Introduce a better system to handle command line input

2 files changed, 160 insertions, 60 deletions

diff --git a/run_tests.bash b/run_tests.bash
index 17cbf01..92e0223 100755
--- a/run_tests.bash
+++ b/run_tests.bash
@@ -32,6 +32,8 @@ print_help() {
     echo "    -q | --queries <path>:"
     echo "        path to a folder containing SPARQL query files to be"
     echo "        executed against the ontology and data."
+    echo "    -j | --jar <path>:"
+    echo "        path to the fat jar to be executed."
     echo "    -p | --prefix <path>:"
     echo "        provides a folder to prefix to the output files."
     echo "        Defaults to './results'."
@@ -43,6 +45,7 @@ print_help() {
 ONTOLOGY=""
 DATA=""
 QUERIES=""
+JAR=""
 PREFIX="./results"
 
 while [[ $# -gt 0 ]]
@@ -72,6 +75,14 @@ do
                 print_help && \
                 exit 2
             ;;
+        -j|--jar)
+            shift
+            JAR="$1"
+            [ ! -r "$JAR" ] && \
+                msg_error "Unable to read jar '$JAR'" && \
+                print_help && \
+                exit 2
+            ;;
         -p|--prefix)
             shift
             PREFIX="$1"
@@ -104,12 +115,17 @@ done
     print_help && \
     exit 3
 
+[ -z "$JAR" ] && \
+    msg_error "Use -j | --jar to provide a jar file" && \
+    print_help && \
+    exit 3
 
 DATAS=`\ls $DATA/*`
 mkdir -p "$PREFIX"
-for QUERY in "$QUERIES"/*.sparql
+for QUERY in "$QUERIES"/query*.sparql
 do
-    sbt "run $QUERY $ONTOLOGY $DATAS" 2>&1 | tee "$PREFIX/answers_$(basename $QUERY .sparql).txt"
+    #sbt "run $QUERY $ONTOLOGY $DATAS" 2>&1 | tee "$PREFIX/answers_$(basename $QUERY .sparql).txt"
+    java -cp ./lib/JRDFox.jar:"$JAR" uk.ac.ox.cs.rsacomb.RSAComb -q "$QUERY" "$ONTOLOGY" "$DATA"/* 2>&1 | tee "$PREFIX/answers_$(basename $QUERY .sparql).txt"
 done
 
 OUTPUT="$PREFIX/results.csv"
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 bf96a31..909cfdd 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 +10,106 @@ import tech.oxfordsemantic.jrdfox.logic.sparql.statement.SelectQuery
 import util.{Logger, RDFoxUtil, RSA}
 import sparql.ConjunctiveQuery
 
+case class RSAOption[+T](opt: T) {
+  def get[T]: T = opt.asInstanceOf[T]
+}
+
+object RSAConfig {
+  type Config = Map[Symbol, RSAOption[Any]]
+
+  private implicit def toRSAOption[T](opt: T) = RSAOption[T](opt)
+
+  /** Help message */
+  private val help: String = """
+  rsacomb - combined approach for CQ answering for RSA ontologies.
+
+  USAGE
+    rsacomb [OPTIONS] <ontology> [<data> ...]
+
+      -h | -? | --help
+          print this help message
+
+      --rsacheck-only
+          only perform the RSA check without performing any query answering.
+
+      -q <file> | --query <file>
+          path to a file containing a single SPARQL query
+
+      <ontology>
+          file containing the ontology
+
+      <data>
+          one or more data files
+
+  """
+
+  /** Default config values */
+  private val default = Map(
+    'rsacheckonly -> RSAOption[Boolean](false)
+  )
+
+  /** Utility to exit the program with a custom message on stderr.
+    *
+    * The program will exit with error code 1 after printing the help
+    * message.
+    *
+    * @param msg message printed to stderr.
+    */
+  private def exit(msg: String): Nothing = {
+    System.err.println(msg)
+    System.err.println()
+    System.err.println(help)
+    sys.exit(1)
+  }
+
+  /** Parse arguments with default options
+    *
+    * @param args arguments list
+    */
+  def parse(args: List[String]): Config = parse(args, default)
+
+  /** Parse arguments
+    *
+    * @param args arguments list
+    * @param config default configuration
+    */
+  def parse(args: List[String], config: Config): Config = {
+    args match {
+      case flag @ ("-h" | "-?" | "--help") :: _ => {
+        println(help)
+        sys.exit(0)
+      }
+      case "--rsacheck-only" :: tail =>
+        parse(tail, config ++ Map('rsacheckonly -> true))
+      case flag @ ("-q" | "--query") :: _query :: tail => {
+        val query = new File(_query)
+        if (!query.isFile)
+          exit(s"'$query' is not a valid filename.")
+        parse(tail, config ++ Map('query -> query))
+      }
+      case _ontology :: _data => {
+        val ontology = new File(_ontology)
+        val data = _data.map(new File(_))
+        (ontology :: data) foreach { (file) =>
+          if (!file.isFile)
+            exit(s"'$file' is not a valid filename.")
+        }
+        finalise(config ++ Map('ontology -> ontology, 'data -> data))
+      }
+      case a => exit(s"Invalid sequence of arguments '${a.mkString(" ")}'.")
+    }
+  }
+
+  /** Perform final checks on parsed options */
+  private def finalise(config: Config): Config = {
+    // Query file is mandatory unless only the RSA check is required.
+    if (!config('rsacheckonly).get[Boolean] && !config.contains('query))
+      exit(s"Query file was not provided.")
+
+    config
+  }
+}
+
 /** Entry point of the program.
   *
   * The executable expects a SPARQL query and a non-empty sequence of
@@ -24,72 +124,56 @@ import sparql.ConjunctiveQuery
   */
 object RSAComb extends App {
 
