4 files changed, 51 insertions, 38 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 22b1f76..24bda1f 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
@@ -88,6 +88,14 @@ object RSAConfig {
     sys.exit(1)
   }
 
+  private def getPath(str: String): os.Path =
+    try {
+      os.Path(str, base = os.pwd)
+    } catch {
+      case e: IllegalArgumentException =>
+        exit(s"'$str' is not a well formed path.")
+    }
+
   /** Parse arguments with default options
     *
     * @param args arguments list
@@ -116,26 +124,20 @@ object RSAConfig {
         }
         parse(tail, config += ('logger -> level))
       }
-      case flag @ ("-o" | "--output") :: _output :: tail =>
-        try {
-          val output = Paths.get(_output)
-          parse(tail, config += ('output -> output))
-        } catch {
-          case e: InvalidPathException =>
-            exit(s"'${_output}' is not a valid filename.")
-        }
+      case flag @ ("-o" | "--output") :: output :: tail =>
+        parse(tail, config += ('output -> getPath(output)))
       case flag @ ("-q" | "--queries") :: _query :: tail => {
-        val query = new File(_query)
-        if (!query.isFile)
-          exit(s"'$query' is not a valid filename.")
+        val query = getPath(_query)
+        if (!os.isFile(query))
+          exit(s"'${_query}' is not a valid filename.")
         parse(tail, config += ('queries -> query))
       }
       case _ontology :: _data => {
-        val ontology = new File(_ontology)
-        val data = _data.map(new File(_))
-        (ontology :: data) foreach { (file) =>
-          if (!file.isFile)
-            exit(s"'$file' is not a valid filename.")
+        val ontology = getPath(_ontology)
+        val data = _data map getPath
+        (ontology :: data) foreach { (path) =>
+          if (!os.isFile(path))
+            exit(s"'$path' is not a valid filename.")
         }
         finalise(config += ('ontology -> ontology) += ('data -> data))
       }
@@ -156,8 +158,8 @@ object RSAComb extends App {
 
   /* Load original ontology and normalize it */
   val ontology = Ontology(
-    config('ontology).get[File],
-    config('data).get[List[File]]
+    config('ontology).get[os.Path],
+    config('data).get[List[os.Path]]
   ).normalize(new Normalizer)
 
   //ontology.axioms foreach println
@@ -168,14 +170,18 @@ object RSAComb extends App {
 
   if (config contains 'queries) {
     val queries =
-      RDFoxUtil.loadQueriesFromFile(config('queries).get[File].getAbsoluteFile)
+      RDFoxUtil.loadQueriesFromFile(
+        config('queries).get[os.Path]
+      )
 
     val answers = rsa ask queries
 
     /* Write answers to output file */
-    val output = new PrintWriter(config('output).get[Path].toFile)
-    output.write(ujson.write(ujson.Arr(answers.map(_.toJSON)), indent = 4))
-    output.close()
+    os.write(
+      config('output).get[os.Path],
+      ujson.write(ujson.Arr(answers.map(_.toJSON)), indent = 4),
+      createFolders = true
+    )
 
     // Logger.print(s"$answers", Logger.VERBOSE)
     // Logger print s"Number of answers: ${answers.length} (${answers.lengthWithMultiplicity})"
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 275f523..e2b0e2f 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
@@ -123,7 +123,7 @@ object RSAOntology {
 
   def apply(
       axioms: List[OWLLogicalAxiom],
-      datafiles: List[File]
+      datafiles: List[os.Path]
   ): RSAOntology = new RSAOntology(axioms, datafiles)
 
   // def apply(
@@ -191,7 +191,7 @@ object RSAOntology {
   * @param ontology the input OWL2 ontology.
   * @param datafiles additinal data (treated as part of the ABox)
   */
-class RSAOntology(axioms: List[OWLLogicalAxiom], datafiles: List[File])
+class RSAOntology(axioms: List[OWLLogicalAxiom], datafiles: List[os.Path])
     extends Ontology(axioms, datafiles) {
 
