Added test on pipeline name

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala

@@ -31,9 +31,11 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
    * Gets location of compiled class of pipeline
    * @return path from classPath to class file
    */
-  def pipeline = "/" + getClass.getName.stripSuffix("$").replaceAll("\\.", "/") + ".class"
+  def pipeline = "/" + getClass.getName.takeWhile(_ != '$').replaceAll("\\.", "/") + ".class"
 
-  def pipelineName = getClass.getSimpleName.takeWhile(_ != '$').toLowerCase
+  def pipelineName = getClass.getName.takeWhile(_ != '$').split("\\.").last.toLowerCase
+
+  protected val globalConfig = Config.global
 
   /** Class can be used directly from java with -cp option */
   def main(args: Array[String]): Unit = {
@@ -41,7 +43,7 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
     for (t <- 0 until argsSize) {
       if (args(t) == "-config" || args(t) == "--config_file") {
         if (args.length <= (t + 1)) throw new IllegalStateException("-config needs a value: <file>")
-        Config.global.loadConfigFile(new File(args(t + 1)))
+        globalConfig.loadConfigFile(new File(args(t + 1)))
       }
 
       if (args(t) == "-cv" || args(t) == "--config_value") {
@@ -52,7 +54,7 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
         val p = v(0).split(":")
         val key = p.last
         val path = p.dropRight(1).toList
-        Config.global.addValue(key, value, path)
+        globalConfig.addValue(key, value, path)
       }
 
       if (args(t) == "--logging_level" || args(t) == "-l") {
@@ -74,8 +76,8 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
 
     val logFile = {
       val pipelineName = this.getClass.getSimpleName.toLowerCase.split("""\$""").head
-      val pipelineConfig = Config.global.map.getOrElse(pipelineName, Map()).asInstanceOf[Map[String, Any]]
-      val pipelineOutputDir = new File(Config.global.map.getOrElse("output_dir", pipelineConfig.getOrElse("output_dir", "./")).toString)
+      val pipelineConfig = globalConfig.map.getOrElse(pipelineName, Map()).asInstanceOf[Map[String, Any]]
+      val pipelineOutputDir = new File(globalConfig.map.getOrElse("output_dir", pipelineConfig.getOrElse("output_dir", "./")).toString)
       val logDir: File = new File(pipelineOutputDir, ".log")
       logDir.mkdirs()
       new File(logDir, "biopet." + BiopetQCommandLine.timestamp + ".log")
@@ -91,7 +93,7 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
       argv ++= List("--log_to_file", new File(logFile.getParentFile, "queue." + BiopetQCommandLine.timestamp + ".log").getAbsolutePath)
     }
     if (!args.contains("-retry") && !args.contains("--retry_failed")) {
-      val retry: Int = Config.global(pipelineName, Nil, "retry", default = 5)
+      val retry: Int = globalConfig(pipelineName, Nil, "retry", default = 5)
       logger.info("No retry flag found, ")
       argv ++= List("-retry", retry.toString)
     }

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala

+package nl.lumc.sasc.biopet.core
+
+import nl.lumc.sasc.biopet.utils.config.Config
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+  * Created by pjvanthof on 17/11/15.
+  */
+class PipelineCommandTest extends TestNGSuite with Matchers {
+  @Test
+  def testPipelineCommand: Unit = {
+    val pipeline = new PipelineCommand {
+      override val globalConfig = new Config(Map())
+      def getConfig = globalConfig
+    }
+
+    pipeline.pipelineName shouldBe this.getClass.getSimpleName.toLowerCase
+    pipeline.pipeline shouldBe s"/${this.getClass.getName.stripSuffix("$").replaceAll("\\.", "/")}.class"
+
+    // Config should be emty if the main method is not yet touched
+    pipeline.getConfig.map shouldBe empty
+
+    //TODO: Main method testing
+  }
+}