-  val help: String = """
-  rsacomb - combined approach for CQ answering for RSA ontologies.
-
-  USAGE
-    rsacomb <query> <ontology> [...]
-
-  where
-    - query: path to a file containing a single SPARQL query
-    - ontology: one or more ontology files
-
-  """
-
-  if (args.length < 2) {
-    println(help)
-    sys.exit;
-  }
-
-  val queryPath = new File(args(0))
-  val ontoPaths = args.drop(1).map(new File(_))
-
-  if (!queryPath.isFile || !ontoPaths.forall(_.isFile)) {
-    println("The provided arguments are not regular files.\n\n")
-    println(help)
-    sys.exit;
-  }
+  val config = RSAConfig.parse(args.toList)
 
-  val ontology = RSAOntology(ontoPaths: _*)
+  val ontology =
+    RSAOntology(config('ontology).get[File], config('data).get[List[File]]: _*)
   if (ontology.isRSA) {
 
     Logger print "Ontology is RSA!"
 
-    val query = RDFoxUtil.loadQueryFromFile(queryPath.getAbsoluteFile)
-
-    ConjunctiveQuery.parse(query) match {
-      case Some(query) => {
-        val answers = ontology ask query
-        Logger.print(s"$answers", Logger.QUIET)
-        Logger print s"Number of answers: ${answers.length} (${answers.lengthWithMultiplicity})"
-
-        /* Additional DEBUG information */
-        if (Logger.level >= Logger.DEBUG) {
-          /* Unfiltered rules */
-          val unfiltered = ontology askUnfiltered query
-          unfiltered map { u =>
-            Logger print s"Number of unfiltered answers: ${u.length} (${u.map(_._1).sum})."
-
-            /* Spurious answers */
-            val spurious = {
-              val variables = query.variables.length
-              val sp = RDFoxUtil.buildDescriptionQuery("SP", variables)
-              ontology.queryDataStore(query, sp, RSA.Prefixes)
-            }
-            spurious map { s =>
-              Logger print s"Number of spurious answers: ${s.length} (${s.map(_._1).sum})"
-
-              /* Spurious/unfiltered percentage */
-              val perc =
-                if (u.length > 0) (s.length / u.length.toFloat) * 100 else 0
-              Logger print s"Percentage of spurious answers: $perc%"
-            }
-          }
+    if (!config('rsacheckonly).get[Boolean]) {
+      val query =
+        RDFoxUtil.loadQueryFromFile(config('query).get[File].getAbsoluteFile)
+
+      ConjunctiveQuery.parse(query) match {
+        case Some(query) => {
+          val answers = ontology ask query
+          Logger.print(s"$answers", Logger.QUIET)
+          Logger print s"Number of answers: ${answers.length} (${answers.lengthWithMultiplicity})"
+
+          //    /* Additional DEBUG information */
+          //    if (Logger.level >= Logger.DEBUG) {
+          //      /* Unfiltered rules */
+          //      val unfiltered = ontology askUnfiltered query
+          //      unfiltered map { u =>
+          //        Logger print s"Number of unfiltered answers: ${u.length} (${u.map(_._1).sum})."
+
+          //        /* Spurious answers */
+          //        val spurious = {
+          //          val variables = query.variables.length
+          //          val sp = RDFoxUtil.buildDescriptionQuery("SP", variables)
+          //          ontology.queryDataStore(query, sp, RSA.Prefixes)
+          //        }
+          //        spurious map { s =>
+          //          Logger print s"Number of spurious answers: ${s.length} (${s.map(_._1).sum})"
+
+          //          /* Spurious/unfiltered percentage */
+          //          val perc =
+          //            if (u.length > 0) (s.length / u.length.toFloat) * 100 else 0
+          //          Logger print s"Percentage of spurious answers: $perc%"
+          //        }
+          //      }
+          //    }
         }
+        case None =>
+          throw new RuntimeException("Submitted query is not conjunctive")
       }
-      case None =>
-        throw new RuntimeException("Submitted query is not conjunctive")
     }
 
+  } else {
+
+    Logger print "Ontology is not RSA!"
+
   }
 }