Add walltime changes to LSF

- Check whether the specified attribute is available
- Add pipeline test (disabled due to missing attribute)

public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSession.java

@@ -210,13 +210,23 @@ public class JnaSession implements Session {
     }
 
     public static void setAttribute(Pointer jt, String name, String value) throws DrmaaException {
-        checkError(LibDrmaa.drmaa_set_attribute(jt, name, value, getError(), LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN));
+        if (getAttrNames().contains(name)) {
+            checkError(LibDrmaa.drmaa_set_attribute(jt, name, value, getError(), LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN));
+        }
+        else {
+            throw new InvalidAttributeValueException("Attribute " + name + " is not supported by this implementation of DRMAA");
+        }
     }
 
     public static String getAttribute(Pointer jt, String name) throws DrmaaException {
-        Memory attrBuffer = new Memory(LibDrmaa.DRMAA_ATTR_BUFFER);
-        checkError(LibDrmaa.drmaa_get_attribute(jt, name, attrBuffer, LibDrmaa.DRMAA_ATTR_BUFFER_LEN, getError(), LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN));
-        return attrBuffer.getString(0);
+        if (getAttrNames().contains(name)) {
+            Memory attrBuffer = new Memory(LibDrmaa.DRMAA_ATTR_BUFFER);
+            checkError(LibDrmaa.drmaa_get_attribute(jt, name, attrBuffer, LibDrmaa.DRMAA_ATTR_BUFFER_LEN, getError(), LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN));
+            return attrBuffer.getString(0);
+        }
+        else {
+            throw new InvalidAttributeValueException("Attribute " + name + " is not supported by this implementation of DRMAA");
+        }
     }
 
     public static void setVectorAttribute(Pointer jt, String name, Collection<String> values) throws DrmaaException {

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

@@ -31,10 +31,6 @@ import org.broadinstitute.sting.commandline.{ClassType, Argument}
  * Default settings settable on the command line and passed to CommandLineFunctions.
  */
 class QSettings {
-  
-  @Argument(fullName="job_walltime", shortName="wallTime", doc="Setting the required walltime when using the drmaa job runner.", required=false)
-  var jobWalltime: Option[Long] = None
-  
   @Argument(fullName="run_name", shortName="runName", doc="A name for this run used for various status messages.", required=false)
   var runName: String = _
 
@@ -76,6 +72,10 @@ class QSettings {
   @Argument(fullName="resident_memory_request_parameter", shortName="resMemReqParam", doc="Parameter for resident memory requests. By default not requested.", required=false)
   var residentRequestParameter: String = _
 
+  @Argument(fullName="job_walltime", shortName="wallTime", doc="Setting the required DRMAA walltime or LSF run limit.", required=false)
+  @ClassType(classOf[Long])
+  var jobWalltime: Option[Long] = None
+
   /** The name of the parallel environment (required for SGE, for example) */
   @Argument(fullName="job_parallel_env", shortName="jobParaEnv", doc="An SGE style parallel environment to use for jobs requesting more than 1 core.  Equivalent to submitting jobs with -pe ARG nt for jobs with nt > 1", required=false)
   var parallelEnvironmentName: String = "smp_pe" // Broad default

public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala

@@ -65,7 +65,7 @@ class DrmaaJobRunner(val session: Session, val function: CommandLineFunction) ex
         drmaaJob.setJoinFiles(true)
       }
 
-      if(function.wallTime != null)
+      if(!function.wallTime.isEmpty)
     	  drmaaJob.setHardWallclockTimeLimit(function.wallTime.get)      
       
       drmaaJob.setNativeSpecification(functionNativeSpec)

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

@@ -151,8 +151,11 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR
           throw new QException("setOption_() returned -1 while setting esub");
       }
 
-      // LSF specific: get the max runtime for the jobQueue and pass it for this job
-      request.rLimits(LibLsf.LSF_RLIMIT_RUN) = Lsf706JobRunner.getRlimitRun(function.jobQueue)
+      if(!function.wallTime.isEmpty)
+        request.rLimits(LibLsf.LSF_RLIMIT_RUN) = function.wallTime.get.toInt
+      else
+        // LSF specific: get the max runtime for the jobQueue and pass it for this job
+        request.rLimits(LibLsf.LSF_RLIMIT_RUN) = Lsf706JobRunner.getRlimitRun(function.jobQueue)
 
       // Run the command as sh <jobScript>
       request.command = "sh " + jobScript

public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala

@@ -33,7 +33,7 @@ import org.broadinstitute.sting.commandline.Argument
 trait CommandLineFunction extends QFunction with Logging {
   def commandLine: String
 
-  /** Setting the wall time request for drmaa job*/
+  /** Setting the wall time request for DRMAA / run limit for LSF */
   var wallTime: Option[Long] = None
   
   /** Upper memory limit */

public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala

@@ -126,4 +126,15 @@ class HelloWorldPipelineTest {
     spec.jobRunners = Seq("GridEngine")
     PipelineTest.executeTest(spec)
   }
+
+  // disabled because our DRMAA implementation doesn't support wallTime
+  @Test(enabled=false, timeOut=36000000)
+  def testHelloWorldWithWalltime() {
+    val spec = new PipelineTestSpec
+    spec.name = "HelloWorldWithWalltime"
+    spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" +
+      " -wallTime 100"
+    spec.jobRunners = PipelineTest.allJobRunners
+    PipelineTest.executeTest(spec)
+  }
 }