Added testing

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

 package nl.lumc.sasc.biopet.core
 
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
+import nl.lumc.sasc.biopet.core.extensions.Md5sum
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.broadinstitute.gatk.queue.QScript
@@ -7,9 +11,7 @@ import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
-import scala.collection.mutable.{ListBuffer, StringBuilder}
-import scalaz._
-import Scalaz._
+import scala.collection.mutable.ListBuffer
 
 /**
   * Created by pjvan_thof on 12/29/15.
@@ -18,27 +20,91 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
   import MultiSampleQScriptTest._
 
   @Test
-  def test: Unit = {
+  def testDefault: Unit = {
+
+    val script = MultiSampleQScriptTest(sample1 :: sample2 :: sample3 :: Nil)
+    script.outputDir = new File("./").getAbsoluteFile
+    script.init()
+    script.biopetScript()
+
+    script.functions.size shouldBe 4
+
+    script.samples.foreach { case (sampleId, sample) =>
+      sample.gender shouldBe Gender.Unknown
+      sample.father shouldBe None
+      sample.mother shouldBe None
+      sample.summaryFiles shouldBe Map()
+      sample.summaryStats shouldBe Map()
+      sample.summarySettings shouldBe Map()
+      sample.sampleDir shouldBe new File(script.outputDir, "samples" + File.separator + sampleId)
+      sample.createFile("bla.txt") shouldBe new File(sample.sampleDir, s"$sampleId.bla.txt")
+
+      sample.libraries.foreach { case (libId, library) =>
+        library.libDir shouldBe new File(sample.sampleDir, s"lib_$libId")
+        library.createFile("bla.txt") shouldBe new File(library.libDir, s"$sampleId-$libId.bla.txt")
+        library.summaryFiles shouldBe Map()
+        library.summaryStats shouldBe Map()
+        library.summarySettings shouldBe Map()
+      }
+    }
+  }
+
+  @Test
+  def testTrio: Unit = {
+    val script = MultiSampleQScriptTest(child :: father :: mother :: Nil)
+    script.init()
+    script.biopetScript()
+
+    script.functions.size shouldBe 4
+
+    script.samples("child").gender shouldBe Gender.Male
+    script.samples("father").gender shouldBe Gender.Male
+    script.samples("mother").gender shouldBe Gender.Female
+    script.samples("child").father shouldBe Some("father")
+    script.samples("child").mother shouldBe Some("mother")
+  }
+
+  @Test
+  def testGroups: Unit = {
+    val script = MultiSampleQScriptTest(sample1 :: sample2 :: sample3 :: Nil)
+    script.init()
+    script.biopetScript()
 
-    val bla = MultiSampleQScriptTest(sample1 :: sample2 :: sample3 :: child :: father :: mother :: Nil)
-    bla.init()
-    bla.biopetScript()
+    script.functions.size shouldBe 4
 
-    bla.samples.foreach(_._2.gender)
+    script.samples("sample1").sampleGroups shouldBe List("1")
+    script.samples("sample1").libraries("lib1").libGroups shouldBe List("1")
+    script.samples("sample2").sampleGroups shouldBe List("2")
+    script.samples("sample2").libraries("lib1").libGroups shouldBe List("3")
 
-    //println(bla.buffer.toString())
+    script.samples("sample3").sampleGroups shouldBe Nil
+  }
+
+  @Test
+  def testOnlySamples: Unit = {
+    val script = MultiSampleQScriptTest(sample1 :: sample2 :: sample3 :: Nil, List("sample1"))
+    script.init()
+    script.biopetScript()
+
+    script.functions.size shouldBe 1
   }
 }
 
 object MultiSampleQScriptTest {
-  val sample1 = Map("samples" -> Map("sample1" -> Map("libraries" -> Map(
-    "lib1" -> Map("test" -> "1-1")
-  ))))
-
-  val sample2 = Map("samples" -> Map("sample2" -> Map("libraries" -> Map(
-    "lib1" -> Map("test" -> "2-1"),
-    "lib2" -> Map("test" -> "2-2")
-  ))))
+  val sample1 = Map("samples" -> Map("sample1" -> Map(
+    "gender" -> "blablablablabla",
+    "groups" -> List("1"),
+    "libraries" -> Map(
+      "lib1" -> Map("test" -> "1-1")
+    )))
+  )
+
+  val sample2 = Map("samples" -> Map("sample2" -> Map(
+    "groups" -> List("2"),
+    "libraries" -> Map(
+      "lib1" -> Map("test" -> "2-1", "groups" -> List("3")),
+      "lib2" -> Map("test" -> "2-2")
+    ))))
 
   val sample3 = Map("samples" -> Map("sample3" -> Map("libraries" -> Map(
     "lib1" -> Map("test" -> "3-1"),
@@ -50,8 +116,10 @@ object MultiSampleQScriptTest {
   val father = Map("samples" -> Map("father" -> Map("gender" -> "male")))
   val mother = Map("samples" -> Map("mother" -> Map("gender" -> "female")))
 
-  def apply(configs: List[Map[String, Any]]) = {
-    new QScript with MultiSampleQScript {
+  def apply(configs: List[Map[String, Any]], only: List[String] = Nil) = {
+    new QScript with MultiSampleQScript { qscript =>
+
+      override val onlySamples = only
 
       var buffer = new ListBuffer[String]()
 
@@ -84,6 +152,7 @@ object MultiSampleQScriptTest {
         protected def addJobs(): Unit = {
           buffer += s"$sampleId"
           addPerLibJobs()
+          add(new Md5sum(qscript))
         }
 
         /** Must return files to store into summary */
@@ -97,6 +166,7 @@ object MultiSampleQScriptTest {
         * Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given.
         */
       def addMultiSampleJobs(): Unit = {
+        add(new Md5sum(qscript))
       }
 
       /**