Merge branch 'patch-rscript' into 'develop'

Patch rscript

See merge request !156

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala

@@ -18,82 +18,65 @@ package nl.lumc.sasc.biopet.extensions
 import java.io.{ FileOutputStream, File }
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.Input
-
-import scala.collection.mutable.ListBuffer
+import scala.sys.process._
 
 /**
  * Created by wyleung on 17-2-15.
  */
 trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
-  /**
-   * Will initially handle Cluster supported commands
-   *
-   */
-  // TODO: write support for running with InProcesFunction
 
-  @Input(doc = "R script", required = false)
-  protected var script: File = _
-  protected var scriptName: String = _
-  protected var arguments: ListBuffer[String] = ListBuffer()
-  override val defaultCoreMemory = 2.0
+  protected var script: File
 
-  executable = config("exe", default = "Rscript", submodule = "R")
+  executable = config("exe", default = "Rscript", submodule = "Rscript")
 
-  /**
-   * Adding arguments in order
-   *
-   * @param argName
-   * @param argValue
-   * @param dash , is the dashsign a - or -- ?
-   * @param sep using a space or "=" to specify the "connector" between argName and argValue
-   */
-  def addArgument(argName: String, argValue: String, dash: String = "-", sep: String = " ") = {
-    arguments += "%s%s%s%s".format(dash, argName, sep, argValue)
-  }
-  def addPositionalArgument(argValue: String, dash: String = "-", sep: String = " ") = {
-    arguments += "%s".format(argValue)
+  override def beforeGraph: Unit = {
+    checkScript()
   }
 
   /**
-   * Set the Rscript to run
-   *
-   * @param filename RScript file location
+   * If script not exist in file system it try to copy it from the jar
+   * @param local if true it use File.createTempFile instead of ".queue/tmp/"
    */
-  def setScript(filename: String): Unit = {
-    val f: File = new File(filename)
-    f.getAbsoluteFile.exists() match {
-      case true => {
-        script = f
-        scriptName = f.getName
+  protected def checkScript(local: Boolean = false): Unit = {
+    if (script.exists()) {
+      script = script.getAbsoluteFile
+    } else {
+      val rScript: File = {
+        if (local) File.createTempFile(script.getName, ".R")
+        else new File(".queue/tmp/" + script)
       }
-      case false => setScript(f, "")
-    }
+      if (!rScript.getParentFile.exists) rScript.getParentFile.mkdirs
 
+      val is = getClass.getResourceAsStream(script.getPath)
+      val os = new FileOutputStream(rScript)
+
+      org.apache.commons.io.IOUtils.copy(is, os)
+      os.close()
+
+      script = rScript
+    }
   }
 
   /**
-   * Gets the R-script from within Biopet
-   *
-   * throws ResourceNotFound if script doesn't exist
+   * Execute rscript on local system
+   * @param logger How to handle stdout and stderr
    */
-  def setScript(filename: File, subpackage: String): Unit = {
-    val RScript: File = new File(".queue/tmp/" + subpackage + filename)
-    if (!RScript.getParentFile.exists) RScript.getParentFile.mkdirs
-
-    val is = getClass.getResourceAsStream(subpackage + RScript.getName)
-    val os = new FileOutputStream(RScript)
+  def runLocal(logger: ProcessLogger): Unit = {
+    checkScript(local = true)
 
-    org.apache.commons.io.IOUtils.copy(is, os)
-    os.close()
+    Process(cmdLine).run(logger)
+  }
 
-    script = RScript
-    scriptName = RScript.getName
+  /**
+   * Execute rscript on local system
+   * Stdout and stderr will go to biopet logger
+   */
+  def runLocal(): Unit = {
+    runLocal(ProcessLogger(logger.info(_)))
   }
 
-  override def cmdLine: String = {
+  def cmdLine: String = {
     required(executable) +
-      required(script) +
-      arguments.mkString(" ")
+      required(script)
   }
 }