Added tests for resources

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala

@@ -43,10 +43,12 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
    * @return number of threads
    */
   private def getThreads(default: Int): Int = {
-    val maxThreads: Int = config("maxthreads", default = 24)
+    val maxThreads: Option[Int] = config("maxthreads")
     val threads: Int = config("threads", default = default)
-    if (maxThreads > threads) threads
-    else maxThreads
+    maxThreads match {
+      case Some(max) => if (max > threads) threads else max
+      case _         => threads
+    }
   }
 
   def setResources(): Unit = {
@@ -79,7 +81,7 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
     if (vmem.isDefined) jobResourceRequests = jobResourceRequests.filterNot(_.contains("h_vmem="))
     if (retry > 0) logger.info("Auto raise memory on retry")
     retry += 1
-    this.freeze()
+    this.freezeFieldValues()
   }
 
   var threadsCorrection = 0

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala

+package nl.lumc.sasc.biopet.core
+
+import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
+import org.broadinstitute.gatk.queue.function.CommandLineFunction
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+import scala.language.reflectiveCalls
+
+/**
+ * Created by pjvanthof on 17/11/15.
+ */
+class CommandLineResourcesTest extends TestNGSuite with Matchers {
+  class CommandLineFunctionMock(c: Map[String, Any] = Map()) extends CommandLineFunction with Configurable {
+    override def freezeFieldValues() {}
+    def commandLine = "command"
+    val root = null
+    override def globalConfig = new Config(c)
+  }
+
+  @Test
+  def testDefaults(): Unit = {
+    val cmd = new CommandLineFunctionMock with CommandLineResources
+    cmd.coreMemory shouldBe 2.0
+    cmd.residentFactor shouldBe 1.2
+    cmd.vmemFactor shouldBe 1.4
+    cmd.retry shouldBe 0
+    cmd.threads shouldBe 1
+
+    cmd.setResources()
+
+    cmd.memoryLimit shouldBe Some(cmd.coreMemory * cmd.threads)
+    cmd.residentLimit shouldBe Some(cmd.coreMemory * cmd.residentFactor)
+    cmd.vmem shouldBe Some((cmd.coreMemory * cmd.vmemFactor) + "G")
+
+    cmd.jobResourceRequests shouldBe empty
+
+    cmd.freezeFieldValues()
+
+    cmd.jobResourceRequests should contain("h_vmem=" + cmd.vmem.get)
+
+    cmd.setupRetry()
+    cmd.retry shouldBe 1
+    cmd.setupRetry()
+    cmd.retry shouldBe 2
+    cmd.setupRetry()
+    cmd.retry shouldBe 3
+
+  }
+
+  @Test
+  def testMaxThreads(): Unit = {
+    val cmd = new CommandLineFunctionMock(Map("maxthreads" -> 5, "threads" -> 10)) with CommandLineResources
+
+    cmd.threads shouldBe 5
+  }
+
+  @Test
+  def testCombine(): Unit = {
+    val cmd1 = new CommandLineFunctionMock with CommandLineResources
+    val cmd2 = new CommandLineFunctionMock with CommandLineResources
+    val mainCmd = new CommandLineFunctionMock with CommandLineResources {
+      def combine(functions: List[CommandLineResources]) = combineResources(functions)
+    }
+    mainCmd.combine(List(cmd1, cmd2))
+
+    mainCmd.coreMemory shouldBe 2.0
+    mainCmd.residentFactor shouldBe 1.2
+    mainCmd.vmemFactor shouldBe 1.4
+    mainCmd.memoryLimit shouldBe Some(4.0)
+    mainCmd.retry shouldBe 0
+    mainCmd.threads shouldBe 2
+
+  }
+}