Copying jobLimitSeconds to clones.

Some cleanup and refactoring around copying values to clones.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5128 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -8,9 +8,6 @@ import org.broadinstitute.sting.queue.util._
 trait CommandLineFunction extends QFunction with Logging {
   def commandLine: String
 
-  /* Is it a gather function? */
-  var isGather: Boolean = true
-
   /** Upper memory limit */
   var memoryLimit: Option[Int] = None
 
@@ -20,6 +17,24 @@ trait CommandLineFunction extends QFunction with Logging {
   /** Job queue to run the command */
   var jobQueue: String = _
 
+  override def copySettingsTo(function: QFunction) {
+    super.copySettingsTo(function)
+    function match {
+      case commandLineFunction: CommandLineFunction =>
+        if (commandLineFunction.memoryLimit.isEmpty)
+          commandLineFunction.memoryLimit = this.memoryLimit
+
+        if (commandLineFunction.jobProject == null)
+          commandLineFunction.jobProject = this.jobProject
+
+        if (commandLineFunction.jobQueue == null)
+          commandLineFunction.jobQueue = this.jobQueue
+
+        commandLineFunction.jobQueue = this.jobQueue
+      case _ => /* ignore */
+    }
+  }
+
   /**
    * Returns set of directories required to run the command.
    * @return Set of directories required to run the command.
@@ -38,7 +53,7 @@ trait CommandLineFunction extends QFunction with Logging {
     if (jobProject == null)
       jobProject = qSettings.jobProject
 
-    if (memoryLimit.isEmpty && qSettings.memoryLimit.isDefined)
+    if (memoryLimit.isEmpty)
       memoryLimit = qSettings.memoryLimit
 
     super.freezeFieldValues

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

@@ -53,6 +53,29 @@ trait QFunction extends Logging {
    */
   var updateJobRun: PartialFunction[Any,Unit] = null
 
+  /**
+   * If true, unless another unfinished function is dependent on this function,
+   * this function will NOT be run even if the outputs have not been created.
+   */
+  var isIntermediate = false
+
+  /**
+   * Copies settings from this function to another function.
+   * @param function QFunction to copy values to.
+   */
+  def copySettingsTo(function: QFunction) {
+    function.analysisName = this.analysisName
+    function.jobName = this.jobName
+    function.qSettings = this.qSettings
+    function.commandDirectory = this.commandDirectory
+    function.jobTempDir = this.jobTempDir
+    function.addOrder = this.addOrder
+    function.jobLimitSeconds = this.jobLimitSeconds
+    function.jobRestartable = this.jobRestartable
+    function.updateJobRun = this.updateJobRun
+    function.isIntermediate = this.isIntermediate
+  }
+
   /** File to redirect any output.  Defaults to <jobName>.out */
   @Output(doc="File to redirect any output", required=false)
   @Gather(classOf[SimpleTextGatherFunction])
@@ -138,12 +161,6 @@ trait QFunction extends Logging {
   /** The @Argument fields on this CommandLineFunction. */
   def argumentFields = QFunction.classFields(this.functionFieldClass).argumentFields
 
-  /**
-   * If true, unless another unfinished function is dependent on this function,
-   * this function will NOT be run even if the outputs have not been created.
-   */
-  var isIntermediate = false
-  
   /**
    * Returns the class that should be used for looking up fields.
    */

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

@@ -70,7 +70,7 @@ trait ScatterGatherableFunction extends CommandLineFunction {
     val outputFieldsWithValues = this.outputFields.filter(hasFieldValue(_))
 
     // Create the scatter function based on @Scatter
-    syncFunction(scatterFunction)
+    this.copySettingsTo(scatterFunction)
     scatterFunction.addOrder = this.addOrder :+ 1
     scatterFunction.commandDirectory = this.scatterGatherTempDir("scatter")
     scatterFunction.originalInputs = this.inputs
@@ -89,11 +89,10 @@ trait ScatterGatherableFunction extends CommandLineFunction {
     for (gatherField <- outputFieldsWithValues) {
       val gatherFunction = this.newGatherFunction(gatherField)
       val gatherOutput = getFieldFile(gatherField)
-      syncFunction(gatherFunction)
+      this.copySettingsTo(gatherFunction)
       gatherFunction.addOrder = this.addOrder :+ gatherAddOrder
       gatherFunction.commandDirectory = this.scatterGatherTempDir("gather-" + gatherField.field.getName)
       gatherFunction.originalOutput = this.getFieldFile(gatherField)
-      gatherFunction.isIntermediate = this.isIntermediate
       initGatherFunction(gatherFunction, gatherField)
       functions :+= gatherFunction
       gatherFunctions += gatherField -> gatherFunction
@@ -106,11 +105,10 @@ trait ScatterGatherableFunction extends CommandLineFunction {
     for (i <- 1 to numClones) {
       val cloneFunction = this.newCloneFunction()
 
-      syncFunction(cloneFunction)
+      this.copySettingsTo(cloneFunction)
       cloneFunction.originalFunction = this
       cloneFunction.index = i
       cloneFunction.addOrder = this.addOrder :+ (i+1)
-      cloneFunction.memoryLimit = this.memoryLimit
       cloneFunction.isIntermediate = true
 
       // Setup the fields on the clone function, outputting each as a relative file in the sg directory.
@@ -224,23 +222,6 @@ trait ScatterGatherableFunction extends CommandLineFunction {
         this.setupCloneFunction(cloneFunction, index)
   }
 
-  /**
-   * Copies standard values from this function to the just created function.
-   * @param newFunction newly created function.
-   */
-  protected def syncFunction(newFunction: QFunction) = {
-    newFunction.analysisName = this.analysisName
-    newFunction.qSettings = this.qSettings
-    newFunction.jobTempDir = this.jobTempDir
-    newFunction.jobName = this.jobName
-    newFunction match {
-      case newCLFFunction: CommandLineFunction =>
-        newCLFFunction.jobQueue = this.jobQueue
-        newCLFFunction.jobProject = this.jobProject
-      case _ => /* ignore */
-    }
-  }
-
   /**
    * The scatter function.
    */

scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala

@@ -92,7 +92,6 @@ class VariantCalling(attribs: Pipeline,gatkJar: File) {
    */
   private def StandardIndelGenotyper(bam : File, output: File, gather: Boolean) : IndelGenotyperV2 = {
     var ig = StandardIndelGenotyper(bam,output)
-    ig.isGather = gather
     return ig
   }
 
@@ -106,7 +105,6 @@ class VariantCalling(attribs: Pipeline,gatkJar: File) {
     cv.genotypemergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNIQUIFY)
     cv.variantmergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION)
     cv.analysisName = "IndelGenotyper"
-    cv.isGather = true
     cv.priority = (igList.map[String,List[String]](ig => swapExt(ig.out,".vcf","").getAbsolutePath)).mkString(",")
     //cv.priority = (igList.foldLeft[List[String]](Nil)( (prLs, ig) =>  prLs ::: List(swapExt(ig.out,".vcf","").getAbsolutePath))).mkString(",")
     cv.rodBind = igList.map[RodBind,List[RodBind]](ig => new RodBind(swapExt(ig.out,".vcf","").getName,"VCF",ig.out))