Update general argument parsing

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala

@@ -6,30 +6,39 @@ import org.apache.log4j.Logger
 import org.apache.log4j.WriterAppender
 import org.apache.log4j.helpers.DateLayout
 import org.apache.log4j.spi.LoggingEvent
-import java.text.DateFormat
+import java.io.File
 
 trait ToolCommand extends MainCommand {
   abstract class AbstractArgs {
   }
   
-  abstract class AbstractOptParser extends scopt.OptionParser[Args](getClass.getSimpleName) {
-    head(getClass.getSimpleName)
-    opt[String]('l', "log") foreach { x =>
+  abstract class AbstractOptParser extends scopt.OptionParser[Args](commandName) {
+    opt[Unit]("log_nostderr") foreach { _ =>
+      logger.removeAppender(stderrAppender) } text("No output to stderr")
+    opt[File]("log_file") foreach { x =>
+      logger.addAppender(new WriterAppender(logLayout, new java.io.PrintStream(x))) } text("Log file") valueName("<file>")
+    opt[String]('l', "log_level") foreach { x =>
         x.toLowerCase match {
           case "debug" => logger.setLevel(org.apache.log4j.Level.DEBUG)
           case "info" => logger.setLevel(org.apache.log4j.Level.INFO)
           case "warn" => logger.setLevel(org.apache.log4j.Level.WARN)
           case "error" => logger.setLevel(org.apache.log4j.Level.ERROR)
           case _ =>
-        } } text("Log level") // TODO: add Enum to validation
+        } } text("Log level") validate { x => x match {
+            case "debug" | "info" | "warn" | "error" => success
+            case _ => failure("Log level must be <debug/info/warn/error>")
+          }
+        }
+    opt[Unit]('h', "help") foreach { _ =>
+      System.err.println(this.usage); sys.exit(1)} text("Print usage")
   }
   
   type Args <: AbstractArgs
   type OptParser <: AbstractOptParser
-   
-  protected val logger = Logger.getLogger(this.getClass.getSimpleName.stripSuffix("$"))
-  logger.setLevel(org.apache.log4j.Level.INFO)
-  logger.addAppender(new WriterAppender(new DateLayout() {
+  
+  protected val logger = Logger.getLogger(commandName)
+  
+  private val logLayout = new DateLayout() {
         val ignoresThrowable = false
         def format(event:org.apache.log4j.spi.LoggingEvent): String = {
           val calendar: Calendar = Calendar.getInstance
@@ -40,5 +49,8 @@ trait ToolCommand extends MainCommand {
           while (logLevel.size < 6) logLevel += " "
           logLevel + " [" + formattedDate + "] [" + event.getLoggerName + "] " + event.getMessage + "\n"
         }
-      }, sys.process.stderr))
+    }
+  private val stderrAppender = new WriterAppender(logLayout, sys.process.stderr)
+  logger.setLevel(org.apache.log4j.Level.INFO)
+  logger.addAppender(stderrAppender)
 }
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