From 16d8360592ef30d00337828e6ce1f4466660c1d2 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 24 Aug 2011 13:59:14 -0400
Subject: [PATCH] QJobReport is now the official capability name

---
 .../sting/queue/QCommandLine.scala            |  5 ++--
 .../sting/queue/engine/QGraphSettings.scala   |  3 +++
 .../{JobLogging.scala => QJobReport.scala}    | 26 ++++++++++---------
 3 files changed, 19 insertions(+), 15 deletions(-)
 rename public/scala/src/org/broadinstitute/sting/queue/util/{JobLogging.scala => QJobReport.scala} (84%)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
index c6d1f3883..668bd9604 100755
--- a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
@@ -115,9 +115,8 @@ class QCommandLine extends CommandLineProgram with Logging {
     // walk over each script, calling onExecutionDone
     for (script <- allQScripts) {
       script.onExecutionDone(qGraph.getFunctionsAndStatus(script.functions), qGraph.success)
-      val reportFile = new File("joblogging.gatkreport.txt")
-      logger.info("Writing JobLogging GATKReport to file " + reportFile)
-      JobLogging.printLogs(qGraph.getFunctionsAndStatus(script.functions), reportFile)
+      logger.info("Writing JobLogging GATKReport to file " + settings.jobReportFile)
+      QJobReport.printReport(qGraph.getFunctionsAndStatus(script.functions), settings.jobReportFile)
     }
 
     if (!qGraph.success) {
diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala
index 6ece600dd..13c841778 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala
@@ -69,6 +69,9 @@ class QGraphSettings {
   @Argument(fullName="expanded_dot_graph", shortName="expandedDot", doc="Outputs the queue graph of scatter gather to a .dot file.  Otherwise overwrites the dot_graph", required=false)
   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")
+
   @ArgumentCollection
   val qSettings = new QSettings
 }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/JobLogging.scala b/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala
similarity index 84%
rename from public/scala/src/org/broadinstitute/sting/queue/util/JobLogging.scala
rename to public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala
index 3bb43508a..882831f6b 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/JobLogging.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala
@@ -32,7 +32,7 @@ import java.io.{FileOutputStream, PrintStream, File}
 /**
  * A mixin to add Job info to the class
  */
-trait JobLogging extends QFunction {
+trait QJobReport extends QFunction {
   private var group: String = _
   private var features: Map[String, String] = null
 
@@ -70,16 +70,18 @@ trait JobLogging extends QFunction {
   }
 }
 
-object JobLogging {
-  def printLogs(jobs: Map[QFunction, JobRunInfo], dest: File) {
-    val jobLogs: List[JobLogging] = jobLoggingSublist(jobs.keys.toList)
-    jobLogs.foreach((job: JobLogging) => job.addRunInfo(jobs.get(job).get))
-    printJobLogging(jobLogs, new PrintStream(new FileOutputStream(dest)))
+object QJobReport {
+  def printReport(jobs: Map[QFunction, JobRunInfo], dest: File) {
+    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))
+    printJobLogging(jobLogs, stream)
+    stream.close()
   }
 
-  private def jobLoggingSublist(l: List[QFunction]): List[JobLogging] = {
-    def asJogLogging(qf: QFunction): JobLogging = qf match {
-      case x: JobLogging => x
+  private def jobLoggingSublist(l: List[QFunction]): List[QJobReport] = {
+    def asJogLogging(qf: QFunction): QJobReport = qf match {
+      case x: QJobReport => x
       case _ => null
     }
 
@@ -90,7 +92,7 @@ object JobLogging {
    * Prints the JobLogging logs to a GATKReport.  First splits up the
    * logs by group, and for each group generates a GATKReportTable
    */
-  private def printJobLogging(logs: List[JobLogging], stream: PrintStream) {
+  private def printJobLogging(logs: List[QJobReport], stream: PrintStream) {
     // create the report
     val report: GATKReport = new GATKReport
 
@@ -112,11 +114,11 @@ object JobLogging {
     report.print(stream)
   }
 
-  private def groupLogs(logs: List[JobLogging]): Map[String, List[JobLogging]] = {
+  private def groupLogs(logs: List[QJobReport]): Map[String, List[QJobReport]] = {
     logs.groupBy(_.getGroup)
   }
 
-  private def logKeys(logs: List[JobLogging]): Set[String] = {
+  private def logKeys(logs: List[QJobReport]): Set[String] = {
     // the keys should be the same for each log, but we will check that
     val keys = Set[String](logs(0).getFeatureNames : _*)