Rework CLI configs

2 files changed, 164 insertions, 124 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 24bda1f..121c65f 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
@@ -19,7 +19,6 @@ package uk.ac.ox.cs.rsacomb
 import java.io.{File, PrintWriter}
 import java.nio.file.{Path, Paths, InvalidPathException}
 import java.util.HashMap
-import scala.collection.mutable.Map
 import scala.collection.JavaConverters._
 import tech.oxfordsemantic.jrdfox.client.UpdateType
 import tech.oxfordsemantic.jrdfox.logic.expression.{IRI, Term}
@@ -32,129 +31,15 @@ import uk.ac.ox.cs.rsacomb.ontology.Ontology
 import uk.ac.ox.cs.rsacomb.converter.Normalizer
 import uk.ac.ox.cs.rsacomb.approximation.{Upperbound, Lowerbound}
 
-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
-
-      -l | --logger <level>
-          specify the logger verbosity. Values are: quiet, normal (default),
-          debug, verbose.
-
-      -o | --output <file>
-        path to the output file for the answers to the query (in JSON
-        format)
-
-      -q | --queries <file>
-          path to a file containing a single SPARQL query. If no query
-          is provided, only the approximation to RSA will be performed.
-
-      <ontology>
-          file containing the ontology
-
-      <data>
-          one or more data files
-
-  """
-
-  /** Default config values */
-  private val default: Config = Map.empty
-
-  /** 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)
-  }
-
-  private def getPath(str: String): os.Path =
-    try {
-      os.Path(str, base = os.pwd)
-    } catch {
-      case e: IllegalArgumentException =>
-        exit(s"'$str' is not a well formed path.")
-    }
-
-  /** Parse arguments with default options
-    *
-    * @param args arguments list
-    * @return map of config options
-    */
-  def parse(args: List[String]): Config = parse(args, default)
-
-  /** Parse arguments
-    *
-    * @param args arguments list
-    * @param config default configuration
-    * @return map of config options
-    */
-  def parse(args: List[String], config: Config): Config = {
-    args match {
-      case flag @ ("-h" | "-?" | "--help") :: _ => {
-        println(help)
-        sys.exit(0)
-      }
-      case flag @ ("-l" | "--logger") :: _level :: tail => {
-        val level = _level match {
-          case "quiet"   => Logger.QUIET
-          case "debug"   => Logger.DEBUG
-          case "verbose" => Logger.VERBOSE
-          case _         => Logger.NORMAL
-        }
-        parse(tail, config += ('logger -> level))
-      }
-      case flag @ ("-o" | "--output") :: output :: tail =>
-        parse(tail, config += ('output -> getPath(output)))
-      case flag @ ("-q" | "--queries") :: _query :: tail => {
-        val query = getPath(_query)
-        if (!os.isFile(query))
-          exit(s"'${_query}' is not a valid filename.")
-        parse(tail, config += ('queries -> query))
-      }
-      case _ontology :: _data => {
-        val ontology = getPath(_ontology)
-        val data = _data map getPath
-        (ontology :: data) foreach { (path) =>
-          if (!os.isFile(path))
-            exit(s"'$path' is not a valid filename.")
-        }
-        finalise(config += ('ontology -> ontology) += ('data -> data))
-      }
-      case a => exit(s"Invalid sequence of arguments '${a.mkString(" ")}'.")
-    }
-  }
-
-  /** Perform final checks on parsed options */
-  private def finalise(config: Config): Config = config
-}
-
 /** Main entry point to the program */
 object RSAComb extends App {
 
   /* Command-line options */
   val config = RSAConfig.parse(args.toList)
-  Logger.level = config('logger).get[Logger.Level]
+
+  /* Set logger level */
+  if (config.contains('logger))
+    Logger.level = config('logger).get[Logger.Level]
 
   /* Load original ontology and normalize it */
   val ontology = Ontology(
@@ -177,11 +62,12 @@ object RSAComb extends App {
     val answers = rsa ask queries
 
