ${queries.length} queries from ${file.getAbsolutePath}"
+    source.close()
+    queries
+  }
+
   /** Parse a SELECT query from a string in SPARQL format.
     *
     * @param query the string containing the SPARQL query