Added sample and library option to config

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

@@ -29,15 +29,27 @@ trait Configurable extends ImplicitConversions {
 
   val config = new ConfigFunctions
 
+  def path(sample: String = null, library: String = null, submodule: String = null) = {
+    (if (sample != null) "samples" :: sample :: Nil else Nil) :::
+      (if (library != null) "libraries" :: library :: Nil else Nil) :::
+      (if (submodule != null) configName :: configPath else configPath)
+  }
+
   protected class ConfigFunctions {
-    def apply(key: String, default: Any = null, submodule: String = null, required: Boolean = false, freeVar: Boolean = true): ConfigValue = {
+    def apply(key: String,
+              default: Any = null,
+              submodule: String = null,
+              required: Boolean = false,
+              freeVar: Boolean = true,
+              sample: String = null,
+              library: String = null): ConfigValue = {
       val m = if (submodule != null) submodule else configName
-      val p = (if (submodule != null) configName :: configPath else configPath)
+      val p = path(sample, library, submodule)
       val d = {
         val value = Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar))
         if (value.isDefined) value.get.value else default
       }
-      if (!contains(key, submodule, freeVar) && d == null) {
+      if (!contains(key, submodule, freeVar, sample = sample, library = library) && d == null) {
         if (required) {
           Logging.logger.error("Value in config could not be found but it is required, key: " + key + "   module: " + m + "   path: " + p)
           throw new IllegalStateException("Value in config could not be found but it is required, key: " + key + "   module: " + m + "   path: " + p)
@@ -47,9 +59,13 @@ trait Configurable extends ImplicitConversions {
       else return Config.global(m, p, key, d, freeVar)
     }
 
-    def contains(key: String, submodule: String = null, freeVar: Boolean = true) = {
+    def contains(key: String,
+                 submodule: String = null,
+                 freeVar: Boolean = true,
+                 sample: String = null,
+                 library: String = null) = {
       val m = if (submodule != null) submodule else configName
-      val p = (if (submodule != null) configName :: configPath else configPath)
+      val p = path(sample, library, submodule)
 
       Config.global.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
     }

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala

@@ -36,12 +36,22 @@ class ConfigurableTest extends TestNGSuite with MockitoSugar with Matchers {
     classC.get("k1", freeVar = false).asString shouldBe "c1"
     classC.classB.get("k1", freeVar = false).asString shouldBe "b1"
     classC.classB.classA.get("k1", freeVar = false).asString shouldBe "a1"
+
+    classC.get("bla", sample = "sample1", library = "library1").asString shouldBe "bla"
+    classC.get("test", sample = "sample1", library = "library1").asString shouldBe "test"
+    classC.get("test", sample = "sample1").asString shouldBe "test"
   }
 }
 
 abstract class Cfg extends Configurable {
-  def get(key: String, default: String = null, submodule: String = null, required: Boolean = false, freeVar: Boolean = true) = {
-    config(key, default, submodule, required, freeVar = freeVar)
+  def get(key: String,
+          default: String = null,
+          submodule: String = null,
+          required: Boolean = false,
+          freeVar: Boolean = true,
+          sample: String = null,
+          library: String = null) = {
+    config(key, default, submodule, required, freeVar = freeVar, sample = sample, library = library)
   }
 }
 
@@ -64,6 +74,15 @@ object ConfigurableTest {
       "k1" -> "b1"
     ), "classc" -> Map(
       "k1" -> "c1"
+    ), "samples" -> Map(
+      "sample1" -> Map(
+        "test" -> "test",
+        "libraries" -> Map(
+          "library1" -> Map(
+            "bla" -> "bla"
+          )
+        )
+      )
     )
   )