JobRunInfo improvements

-- dry-run now adds some info, for testing
-- InProcessRunner adds some, but not all, of the information we want

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

@@ -23,7 +23,7 @@ class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNod
    */
   var depth = -1
 
-  var runInfo: JobRunInfo = JobRunInfo.default // todo: replace after testing with _
+  val myRunInfo: JobRunInfo = JobRunInfo.default // purely for dryRun testing
 
   /**
    * Initializes with the current status of the function.
@@ -90,7 +90,6 @@ class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNod
             tailError()
           } else if (currentStatus == RunnerStatus.DONE) {
             try {
-              runInfo = runner.getRunInfo
               runner.cleanup()
               function.doneOutputs.foreach(_.createNewFile())
             } catch {
@@ -182,4 +181,8 @@ class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNod
     printWriter.close
     IOUtils.writeContents(functionErrorFile, stackTrace.toString)
   }
+
+  def getRunInfo = {
+    if ( runner == null ) myRunInfo else runner.getRunInfo
+  }
 }

public/scala/src/org/broadinstitute/sting/queue/engine/InProcessRunner.scala

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.queue.engine
 
 import org.broadinstitute.sting.queue.function.InProcessFunction
 import org.broadinstitute.sting.queue.util.IOUtils
+import java.util.Date
 
 /**
  * Runs a function that executes in process and does not fork out an external process.
@@ -10,8 +11,12 @@ class InProcessRunner(val function: InProcessFunction) extends JobRunner[InProce
   private var runStatus: RunnerStatus.Value = _
 
   def start() = {
+    runInfo.startTime = new Date()
     runStatus = RunnerStatus.RUNNING
+
     function.run()
+
+    runInfo.doneTime = new Date()
     val content = "%s%nDone.".format(function.description)
     IOUtils.writeContents(function.jobOutputFile, content)
     runStatus = RunnerStatus.DONE

public/scala/src/org/broadinstitute/sting/queue/engine/JobRunInfo.scala

@@ -53,7 +53,13 @@ import java.util.Date
 /**
  * Base class containing all of the information about a job run.
  */
-class JobRunInfo(startTime: Date, doneTime: Date, memUsedInGb: Int, hostName: String, status: RunnerStatus.Value) {
+class JobRunInfo {
+  var startTime: Date = _
+  var doneTime: Date = _
+  var memUsedInGb: Int = -1
+  var hostName: String = "localhost"
+  var status: RunnerStatus.Value = RunnerStatus.DONE
+
   def getStatus = status
   def getStartTime = startTime
   def getDoneTime = doneTime
@@ -69,7 +75,5 @@ class JobRunInfo(startTime: Date, doneTime: Date, memUsedInGb: Int, hostName: St
 }
 
 object JobRunInfo {
-  def default = new JobRunInfo(new Date(), new Date(), 1, "localhost", RunnerStatus.DONE)
-  def detailed(startTime: Date, doneTime: Date, memUsedInGb: Int, hostName: String) =
-    new JobRunInfo(startTime, doneTime, memUsedInGb, hostName, RunnerStatus.DONE)
+  def default: JobRunInfo = new JobRunInfo()
 }

public/scala/src/org/broadinstitute/sting/queue/engine/JobRunner.scala

@@ -72,7 +72,8 @@ trait JobRunner[TFunction <: QFunction] {
   /**
    * Must be overloaded
    */
-  def getRunInfo: JobRunInfo = JobRunInfo.default
+  val runInfo = JobRunInfo.default
+  def getRunInfo = runInfo
 
   /**
    * Calls back to a hook that an expert user can setup to modify a job.

public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala

@@ -320,7 +320,9 @@ class QGraph extends Logging {
       logger.debug("+++++++")
       foreachFunction(readyJobs.toList, edge => {
         if (running) {
+          edge.myRunInfo.startTime = new Date()
           logEdge(edge)
+          edge.myRunInfo.doneTime = new Date()
           edge.markAsDone
         }
       })
@@ -1038,7 +1040,7 @@ class QGraph extends Logging {
   def isShutdown = !running
 
   def getFunctionsAndStatus(functions: List[QFunction]): Map[QFunction, JobRunInfo] = {
-    getFunctionEdges.map(edge => (edge.function, edge.runInfo)).toMap
+    getFunctionEdges.map(edge => (edge.function, edge.getRunInfo)).toMap
   }
 
   /**