     /* Write answers to output file */
-    os.write(
-      config('output).get[os.Path],
-      ujson.write(ujson.Arr(answers.map(_.toJSON)), indent = 4),
-      createFolders = true
-    )
+    if (config.contains('answers))
+      os.write(
+        config('answers).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/RSAConfig.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/RSAConfig.scala
new file mode 100644
index 0000000..4d96850
--- /dev/null
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/RSAConfig.scala
@@ -0,0 +1,154 @@
+/*
+ * Copyright 2020, 2021 KRR Oxford
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package uk.ac.ox.cs.rsacomb
+
+import scala.collection.mutable.Map
+import util.Logger
+
+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
+
+      -l | --logger <level>
+          specify the logger verbosity. Values are: quiet, normal (default),
+          debug, verbose.
+
+      -a | --answers <file>
+        path to the output file for the answers to the query (in JSON
+        format)
+
+      -q | --queries <file>
+          path to a file containing a single SPARQL query. If no query
+          is provided, only the approximation to RSA will be performed.
+
+      -o | --ontology <file>
+          ontology file in OWL format.
+
+      -d | --data <file>
+          data files to be used alongside the ontology file. If a
+          directory is provided, all files in the directory (recursively)
+          will be considered.
+
+  """
+
+  /** Default config values */
+  private val default: Config = Map.empty
+
+  /** 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)
+  }
+
+  private def getPath(str: String): os.Path =
+    try {
+      os.Path(str, base = os.pwd)
+    } catch {
+      case e: IllegalArgumentException =>
+        exit(s"'$str' is not a well formed path.")
+    }
+
+  /** Parse arguments with default options
+    *
+    * @param args arguments list
+    * @return map of config options
+    */
+  def parse(args: List[String]): Config = parse(args, default)
+
+  /** Parse arguments
+    *
+    * @param args arguments list
+    * @param config default configuration
+    * @return map of config options
+    */
+  def parse(args: List[String], config: Config): Config = {
+    args match {
+      case Nil => finalise(config)
+      case flag @ ("-h" | "-?" | "--help") :: _ => {
+        println(help)
+        sys.exit(0)
+      }
+      case flag @ ("-l" | "--logger") :: _level :: tail => {
+        val level = _level match {
+          case "quiet"   => Logger.QUIET
+          case "debug"   => Logger.DEBUG
+          case "verbose" => Logger.VERBOSE
+          case _         => Logger.NORMAL
+        }
+        parse(tail, config += ('logger -> level))
+      }
+      case flag @ ("-a" | "--answers") :: answers :: tail =>
+        parse(tail, config += ('answers -> getPath(answers)))
+      case flag @ ("-q" | "--queries") :: _query :: tail => {
+        val query = getPath(_query)
+        if (!os.isFile(query))
+          exit(s"'${_query}' is not a valid filename.")
+        parse(tail, config += ('queries -> query))
+      }
+      case flag @ ("-o" | "--ontology") :: _ontology :: tail => {
+        val ontology = getPath(_ontology)
+        if (!os.isFile(ontology))
+          exit(s"'${_ontology}' is not a valid filename.")
+        parse(tail, config += ('ontology -> ontology))
+      }
+      case flag @ ("-d" | "--data") :: _data :: tail => {
+        val data = getPath(_data)
+        val files =
+          if (os.isFile(data))
+            Seq(data)
+          else if (os.isDir(data))
+            os.walk(data).filter(os.isFile)
+          else
+            exit(s"'${_data}' is not a valid path.")
+        parse(tail, config += ('data -> files))
+      }
+      case a => exit(s"Invalid sequence of arguments '${a.mkString(" ")}'.")
+    }
+  }
+
+  /** Perform final checks on parsed options */
+  private def finalise(config: Config): Config = {
+    if (!config.contains('ontology))
+      exit("The following flag is mandatory: '-o' or '--ontology'.")
+    if (!config.contains('data))
+      config += ('data -> List.empty[os.Path])
+    config
+  }
+}