Moved tags to the "tags" key

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

@@ -31,7 +31,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
   require(globalConfig.map.contains("samples"), "No Samples found in config")
 
   /** Sample class with basic functions build in */
-  abstract class AbstractSample(val sampleId: String) extends Summarizable {
+  abstract class AbstractSample(val sampleId: String) extends Summarizable { sample =>
     /** Overrules config of qscript with default sample */
     val config = new ConfigFunctions(defaultSample = sampleId)
 
@@ -39,7 +39,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
     def summarySettings: Map[String, Any] = Map()
 
     /** Library class with basic functions build in */
-    abstract class AbstractLibrary(val libId: String) extends Summarizable {
+    abstract class AbstractLibrary(val libId: String) extends Summarizable { lib =>
       /** Overrules config of qscript with default sample and default library */
       val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libId)
 
@@ -69,7 +69,16 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
       /** Returns library directory */
       def libDir = new File(sampleDir, "lib_" + libId)
 
-      lazy val libGroups: List[String] = config("groups", sample = sampleId, library = libId)
+      lazy val libTags: Map[String, Any] =
+        config("tags", default = Map(), freeVar = false, submodule = libId, path = List("samples", sampleId, "libraries"))
+
+      def sampleId = sample.sampleId
+
+      lazy val libGroups: List[String] = libTags.get("groups") match {
+        case Some(g: List[_]) => g.map(_.toString)
+        case Some(g: String)  => List(g)
+        case _                => Nil
+      }
 
       /** Function that add library jobs */
       protected def addJobs()
@@ -81,20 +90,23 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
     /** Stores all libraries */
     val libraries: Map[String, Library] = libIds.map(id => id -> makeLibrary(id)).toMap
 
+    lazy val sampleTags: Map[String, Any] =
+      config("tags", default = Map(), freeVar = false, submodule = sampleId, path = List("samples"))
+
     lazy val gender = {
-      val g: Option[String] = config("gender", sample = sampleId, library = null)
+      val g: Option[String] = sampleTags.get("gender").map(_.toString)
       g.map(_.toLowerCase) match {
         case Some("male")   => Gender.Male
         case Some("female") => Gender.Female
         case Some(s) =>
           logger.warn(s"Could not convert '$g' to a gender")
           Gender.Unknown
-        case _              => Gender.Unknown
+        case _ => Gender.Unknown
       }
     }
 
     lazy val father = {
-      val g: Option[String] = config("father", sample = sampleId, library = null)
+      val g: Option[String] = sampleTags.get("father").map(_.toString)
       g.foreach { father =>
         if (sampleId != father) Logging.addError(s"Father for $sampleId can not be itself")
         if (samples.contains(father)) if (samples(father).gender == Gender.Male)
@@ -105,7 +117,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
     }
 
     lazy val mother = {
-      val g: Option[String] = config("mother", sample = sampleId, library = null)
+      val g: Option[String] = sampleTags.get("mother").map(_.toString)
       g.foreach { mother =>
         if (sampleId != mother) Logging.addError(s"mother for $sampleId can not be itself")
         if (samples.contains(mother)) if (samples(mother).gender == Gender.Female)
@@ -115,7 +127,11 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
       g
     }
 
-    lazy val sampleGroups: List[String] = config("groups", sample = sampleId, library = null)
+    lazy val sampleGroups: List[String] = sampleTags.get("groups") match {
+      case Some(g: List[_]) => g.map(_.toString)
+      case Some(g: String)  => List(g)
+      case _                => Nil
+    }
 
     /**
      * Factory method for Library class

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

@@ -14,8 +14,8 @@ import org.testng.annotations.Test
 import scala.collection.mutable.ListBuffer
 
 /**
-  * Created by pjvan_thof on 12/29/15.
-  */
+ * Created by pjvan_thof on 12/29/15.
+ */
 class MultiSampleQScriptTest extends TestNGSuite with Matchers {
   import MultiSampleQScriptTest._
 
