Minor updates to previous ParallelShell commit.

Changed `--maximumNumberOfJobsToRunConcurrently`/`-maxConcurrentRun` to `Option[Int]`.
Updated licenses.
Added basic tests.
Removed some IntelliJ warnings.

public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala

@@ -149,4 +149,23 @@ class HelloWorldQueueTest {
     spec.expectedFilePaths = Seq("pipelineLogDir/HelloWorld-1.out")
     QueueTest.executeTest(spec)
   }
+
+  @Test(timeOut=36000000)
+  def testHelloWorldParallelShell() {
+    val spec = new QueueTestSpec
+    spec.name = "HelloWorldWithLogDirectory"
+    spec.args = "-S " + QueueTest.publicQScriptsPackageDir + "examples/HelloWorld.scala"
+    spec.jobRunners = Seq("ParallelShell")
+    QueueTest.executeTest(spec)
+  }
+
+  @Test(timeOut=36000000)
+  def testHelloWorldParallelShellMaxConcurrentRun() {
+    val spec = new QueueTestSpec
+    spec.name = "HelloWorldWithLogDirectory"
+    spec.args = "-S " + QueueTest.publicQScriptsPackageDir + "examples/HelloWorld.scala" +
+      " -maxConcurrentRun 10"
+    spec.jobRunners = Seq("ParallelShell")
+    QueueTest.executeTest(spec)
+  }
 }

public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraph.scala

@@ -437,8 +437,8 @@ class QGraph extends Logging {
         def startJobs: Boolean = {
 
           def canRunMoreConcurrentJobs: Boolean =
-            if(settings.maximumNumberOfConcurrentJobs > 0)
+            if(settings.maximumNumberOfConcurrentJobs.isDefined)
-              runningJobs.size + startedJobs.size < settings.maximumNumberOfConcurrentJobs
+              runningJobs.size + startedJobs.size < settings.maximumNumberOfConcurrentJobs.get
             else
               true
 

public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraphSettings.scala

@@ -28,7 +28,7 @@ package org.broadinstitute.gatk.queue.engine
 import java.io.File
 import org.broadinstitute.gatk.queue.QSettings
 import org.broadinstitute.gatk.queue.util.{EmailSettings, SystemUtils}
-import org.broadinstitute.gatk.utils.commandline.{Advanced, ArgumentCollection, Argument}
+import org.broadinstitute.gatk.utils.commandline.{ClassType, Advanced, ArgumentCollection, Argument}
 
 /**
  * Command line options for a QGraph.
@@ -81,8 +81,9 @@ class QGraphSettings {
   var disableJobReport: Boolean = false
 
   @Advanced
+  @ClassType(classOf[Int])
   @Argument(fullName="maximumNumberOfJobsToRunConcurrently", shortName="maxConcurrentRun", doc="The maximum number of jobs to start at any given time. (Default is no limit)", required=false)
-  var maximumNumberOfConcurrentJobs: Int = -1
+  var maximumNumberOfConcurrentJobs: Option[Int] = None
 
   @ArgumentCollection
   val emailSettings = new EmailSettings

public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobManager.scala

@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -67,4 +67,4 @@ class ParallelShellJobManager extends CommandLineJobManager[ParallelShellJobRunn
    */
   override def tryStop(runners: Set[ParallelShellJobRunner]) =
     runners.foreach(_.tryStop())
-}
+}

public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobRunner.scala

@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -63,7 +63,7 @@ class ParallelShellJobRunner(val function: CommandLineFunction) extends CommandL
     val commandLine = Array("sh", jobScript.getAbsolutePath)
     val stdoutSettings = new OutputStreamSettings
     val stderrSettings = new OutputStreamSettings
-    val mergeError = (function.jobErrorFile == null)
+    val mergeError = function.jobErrorFile == null
 
     stdoutSettings.setOutputFile(function.jobOutputFile, true)
     if (function.jobErrorFile != null)
@@ -90,25 +90,20 @@ class ParallelShellJobRunner(val function: CommandLineFunction) extends CommandL
 
     // Register a callback on the completion of the future, making sure that
     // the status of the job is updated accordingly. 
-    executedFuture.onComplete { tryExitStatus =>
+    executedFuture.onComplete {
-
+      case Success(exitStatus) =>
-      tryExitStatus match {
+        logger.debug(commandLine.mkString(" ") + " :: Got return on exit status in future: " + exitStatus)
-        case Success(exitStatus) => {
+        finalExitStatus.success(exitStatus)
-          logger.debug(commandLine.mkString(" ") + " :: Got return on exit status in future: " + exitStatus)
+        getRunInfo.doneTime = new Date()
-          finalExitStatus.success(exitStatus)
+        exitStatusUpdateJobRunnerStatus(exitStatus)
-          getRunInfo.doneTime = new Date()
+      case Failure(throwable) =>
-          exitStatusUpdateJobRunnerStatus(exitStatus)
+        logger.debug(
-        }
+          "Failed in return from run with: " +
-        case Failure(throwable) => {
+            throwable.getClass.getCanonicalName + " :: " +
-          logger.debug(
+            throwable.getMessage)
-            "Failed in return from run with: " +
+        finalExitStatus.failure(throwable)
-              throwable.getClass.getCanonicalName + " :: " +
+        getRunInfo.doneTime = new Date()
-              throwable.getMessage)
+        updateStatus(RunnerStatus.FAILED)
-          finalExitStatus.failure(throwable)
-          getRunInfo.doneTime = new Date()
-          updateStatus(RunnerStatus.FAILED)
-        }
-      }
     }
   }
 
@@ -153,4 +148,4 @@ class ParallelShellJobRunner(val function: CommandLineFunction) extends CommandL
       false
     }
   }
-}
+}

public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ThreadSafeProcessController.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
 package org.broadinstitute.gatk.queue.engine.parallelshell
 
 import java.io.PrintWriter
@@ -78,4 +103,4 @@ class ThreadSafeProcessController extends Logging {
     }.destroy()
   }
 
-}
+}

public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala

@@ -53,7 +53,7 @@ object QueueTest extends BaseTest with Logging {
   /**
    * All the job runners configured to run QueueTests at The Broad.
    */
-  final val allJobRunners = Seq("GridEngine", "Shell")
+  final val allJobRunners = Seq("GridEngine", "Shell", "ParallelShell")
 
   /**
    * The default job runners to run.