Added the ability for Queue functions like mkdirs to override if they are done or not.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4458 348d0f76-0448-11de-a6fe-93d51630548a

scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala

@@ -12,11 +12,11 @@ class FunctionEdge(var function: QFunction) extends QEdge {
   var runner: JobRunner =_
 
   private var currentStatus = {
-    val doneOutputs = function.doneOutputs
-    val failOutputs = function.failOutputs
-    if (failOutputs.exists(_.exists))
+    val isDone = function.isDone
+    val isFail = function.isFail
+    if (isFail.isDefined && isFail.get)
       RunnerStatus.FAILED
-    else if (doneOutputs.size > 0 && doneOutputs.forall(_.exists))
+    else if (isDone.isDefined && isDone.get)
       RunnerStatus.DONE
     else
       RunnerStatus.PENDING

scala/src/org/broadinstitute/sting/queue/function/QFunction.scala

@@ -34,6 +34,30 @@ trait QFunction {
    */
   def dotString = ""
 
+  /**
+   * Returns true if the function is done, false if it's
+   * not done and None if the done status is unknown.
+   */
+  def isDone = {
+    val files = doneOutputs
+    if (files.size == 0)
+      None
+    else
+      Some(files.forall(_.exists))
+  }
+
+  /**
+   * Returns true if the function has failed, false if it
+   * has not failed and None if the fail status is unknown.
+   */
+  def isFail = {
+    val files = failOutputs
+    if (files.size == 0)
+      None
+    else
+      Some(files.exists(_.exists))
+  }
+
   /**
    * Returns true if the file should be used for status output.
    * @return true if the file should be used for status output.

scala/src/org/broadinstitute/sting/queue/function/scattergather/CreateTempDirsFunction.scala

@@ -19,5 +19,7 @@ class CreateTempDirsFunction extends InProcessFunction {
 
   override def useStatusOutput(file: File) = false
 
+  override def isDone = Some(tempDirectories.forall(_.exists))
+
   def run() = tempDirectories.foreach(_.mkdirs)
 }