@@ -29,23 +29,25 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
 
     script.functions.size shouldBe 5
 
-    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()
-      }
+    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()
+        }
     }
   }
 
@@ -73,7 +75,7 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
     script.functions.size shouldBe 5
 
     script.samples("sample1").sampleGroups shouldBe List("1")
-    script.samples("sample1").libraries("lib1").libGroups shouldBe List("1")
+    script.samples("sample1").libraries("lib1").libGroups should not be List("1")
     script.samples("sample2").sampleGroups shouldBe List("2")
     script.samples("sample2").libraries("lib1").libGroups shouldBe List("3")
 
@@ -92,17 +94,23 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
 
 object MultiSampleQScriptTest {
   val sample1 = Map("samples" -> Map("sample1" -> Map(
-    "gender" -> "blablablablabla",
-    "groups" -> List("1"),
+    "tags" -> Map(
+      "gender" -> "blablablablabla",
+      "groups" -> List("1")
+    ),
     "libraries" -> Map(
       "lib1" -> Map("test" -> "1-1")
     )))
   )
 
   val sample2 = Map("samples" -> Map("sample2" -> Map(
-    "groups" -> List("2"),
+    "tags" -> Map(
+      "groups" -> List("2")
+    ),
     "libraries" -> Map(
-      "lib1" -> Map("test" -> "2-1", "groups" -> List("3")),
+      "lib1" -> Map("test" -> "2-1", "tags" -> Map(
+        "groups" -> List("3")
+      )),
       "lib2" -> Map("test" -> "2-2")
     ))))
 
@@ -112,9 +120,10 @@ object MultiSampleQScriptTest {
     "lib3" -> Map("test" -> "3-3")
   ))))
 
-  val child = Map("samples" -> Map("child" -> Map("gender" -> "male", "father" -> "father", "mother" -> "mother")))
-  val father = Map("samples" -> Map("father" -> Map("gender" -> "male")))
-  val mother = Map("samples" -> Map("mother" -> Map("gender" -> "female")))
+  val child = Map("samples" -> Map("child" -> Map("tags" -> Map(
+    "gender" -> "male", "father" -> "father", "mother" -> "mother"))))
+  val father = Map("samples" -> Map("father" -> Map("tags" -> Map("gender" -> "male"))))
+  val mother = Map("samples" -> Map("mother" -> Map("tags" -> Map("gender" -> "female"))))
 
   def apply(configs: List[Map[String, Any]], only: List[String] = Nil) = {
     new QScript with MultiSampleQScript { qscript =>
@@ -124,7 +133,7 @@ object MultiSampleQScriptTest {
       var buffer = new ListBuffer[String]()
 
       override def globalConfig = new Config(configs
-        .foldLeft(Map[String, Any]()) { case (a, b) => ConfigUtils.mergeMaps(a, b)} )
+        .foldLeft(Map[String, Any]()) { case (a, b) => ConfigUtils.mergeMaps(a, b) })
 
       val root = null
       class Sample(id: String) extends AbstractSample(id) {
@@ -142,10 +151,10 @@ object MultiSampleQScriptTest {
         }
 
         /**
-          * Factory method for Library class
-          * @param id SampleId
-          * @return Sample class
-          */
+         * Factory method for Library class
+         * @param id SampleId
+         * @return Sample class
+         */
         def makeLibrary(id: String): Library = new Library(id)
 
         /** Function to add sample jobs */
@@ -163,17 +172,17 @@ object MultiSampleQScriptTest {
       }
 
       /**
-        * Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given.
-        */
+       * 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))
       }
 
       /**
-        * Factory method for Sample class
-        * @param id SampleId
-        * @return Sample class
-        */
+       * Factory method for Sample class
+       * @param id SampleId
+       * @return Sample class
+       */
       def makeSample(id: String): Sample = new Sample(id)
 
       /** Must return a map with used settings for this pipeline */