Assign queries integer identifier

The ID needs to be specified at creation time or in a query file
preceeding the query with the syntax

```
^[Query<id>]
```

where `<id>` is the id of the query.

2 files changed, 14 insertions, 12 deletions

diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/sparql/ConjunctiveQuery.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/sparql/ConjunctiveQuery.scala
index 105f425..693a9af 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/sparql/ConjunctiveQuery.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/sparql/ConjunctiveQuery.scala
@@ -32,14 +32,12 @@ import uk.ac.ox.cs.rsacomb.util.RDFoxUtil
 /** Factory for [[uk.ac.ox.cs.rsacomb.sparql.ConjunctiveQuery]]. */
 object ConjunctiveQuery {
 
-  private var idCounter: Int = 0;
-
   /** Creates a new ConjunctiveQuery instance.
     *
     * @param query `SelectQuery` instance representing the actual query
     */
-  def apply(query: SelectQuery): ConjunctiveQuery =
-    new ConjunctiveQuery({ idCounter += 1; idCounter }, query)
+  def apply(id: Int, query: SelectQuery): ConjunctiveQuery =
+    new ConjunctiveQuery(id, query)
 
   /** Creates a new ConjunctiveQuery from a query string
     *
@@ -50,10 +48,11 @@ object ConjunctiveQuery {
     *         input query represents one, None is returned otherwise.
     */
   def parse(
+      id: Int,
       query: String,
       prefixes: Prefixes = new Prefixes()
   ): Option[ConjunctiveQuery] =
-    RDFoxUtil.parseSelectQuery(query, prefixes).map(ConjunctiveQuery(_))
+    RDFoxUtil.parseSelectQuery(query, prefixes).map(ConjunctiveQuery(id, _))
 
 }
 
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 aa501cd..46f1160 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
@@ -243,21 +243,24 @@ object RDFoxUtil {
       path: os.Path,
       prefixes: Prefixes = new Prefixes()
   ): List[ConjunctiveQuery] = {
+    val pattern = raw"\^\[Query(\d+)\]".r
     val queries = os.read
       .lines(path)
       .map(_.trim.filter(_ >= ' '))
       .filterNot(_ == "")
-      .foldRight((List.empty[List[String]], List.empty[String])) {
+      .foldRight((List.empty[Option[ConjunctiveQuery]], List.empty[String])) {
         case (line, (acc, query)) => {
-          if ("^#\\^\\[Query\\d+\\]$".r.matches(line))
-            (query :: acc, List.empty)
-          else
-            (acc, line :: query)
+          line match {
+            case pattern(id) => {
+              val cq =
+                ConjunctiveQuery.parse(id.toInt, query.mkString(" "), prefixes)
+              (cq :: acc, List.empty)
+            }
+            case _ => (acc, line :: query)
+          }
         }
       }
       ._1
-      .map(_.mkString(" "))
-      .map(ConjunctiveQuery.parse(_, prefixes))
       .collect { case Some(q) => q }
     Logger print s"Loaded ${queries.length} queries from $path"
     queries