Now captures the exechost in the job report

-- Works for in process, shell, and LSF runners
-- Cleanup of debugging output

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

@@ -64,7 +64,8 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon
    */
   def onExecutionDone(jobs: Map[QFunction, JobRunInfo], success: Boolean) {
     logger.info("Script %s with %d total jobs".format(if (success) "completed successfully" else "failed", jobs.size))
-    for ( (f, info) <- jobs ) logger.info("  %s %s".format(f.jobName, info))
+    // this is too much output
+    // for ( (f, info) <- jobs ) logger.info("  %s %s".format(f.jobName, info))
   }
 
   /**

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

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.queue.engine
 import org.broadinstitute.sting.queue.function.InProcessFunction
 import java.util.Date
 import org.broadinstitute.sting.queue.util.{Logging, IOUtils}
+import org.broadinstitute.sting.utils.Utils
 
 /**
  * Runs a function that executes in process and does not fork out an external process.
@@ -12,6 +13,7 @@ class InProcessRunner(val function: InProcessFunction) extends JobRunner[InProce
 
   def start() = {
     getRunInfo.startTime = new Date()
+    getRunInfo.exechosts = Utils.resolveHostname()
     runStatus = RunnerStatus.RUNNING
 
     function.run()

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

@@ -39,6 +39,7 @@ class JobRunInfo {
   var startTime: Date = _
   /** The done time with millisecond resolution of this job */
   var doneTime: Date = _
+  var exechosts: String = "localhost"
 
   def getStartTime = startTime
   def getDoneTime = doneTime
@@ -48,6 +49,8 @@ class JobRunInfo {
   /** Helper function that pretty prints the date */
   private def formatTime(d: Date) = if ( d != null ) formatter.format(d) else "null"
 
+  def getExecHosts = exechosts
+
   /**
    * Was any information set for this jobInfo?  JobInfo can be unset because
    * the job never ran or because it already completed.

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

@@ -39,6 +39,7 @@ import org.broadinstitute.sting.queue.util._
 import collection.immutable.{TreeSet, TreeMap}
 import org.broadinstitute.sting.queue.function.scattergather.{ScatterFunction, CloneFunction, GatherFunction, ScatterGatherableFunction}
 import java.util.Date
+import org.broadinstitute.sting.utils.Utils
 
 /**
  * The internal dependency tracker between sets of function input and output files.
@@ -321,6 +322,7 @@ class QGraph extends Logging {
       foreachFunction(readyJobs.toList, edge => {
         if (running) {
           edge.myRunInfo.startTime = new Date()
+          edge.getRunInfo.exechosts = Utils.resolveHostname()
           logEdge(edge)
           edge.myRunInfo.doneTime = new Date()
           edge.markAsDone

public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala

@@ -276,6 +276,13 @@ object Lsf706JobRunner extends Logging {
       // the platform LSF startTimes are in seconds, not milliseconds, so convert to the java convention
       runner.getRunInfo.startTime = new Date(jobInfo.startTime.longValue * 1000)
       runner.getRunInfo.doneTime = new Date(jobInfo.endTime.longValue * 1000)
+      val exHostsRaw = jobInfo.exHosts.getStringArray(0)
+      //logger.warn("exHostsRaw = " + exHostsRaw)
+      val exHostsList = exHostsRaw.toList
+      //logger.warn("exHostsList = " + exHostsList)
+      val exHosts = exHostsList.reduceLeft(_ + "," + _)
+      //logger.warn("exHosts = " + exHosts)
+      runner.getRunInfo.exechosts = exHosts
     }
 
     runner.updateStatus(

public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala

@@ -28,6 +28,8 @@ import org.broadinstitute.sting.queue.function.CommandLineFunction
 import org.broadinstitute.sting.queue.util.ShellJob
 import org.broadinstitute.sting.queue.engine.{RunnerStatus, CommandLineJobRunner}
 import java.util.Date
+import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
+import org.broadinstitute.sting.utils.Utils
 
 /**
  * Runs jobs one at a time locally
@@ -52,6 +54,7 @@ class ShellJobRunner(val function: CommandLineFunction) extends CommandLineJobRu
     updateJobRun(job)
 
     getRunInfo.startTime = new Date()
+    getRunInfo.exechosts = Utils.resolveHostname()
     updateStatus(RunnerStatus.RUNNING)
     job.run()
     getRunInfo.doneTime = new Date()

public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala

@@ -48,12 +48,13 @@ trait QJobReport extends Logging {
   def disableReport() { reportEnabled = false }
 
   def setRunInfo(info: JobRunInfo) {
-    logger.info("info " + info)
+    //logger.info("info " + info)
     reportFeatures = Map(
       "iteration" -> 1,
       "analysisName" -> getReportGroup,
       "jobName" -> QJobReport.workAroundSameJobNames(this),
       "intermediate" -> self.isIntermediate,
+      "exechosts" -> info.getExecHosts,
       "startTime" -> info.getStartTime.getTime,
       "doneTime" -> info.getDoneTime.getTime,
       "formattedStartTime" -> info.getFormattedStartTime,