Refactor code

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

 package nl.lumc.sasc.biopet.core
 
-import nl.lumc.sasc.biopet.core.apps.WipeReads
-import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
-import nl.lumc.sasc.biopet.pipelines.basty.Basty
-import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
-import nl.lumc.sasc.biopet.pipelines.gatk.GatkBenchmarkGenotyping
-import nl.lumc.sasc.biopet.pipelines.gatk.GatkGenotyping
-import nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline
-import nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantRecalibration
-import nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling
-import nl.lumc.sasc.biopet.pipelines.gatk.GatkVcfSampleCompare
-import nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap
-import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-import nl.lumc.sasc.biopet.pipelines.sage.Sage
-
 object BiopetExecutable {
 
-  val pipelines: List[MainCommand] = List(
-    Flexiprep,
-    Mapping,
-    Gentrap,
-    BamMetrics,
-    GatkBenchmarkGenotyping,
-    GatkGenotyping,
-    GatkVariantcalling,
-    GatkPipeline,
-    GatkVariantRecalibration,
-    GatkVcfSampleCompare,
-    Sage,
-    Basty)
-
-  val tools: List[MainCommand] = List(
-    WipeReads)
-
+  val modules: Map[String, List[MainCommand]] = Map(
+    "pipeline" -> List(
+      nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep,
+      nl.lumc.sasc.biopet.pipelines.mapping.Mapping,
+      nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap,
+      nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics,
+      nl.lumc.sasc.biopet.pipelines.gatk.GatkBenchmarkGenotyping,
+      nl.lumc.sasc.biopet.pipelines.gatk.GatkGenotyping,
+      nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling,
+      nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline,
+      nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantRecalibration,
+      nl.lumc.sasc.biopet.pipelines.gatk.GatkVcfSampleCompare,
+      nl.lumc.sasc.biopet.pipelines.sage.Sage,
+      nl.lumc.sasc.biopet.pipelines.basty.Basty),
+    "tool" -> List(
+      nl.lumc.sasc.biopet.core.apps.WipeReads)
+  )
+  
   /**
    * @param args the command line arguments
    */
   def main(args: Array[String]): Unit = {
 
     def toBulletedList(m: List[MainCommand], kind: String = "", bullet: String = "-") =
-      "Available %s:\n  ".format(kind) + bullet + " " + m.map(x => x.name).sorted.mkString("\n  " + bullet + " ")
-
-    lazy val pipelineList: String = toBulletedList(pipelines, "pipelines")
-
-    lazy val toolList: String = toBulletedList(tools, "tools")
-
-    lazy val addendum: String =
-      """Questions or comments? Email sasc@lumc.nl or check out the project page at https://git.lumc.nl/biopet/biopet.git""".stripMargin
-
-    lazy val baseUsage: String =
+      "Available %ss:\n  ".format(kind) + bullet + " " + m.map(x => x.name).sorted.mkString("\n  " + bullet + " ")
+
+    def usage(module:String = null): String = {
+      if (module != null) checkModule(module)
+      val usage: String = {
+        val set = if (module == null) modules.keySet else Set(module)
+        val u = for (m <- set) yield toBulletedList(modules(m), m)
+        u.mkString("\n\n")
+      }
       """
-        |Usage: java -jar BiopetFramework.jar {pipeline,tool} {pipeline/tool name} {pipeline/tool-specific options}
+        |Usage: java -jar BiopetFramework.jar {%s} <name> [args]
         |
         |%s
         |
-        |%s
-      """.stripMargin.format("%s", addendum)
-
-    lazy val mainUsage: String =
-      baseUsage.format(pipelineList + "\n\n" + toolList)
-
-    lazy val pipelineUsage: String = baseUsage
-      .replaceFirst("""\{pipeline,tool\}""", "pipeline")
-      .replace("""pipeline/tool""", "pipeline")
-      .format(pipelineList)
-
-    lazy val toolUsage: String = baseUsage
-      .replaceFirst("""\{pipeline,tool\}""", "tool")
-      .replace("""pipeline/tool""", "tool")
-      .format(toolList)
-
-    if (args.isEmpty) {
-      System.err.println(mainUsage)
-      System.exit(1)
+        |Questions or comments? Email sasc@lumc.nl or check out the project page at https://git.lumc.nl/biopet/biopet.git
+      """.stripMargin.format(modules.keys.mkString(","),usage)
     }
 
-    def retrieveCommand(q: String, cl: List[MainCommand]): Option[MainCommand] =
-      cl match {
-        case head :: tail if head.name.toLowerCase == q   => Some(head)
-        case Nil                                          => None
-        case head :: tail                                 => retrieveCommand(q, tail)
+    def checkModule(module:String) {
+      if (!modules.contains(module)) {
+          System.err.println(s"ERROR: module '$module' does not exist\n" + usage())
+          System.exit(1)
       }
-
-    args match {
-      case Array("pipeline", pipelineName, pipelineArgs @ _*) =>
-        retrieveCommand(pipelineName.toLowerCase, pipelines) match {
-          case Some(pipeline)  =>
-            pipeline.main(pipelineArgs.toArray)
-            System.exit(0)
-          case None            =>
-            System.err.println(s"ERROR: pipeline '$pipelineName' does not exist")
-            System.err.println(pipelineUsage)
-            System.exit(1)
-        }
-      case Array("pipeline") =>
-        System.err.println(pipelineUsage)
-        System.exit(1)
-      case Array("tool", toolName, toolArgs @ _*) =>
-        retrieveCommand(toolName.toLowerCase, tools) match {
-          case Some(tool)  =>
-            tool.main(toolArgs.toArray)
-            System.exit(0)
-          case None            =>
-            System.err.println(s"ERROR: tool '$toolName' does not exist")
-            System.err.println(toolUsage)
-            System.exit(1)
-        }
-      case Array("tool") =>
-        System.err.println(toolUsage)
-        System.exit(1)
-      case _ =>
-        println(mainUsage)
+    }
+    
+    def getCommand(module:String, name:String) : MainCommand = {
+      checkModule(module)
+      val command = modules(module).find(p => p.name.toLowerCase == name.toLowerCase)
+      if (command == None) {
+        System.err.println(s"ERROR: command '$name' does not exist in module '$module'\n" + usage(module))
         System.exit(1)
+      }
+      return command.get
+    }
+    
+    args match {
+      case Array(module, name, passArgs @ _*) => {
+          getCommand(module, name).main(passArgs.toArray)
+      }
+      case Array(module) => {
+          System.err.println(usage(module))
+          System.exit(1)
+      }
+      case _ => {
+          System.err.println(usage())
+          System.exit(1)
+      }
     }
   }
 }