Fixes throughout for getting job information

-- no more hostname -- it's just not going to be important

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

@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.queue.engine
 
 import org.broadinstitute.sting.queue.function.InProcessFunction
-import org.broadinstitute.sting.queue.util.IOUtils
 import java.util.Date
+import org.broadinstitute.sting.queue.util.{Logging, IOUtils}
 
 /**
  * Runs a function that executes in process and does not fork out an external process.
@@ -11,12 +11,12 @@ class InProcessRunner(val function: InProcessFunction) extends JobRunner[InProce
   private var runStatus: RunnerStatus.Value = _
 
   def start() = {
-    runInfo.startTime = new Date()
+    getRunInfo.startTime = new Date()
     runStatus = RunnerStatus.RUNNING
 
     function.run()
 
-    runInfo.doneTime = new Date()
+    getRunInfo.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

@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.queue.engine
 
 import java.util.Date
+import java.text.SimpleDateFormat
 
 /*
  * Copyright (c) 2011, The Broad Institute
@@ -57,14 +58,20 @@ 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
+  def getFormattedStartTime = formatTime(getStartTime)
+  def getFormattedDoneTime = formatTime(getDoneTime)
+
+  val formatter = new SimpleDateFormat("dd.MM.yy/H:mm:ss:SSS");
+  private def formatTime(d: Date) = if ( d != null ) formatter.format(d) else "null"
+
   def getMemoryUsedInGb = memUsedInGb
-  def getHostname = hostName
+  def isFilledIn = startTime != null
 
   def getRuntimeInMs: Long = {
     if ( getDoneTime != null && getStartTime != null )
@@ -74,7 +81,7 @@ class JobRunInfo {
   }
 
   override def toString: String =
-    "started %s ended %s runtime %s on host %s using %d Gb memory".format(getStartTime, getDoneTime, getRuntimeInMs, getHostname, getMemoryUsedInGb)
+    "started %s ended %s runtime %s using %d Gb memory".format(getFormattedStartTime, getFormattedDoneTime, getRuntimeInMs, getMemoryUsedInGb)
 }
 
 object JobRunInfo {

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

@@ -70,7 +70,7 @@ class QGraphSettings {
   var expandedDotFile: File = _
 
   @Argument(fullName="jobReport", shortName="jobReport", doc="File where we will write the Queue job report", required=false)
-  var jobReportFile: File = new File("queue_job_report.gatkreport.txt")
+  var jobReportFile: File = new File("/dev/stdout")
 
   @ArgumentCollection
   val qSettings = new QSettings

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

@@ -31,11 +31,12 @@ import org.broadinstitute.sting.jna.lsf.v7_0_6.{LibLsf, LibBat}
 import org.broadinstitute.sting.utils.Utils
 import org.broadinstitute.sting.jna.clibrary.LibC
 import org.broadinstitute.sting.jna.lsf.v7_0_6.LibBat.{submitReply, submit}
-import com.sun.jna.ptr.IntByReference
 import org.broadinstitute.sting.queue.engine.{RunnerStatus, CommandLineJobRunner}
-import com.sun.jna.{Structure, StringArray, NativeLong}
 import java.util.regex.Pattern
 import java.lang.StringBuffer
+import java.util.Date
+import com.sun.jna.{Pointer, Structure, StringArray, NativeLong}
+import com.sun.jna.ptr.{PointerByReference, IntByReference}
 
 /**
  * Runs jobs on an LSF compute cluster.
@@ -271,12 +272,21 @@ object Lsf706JobRunner extends Logging {
 
     logger.debug("Job Id %s status / exitStatus / exitInfo: 0x%02x / 0x%02x / 0x%02x".format(runner.jobId, jobStatus, exitStatus, exitInfo))
 
+    def updateRunInfo() {
+      runner.getRunInfo.startTime = new Date(jobInfo.startTime.longValue)
+      runner.getRunInfo.doneTime = new Date(jobInfo.endTime.longValue)
+      runner.getRunInfo.hostName = "unavailable" // TODO : exHosts
+      runner.getRunInfo.memUsedInGb = jobInfo.runRusage.mem
+    }
+
     runner.updateStatus(
       if (Utils.isFlagSet(jobStatus, LibBat.JOB_STAT_DONE)) {
         // Done successfully.
+        updateRunInfo()
         RunnerStatus.DONE
       } else if (Utils.isFlagSet(jobStatus, LibBat.JOB_STAT_EXIT) && !willRetry(exitInfo, endTime)) {
         // Exited function that (probably) won't be retried.
+        updateRunInfo()
         RunnerStatus.FAILED
       } else {
         // Note that we still saw the job in the system.

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

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.queue.engine.shell
 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
 
 /**
  * Runs jobs one at a time locally
@@ -50,8 +51,10 @@ class ShellJobRunner(val function: CommandLineFunction) extends CommandLineJobRu
     // Allow advanced users to update the job.
     updateJobRun(job)
 
+    getRunInfo.startTime = new Date()
     updateStatus(RunnerStatus.RUNNING)
     job.run()
+    getRunInfo.doneTime = new Date()
     updateStatus(RunnerStatus.DONE)
   }
 

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

@@ -49,15 +49,15 @@ trait QJobReport extends QFunction {
   def getName: String = features.get("jobName").get
 
   private def addRunInfo(info: JobRunInfo) {
+    logger.info("info " + info)
     features = features ++ Map(
       "analysisName" -> this.analysisName,
       "jobName" -> this.jobName,
       "intermediate" -> this.isIntermediate,
-      "startTime" -> info.getStartTime,
+      "startTime" -> info.getFormattedStartTime,
-      "doneTime" -> info.getDoneTime,
+      "doneTime" -> info.getFormattedDoneTime,
       "memUsedInGb" -> info.getMemoryUsedInGb,
-      "runtime" -> info.getRuntimeInMs,
+      "runtime" -> info.getRuntimeInMs).mapValues((x:Any) => if (x != null) x.toString else "null")
-      "hostName" -> info.getHostname).mapValues(_.toString)
   }
 
   def setJobLogging(group: String) {
@@ -71,7 +71,8 @@ trait QJobReport extends QFunction {
 }
 
 object QJobReport {
-  def printReport(jobs: Map[QFunction, JobRunInfo], dest: File) {
+  def printReport(jobsRaw: Map[QFunction, JobRunInfo], dest: File) {
+    val jobs = jobsRaw.filter(_._2.isFilledIn)
     val jobLogs: List[QJobReport] = jobLoggingSublist(jobs.keys.toList)
     jobLogs.foreach((job: QJobReport) => job.addRunInfo(jobs.get(job).get))
     val stream = new PrintStream(new FileOutputStream(dest))