Merge branch 'feature-core_testing' into 'develop'

Added unit tests

see also #51 

See merge request !278

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/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala

@@ -31,9 +31,11 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
    * Gets location of compiled class of pipeline
    * @return path from classPath to class file
    */
-  def pipeline = "/" + getClass.getName.stripSuffix("$").replaceAll("\\.", "/") + ".class"
+  def pipeline = "/" + getClass.getName.takeWhile(_ != '$').replaceAll("\\.", "/") + ".class"
 
-  def pipelineName = getClass.getSimpleName.takeWhile(_ != '$').toLowerCase
+  def pipelineName = getClass.getName.takeWhile(_ != '$').split("\\.").last.toLowerCase
+
+  protected val globalConfig = Config.global
 
   /** Class can be used directly from java with -cp option */
   def main(args: Array[String]): Unit = {
@@ -41,7 +43,7 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
     for (t <- 0 until argsSize) {
       if (args(t) == "-config" || args(t) == "--config_file") {
         if (args.length <= (t + 1)) throw new IllegalStateException("-config needs a value: <file>")
-        Config.global.loadConfigFile(new File(args(t + 1)))
+        globalConfig.loadConfigFile(new File(args(t + 1)))
       }
 
       if (args(t) == "-cv" || args(t) == "--config_value") {
@@ -52,7 +54,7 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
         val p = v(0).split(":")
         val key = p.last
         val path = p.dropRight(1).toList
-        Config.global.addValue(key, value, path)
+        globalConfig.addValue(key, value, path)
       }
 
       if (args(t) == "--logging_level" || args(t) == "-l") {
@@ -74,8 +76,8 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
 
     val logFile = {
       val pipelineName = this.getClass.getSimpleName.toLowerCase.split("""\$""").head
-      val pipelineConfig = Config.global.map.getOrElse(pipelineName, Map()).asInstanceOf[Map[String, Any]]
-      val pipelineOutputDir = new File(Config.global.map.getOrElse("output_dir", pipelineConfig.getOrElse("output_dir", "./")).toString)
+      val pipelineConfig = globalConfig.map.getOrElse(pipelineName, Map()).asInstanceOf[Map[String, Any]]
+      val pipelineOutputDir = new File(globalConfig.map.getOrElse("output_dir", pipelineConfig.getOrElse("output_dir", "./")).toString)
       val logDir: File = new File(pipelineOutputDir, ".log")
       logDir.mkdirs()
       new File(logDir, "biopet." + BiopetQCommandLine.timestamp + ".log")
@@ -91,7 +93,7 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
       argv ++= List("--log_to_file", new File(logFile.getParentFile, "queue." + BiopetQCommandLine.timestamp + ".log").getAbsolutePath)
     }
     if (!args.contains("-retry") && !args.contains("--retry_failed")) {
-      val retry: Int = Config.global(pipelineName, Nil, "retry", default = 5)
+      val retry: Int = globalConfig(pipelineName, Nil, "retry", default = 5)
       logger.info("No retry flag found, ")
       argv ++= List("-retry", retry.toString)
     }

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

@@ -17,9 +17,4 @@ trait ToolCommandFunction extends BiopetJavaCommandLineFunction with Version {
     javaMainClass = toolObject.getClass.getName.takeWhile(_ != '$')
     super.beforeGraph()
   }
-
-  override def freezeFieldValues(): Unit = {
-    javaMainClass = toolObject.getClass.getName.takeWhile(_ != '$')
-    super.freezeFieldValues()
-  }
 }

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
+
+  }
+}

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

+package nl.lumc.sasc.biopet.core
+
+import nl.lumc.sasc.biopet.utils.config.Config
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 17/11/15.
+ */
+class PipelineCommandTest extends TestNGSuite with Matchers {
+  @Test
+  def testPipelineCommand: Unit = {
+    val pipeline = new PipelineCommand {
+      override val globalConfig = new Config(Map())
+      def getConfig = globalConfig
+    }
+
+    pipeline.pipelineName shouldBe this.getClass.getSimpleName.toLowerCase
+    pipeline.pipeline shouldBe s"/${this.getClass.getName.stripSuffix("$").replaceAll("\\.", "/")}.class"
+
+    // Config should be emty if the main method is not yet touched
+    pipeline.getConfig.map shouldBe empty
+
+    //TODO: Main method testing
+  }
+}

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

+package nl.lumc.sasc.biopet.core
+
+import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 17/11/15.
+ */
+class SampleLibraryTagTest extends TestNGSuite with Matchers {
+  @Test
+  def testDefault: Unit = {
+    val o = new SampleLibraryTag {
+      override def root: Configurable = null
+      override def globalConfig = new Config(Map())
+    }
+    o.sampleId shouldBe None
+    o.libId shouldBe None
+  }
+
+  @Test
+  def testInherit: Unit = {
+    val o1 = new SampleLibraryTag {
+      override def root: Configurable = null
+      override def globalConfig = new Config(Map())
+    }
+    o1.sampleId = Some("sampleName")
+    o1.libId = Some("libName")
+    o1.sampleId shouldBe Some("sampleName")
+    o1.libId shouldBe Some("libName")
+
+    val o2 = new SampleLibraryTag {
+      override def root: Configurable = o1
+      override def globalConfig = new Config(Map())
+    }
+    o2.sampleId shouldBe o1.sampleId
+    o2.libId shouldBe o1.libId
+
+  }
+}

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

+package nl.lumc.sasc.biopet.core
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+import nl.lumc.sasc.biopet.FullVersion
+
+/**
+ * Created by pjvanthof on 16/11/15.
+ */
+class ToolCommandTest extends TestNGSuite with Matchers {
+  @Test
+  def testToolCommand: Unit = {
+    val tool = new ToolCommandFunction {
+      val root = null
+      val toolObject = ToolCommandTest
+    }
+
+    tool.versionCommand shouldBe empty
+    tool.versionRegex.toString() shouldBe empty
+    tool.getVersion shouldBe Some("Biopet " + FullVersion)
+    tool.beforeGraph
+
+    tool.javaMainClass shouldBe ToolCommandTest.getClass.getName.takeWhile(_ != '$')
+  }
+}
+
+object ToolCommandTest {
+
+}
\ No newline at end of file

public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala

@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
 
 trait Configurable extends ImplicitConversions {
   /** Should be object of parant object */
-  val root: Configurable
+  def root: Configurable
   def globalConfig: Config = if (root != null) root.globalConfig else Config.global
 
   /** suffix to the path */