Sending a version of per job status messages.

In addition to outputs, inputs are passed to QStatusMessenger.done()
CloneFunction.cloneIndex has a new CloneFunction.cloneCount companion useful for display purposes.

public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala

@@ -123,6 +123,8 @@ class QCommandLine extends CommandLineProgram with Logging {
         commandPlugin.statusMessenger.started()
     }
 
+    qGraph.messengers = allCommandPlugins.filter(_.statusMessenger != null).map(_.statusMessenger).toSeq
+
     // TODO: Default command plugin argument?
     val remoteFileConverter = (
       for (commandPlugin <- allCommandPlugins if (commandPlugin.remoteFileConverter != null))
@@ -178,14 +180,17 @@ class QCommandLine extends CommandLineProgram with Logging {
       qGraph.logFailed()
       for (commandPlugin <- allCommandPlugins)
         if (commandPlugin.statusMessenger != null)
-          commandPlugin.statusMessenger.exit("Done with errors")
+          commandPlugin.statusMessenger.exit("Done with errors: %s".format(qGraph.formattedStatusCounts))
       1
     } else {
       if (settings.run) {
         allQScripts.foreach(_.pushOutputs())
         for (commandPlugin <- allCommandPlugins)
-          if (commandPlugin.statusMessenger != null)
+          if (commandPlugin.statusMessenger != null) {
-            commandPlugin.statusMessenger.done(allQScripts.map(_.remoteOutputs))
+            val allInputs = allQScripts.map(_.remoteInputs)
+            val allOutputs = allQScripts.map(_.remoteOutputs)
+            commandPlugin.statusMessenger.done(allInputs, allOutputs)
+          }
       }
       0
     }

public/scala/src/org/broadinstitute/sting/queue/QScript.scala

@@ -149,8 +149,17 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon
    * List out the remote outputs
    * @return the RemoteFile outputs by argument source
    */
-  def remoteOutputs: Map[ArgumentSource, Seq[RemoteFile]] =
+  def remoteInputs: Map[ArgumentSource, Seq[RemoteFile]] = remoteFieldMap(inputFields)
-    outputFields.map(field => (field -> filterRemoteFiles(ClassFieldCache.getFieldFiles(this, field)))).filter(tuple => !tuple._2.isEmpty).toMap
+
+  /**
+   * List out the remote outputs
+   * @return the RemoteFile outputs by argument source
+   */
+  def remoteOutputs: Map[ArgumentSource, Seq[RemoteFile]] = remoteFieldMap(outputFields)
+
+  private def remoteFieldMap(fields: Seq[ArgumentSource]): Map[ArgumentSource, Seq[RemoteFile]] = {
+    fields.map(field => (field -> filterRemoteFiles(ClassFieldCache.getFieldFiles(this, field)))).filter(tuple => !tuple._2.isEmpty).toMap
+  }
 
   private def filterRemoteFiles(fields: Seq[File]): Seq[RemoteFile] =
     fields.filter(field => field != null && field.isInstanceOf[RemoteFile]).map(_.asInstanceOf[RemoteFile])

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

@@ -47,6 +47,7 @@ import java.io.{OutputStreamWriter, File}
  */
 class QGraph extends Logging {
   var settings: QGraphSettings = _
+  var messengers: Seq[QStatusMessenger] = Nil
 
   private def dryRun = !settings.run
   private var numMissingValues = 0
@@ -95,7 +96,7 @@ class QGraph extends Logging {
    * The settings aren't necessarily available until after this QGraph object has been constructed, so
    * this function must be called once the QGraphSettings have been filled in.
    *
-   * @param settings
+   * @param settings QGraphSettings
    */
   def initializeWithSettings(settings: QGraphSettings) {
     this.settings = settings
@@ -430,6 +431,7 @@ class QGraph extends Logging {
           val edge = readyJobs.head
           edge.runner = newRunner(edge.function)
           edge.start()
+          messengers.foreach(_.started(jobShortName(edge.function)))
           startedJobs += edge
           readyJobs -= edge
           logNextStatusCounts = true
@@ -465,8 +467,14 @@ class QGraph extends Logging {
         updateStatus()
 
