From 296bcc7fb14369f2ec3e40229e47273798e220aa Mon Sep 17 00:00:00 2001
From: Phillip Dexheimer <phillip.dexheimer@cchmc.org>
Date: Tue, 12 Nov 2013 11:42:09 -0500
Subject: [PATCH] Changed name of jobs submitted to cluster job runners

-- Added 'jobRunnerJobName' definition to QFunction, defaults to value of shortDescription
-- Edited Lsf and Drmaa JobRunners to use this string instead of description for naming jobs in the scheduler

Signed-off-by: Joel Thibault <thibault@broadinstitute.org>
---
 .../sting/queue/engine/drmaa/DrmaaJobRunner.scala            | 2 +-
 .../sting/queue/engine/lsf/Lsf706JobRunner.scala             | 2 +-
 .../org/broadinstitute/sting/queue/function/QFunction.scala  | 5 +++++
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala
index 79fc8589f..b405c91a2 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala
@@ -50,7 +50,7 @@ class DrmaaJobRunner(val session: Session, val function: CommandLineFunction) ex
     session.synchronized {
       val drmaaJob: JobTemplate = session.createJobTemplate
 
-      drmaaJob.setJobName(function.description.take(jobNameLength).replaceAll(jobNameFilter, "_"))
+      drmaaJob.setJobName(function.jobRunnerJobName.take(jobNameLength).replaceAll(jobNameFilter, "_"))
 
       // Set the current working directory
       drmaaJob.setWorkingDirectory(function.commandDirectory.getPath)
diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
index ead29bbf5..e9f141880 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
@@ -71,7 +71,7 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR
       for (i <- 0 until LibLsf.LSF_RLIM_NLIMITS)
         request.rLimits(i) = LibLsf.DEFAULT_RLIMIT;
 
-      request.jobName = function.description.take(LibBat.MAX_JOB_NAME_LEN)
+      request.jobName = function.jobRunnerJobName.take(LibBat.MAX_JOB_NAME_LEN)
       request.options |= LibBat.SUB_JOB_NAME
 
       // Set the output file for stdout
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
index abbb63271..3afd289af 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
@@ -150,6 +150,11 @@ trait QFunction extends Logging with QJobReport {
       case _ => analysisName
     }
   }
+  
+  /**
+   * The name of the job as submitted to the job runner
+   */
+  def jobRunnerJobName = shortDescription
 
   /**
    * Returns true if the function is done.