   /** Simplify conversion between OWLAPI and RDFox concepts */
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/ontology/Ontology.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/ontology/Ontology.scala
index 8d46646..9d80dd5 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/ontology/Ontology.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/ontology/Ontology.scala
@@ -77,7 +77,7 @@ object Ontology {
     */
   def dependencyGraph(
       axioms: List[OWLLogicalAxiom],
-      datafiles: List[File],
+      datafiles: List[os.Path],
       unsafe: List[OWLObjectPropertyExpression]
   ): DependencyGraph = {
 
@@ -167,10 +167,10 @@ object Ontology {
     (graph, nodemap)
   }
 
-  def apply(axioms: List[OWLLogicalAxiom], datafiles: List[File]): Ontology =
+  def apply(axioms: List[OWLLogicalAxiom], datafiles: List[os.Path]): Ontology =
     new Ontology(axioms, datafiles)
 
-  def apply(ontology: OWLOntology, datafiles: List[File]): Ontology = {
+  def apply(ontology: OWLOntology, datafiles: List[os.Path]): Ontology = {
 
     /** TBox axioms */
     var tbox: List[OWLLogicalAxiom] =
@@ -202,8 +202,8 @@ object Ontology {
     Ontology(abox ::: tbox ::: rbox, datafiles)
   }
 
-  def apply(ontofile: File, datafiles: List[File]): Ontology = {
-    val ontology = manager.loadOntologyFromOntologyDocument(ontofile)
+  def apply(ontofile: os.Path, datafiles: List[os.Path]): Ontology = {
+    val ontology = manager.loadOntologyFromOntologyDocument(ontofile.toIO)
     Ontology(ontology, datafiles)
   }
 
@@ -214,7 +214,10 @@ object Ontology {
   * @param axioms list of axioms (roughly) corresponding to the TBox.
   * @param datafiles files containing ABox data.
   */
-class Ontology(val axioms: List[OWLLogicalAxiom], val datafiles: List[File]) {
+class Ontology(
+    val axioms: List[OWLLogicalAxiom],
+    val datafiles: List[os.Path]
+) {
 
   /** Extend OWLAxiom functionalities */
   import uk.ac.ox.cs.rsacomb.implicits.RSAAxiom._
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 217fa7f..aa501cd 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
@@ -186,10 +186,15 @@ object RDFoxUtil {
     * @param graph named graph where the data should be uploaded
     * @param files sequence of files to upload.
     */
-  def addData(data: DataStoreConnection, graph: IRI, files: File*): Unit =
+  def addData(data: DataStoreConnection, graph: IRI, files: os.Path*): Unit =
     Logger.timed(
-      files.foreach {
-        data.importData(graph.getIRI, UpdateType.ADDITION, RSA.Prefixes, _)
+      files.foreach { path =>
+        data.importData(
+          graph.getIRI,
+          UpdateType.ADDITION,
+          RSA.Prefixes,
+          path.toIO
+        )
       },
       "Loading data files",
       Logger.DEBUG
@@ -235,11 +240,11 @@ object RDFoxUtil {
     * @return a list of [[tech.oxfordsemantic.jrdfox.logic.sparql.statement.SelectQuery SelectQuery]] queries.
     */
   def loadQueriesFromFile(
-      file: File,
+      path: os.Path,
       prefixes: Prefixes = new Prefixes()
   ): List[ConjunctiveQuery] = {
-    val source = io.Source.fromFile(file)
-    val queries = source.getLines
+    val queries = os.read
+      .lines(path)
       .map(_.trim.filter(_ >= ' '))
       .filterNot(_ == "")
       .foldRight((List.empty[List[String]], List.empty[String])) {
@@ -254,8 +259,7 @@ object RDFoxUtil {
       .map(_.mkString(" "))
       .map(ConjunctiveQuery.parse(_, prefixes))
       .collect { case Some(q) => q }
-    Logger print s"Loaded ${queries.length} queries from ${file.getAbsolutePath}"
-    source.close()
+    Logger print s"Loaded ${queries.length} queries from $path"
     queries
   }