         runningJobs.foreach(edge => edge.status match {
-          case RunnerStatus.DONE => doneJobs += edge
+          case RunnerStatus.DONE => {
-          case RunnerStatus.FAILED => failedJobs += edge
+            doneJobs += edge
+            messengers.foreach(_.done(jobShortName(edge.function)))
+          }
+          case RunnerStatus.FAILED => {
+            failedJobs += edge
+            messengers.foreach(_.exit(jobShortName(edge.function), edge.function.jobErrorLines.mkString("%n".format())))
+          }
           case RunnerStatus.RUNNING => /* do nothing while still running */
         })
 
@@ -493,7 +501,7 @@ class QGraph extends Logging {
         // incremental
         if ( logNextStatusCounts && INCREMENTAL_JOBS_REPORT ) {
           logger.info("Writing incremental jobs reports...")
-          writeJobsReport(false)
+          writeJobsReport(plot = false)
         }
 
         readyJobs ++= getReadyJobs
@@ -516,9 +524,13 @@ class QGraph extends Logging {
   private def nextRunningCheck(lastRunningCheck: Long) =
     ((30 * 1000L) - (System.currentTimeMillis - lastRunningCheck))
 
+  def formattedStatusCounts: String = {
+    "%d Pend, %d Run, %d Fail, %d Done".format(
+      statusCounts.pending, statusCounts.running, statusCounts.failed, statusCounts.done)
+  }
+
   private def logStatusCounts() {
-    logger.info("%d Pend, %d Run, %d Fail, %d Done".format(
+    logger.info(formattedStatusCounts)
-      statusCounts.pending, statusCounts.running, statusCounts.failed, statusCounts.done))
   }
 
   /**
@@ -533,6 +545,16 @@ class QGraph extends Logging {
     traverseFunctions(edge => recheckDone(edge))
   }
 
+  // TODO: Yet another field to add (with overloads) to QFunction?
+  private def jobShortName(function: QFunction): String = {
+    var name = function.analysisName
+    if (function.isInstanceOf[CloneFunction]) {
+      val cloneFunction = function.asInstanceOf[CloneFunction]
+      name += " %d of %d".format(cloneFunction.cloneIndex, cloneFunction.cloneCount)
+    }
+    name
+  }
+
   /**
    * First pass that checks if an edge is done or if it's an intermediate edge if it can be skipped.
    * This function may modify the status of previous edges if it discovers that the edge passed in

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

@@ -8,6 +8,10 @@ import org.broadinstitute.sting.queue.util.RemoteFile
  */
 trait QStatusMessenger {
   def started()
-  def done(files: Seq[Map[ArgumentSource, Seq[RemoteFile]]])
+  def done(inputs: Seq[Map[ArgumentSource, Seq[RemoteFile]]], outputs: Seq[Map[ArgumentSource, Seq[RemoteFile]]])
   def exit(message: String)
+
+  def started(job: String)
+  def done(job: String)
+  def exit(job: String, message: String)
 }

public/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala

@@ -38,6 +38,7 @@ object CloneFunction {
 class CloneFunction extends CommandLineFunction {
   var originalFunction: ScatterGatherableFunction = _
   var cloneIndex: Int = _
+  var cloneCount: Int = _
 
   private var overriddenFields = Map.empty[ArgumentSource, Any]
   private var withScatterPartCount = 0

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

@@ -176,6 +176,7 @@ trait ScatterGatherableFunction extends CommandLineFunction {
       cloneFunction.originalFunction = this
       cloneFunction.analysisName = this.analysisName
       cloneFunction.cloneIndex = i
+      cloneFunction.cloneCount = numClones
       cloneFunction.commandDirectory = this.scatterGatherTempDir(dirFormat.format(i))
       cloneFunction.jobOutputFile = if (IOUtils.isSpecialFile(this.jobOutputFile)) this.jobOutputFile else new File(this.jobOutputFile.getName)
       if (this.jobErrorFile != null)