Added check on unused config values

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

@@ -30,6 +30,33 @@ import scala.collection.JavaConversions._
  *
  */
 object ConfigUtils extends Logging {
+  /**
+   * This method give back all nested values that does exist in map1 but not in map2
+   * @param map1 input map
+   * @param map2 input map
+   * @return Uniqe map1
+   */
+  def uniqeKeys(map1: Map[String, Any], map2: Map[String, Any]): Map[String, Any] = {
+    filterEmtpyMapValues(map1
+      .flatMap {
+        case (key, value: Map[_, _])             => Some(key -> uniqeKeys(value.asInstanceOf[Map[String, Any]], map2.getOrElse(key, Map()).asInstanceOf[Map[String, Any]]))
+        case (key, value) if !map2.contains(key) => Some(key -> value)
+        case _                                   => None
+      })
+  }
+
+  /**
+   * Filter values that are a map but are empty
+   * @param map input map
+   * @return output map
+   */
+  def filterEmtpyMapValues(map: Map[String, Any]): Map[String, Any] = {
+    map.filter {
+      case (key, value: Map[_, _]) => value.nonEmpty
+      case _                       => true
+    }
+  }
+
   /**
    * Merge 2 maps, when value is in a map in map1 and map2 the value calls recursively this function
    * @param map1 Prio over map2

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

@@ -215,6 +215,17 @@ class Config(protected var _map: Map[String, Any],
     // Positions where values are found
     val found = convertIndexValuesToMap(foundCache.filter(!_._2.default).toList.map(x => (x._2.foundIndex, x._2.value)))
     val fixed = convertIndexValuesToMap(fixedCache.filter(!_._2.default).toList.map(x => (x._2.foundIndex, x._2.value)))
+    val unused = uniqeKeys(map, found)
+
+    def reportUnused(map: Map[String, Any], path: List[String] = Nil): Unit = {
+      map.foreach {
+        case (key, value: Map[_, _]) => reportUnused(value.asInstanceOf[Map[String, Any]], path :+ key)
+        case (key, value) => logger.warn(s"config key in user config is never used, key: $key" +
+          (if (path.nonEmpty) s", path: ${path.mkString(" -> ")}" else ""))
+      }
+    }
+
+    reportUnused(unused)
 
     // Positions where to start searching
     val effectiveFound = convertIndexValuesToMap(foundCache.filter(!_._2.default).toList.map(x => (x._2.requestIndex, x._2.value)), Some(false))
@@ -226,7 +237,8 @@ class Config(protected var _map: Map[String, Any],
     val fullEffective = ConfigUtils.mergeMaps(effectiveFound, effectiveDefaultFound)
     val fullEffectiveWithNotFound = ConfigUtils.mergeMaps(fullEffective, notFound)
 
-    writeMapToJsonFile(_map, "input")
+    writeMapToJsonFile(map, "input")
+    writeMapToJsonFile(unused, "unused")
     writeMapToJsonFile(_defaults, "defaults")
     writeMapToJsonFile(found, "found")
     writeMapToJsonFile(fixed, "fixed")
@@ -238,7 +250,7 @@ class Config(protected var _map: Map[String, Any],
     writeMapToJsonFile(fullEffectiveWithNotFound, "effective.full.notfound")
   }
 
-  override def toString: String = _map.toString()
+  override def toString: String = map.toString()
 }
 
 object Config extends Logging {

biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala

@@ -223,6 +223,21 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
     mergeMaps(map2, map1, (a, b, k) => a.toString + b.toString) shouldBe Map("c" -> Map("x" -> "21"))
     mergeMaps(map2, map2, (a, b, k) => a.toString + b.toString) shouldBe Map("c" -> Map("x" -> "22"))
   }
+
+  @Test def testFilterEmtpyMapValues: Unit = {
+    ConfigUtils.filterEmtpyMapValues(Map("bla" -> "bla")) shouldBe Map("bla" -> "bla")
+    ConfigUtils.filterEmtpyMapValues(Map("bla" -> Map())) shouldBe Map()
+    ConfigUtils.filterEmtpyMapValues(Map("bla" -> Map("bla" -> "bla"))) shouldBe Map("bla" -> Map("bla" -> "bla"))
+    ConfigUtils.filterEmtpyMapValues(Map("bla" -> Map("bla" -> "bla"))) shouldBe Map("bla" -> Map("bla" -> "bla"))
+    ConfigUtils.filterEmtpyMapValues(Map("bla" -> Map("bla" -> "bla"), "bla2" -> "bla")) shouldBe Map("bla" -> Map("bla" -> "bla"), "bla2" -> "bla")
+  }
+
+  @Test def testUniqeKeys: Unit = {
+    ConfigUtils.uniqeKeys(Map("bla" -> "bla"), Map("bla" -> "bla")) shouldBe Map()
+    ConfigUtils.uniqeKeys(Map("bla" -> "bla"), Map()) shouldBe Map("bla" -> "bla")
+    ConfigUtils.uniqeKeys(Map("bla" -> Map("bla" -> "bla")), Map("bla" -> Map("bla" -> "bla"))) shouldBe Map()
+    ConfigUtils.uniqeKeys(Map("bla" -> Map("bla" -> "bla")), Map("bla" -> Map())) shouldBe Map("bla" -> Map("bla" -> "bla"))
+  }
 }
 
 object ConfigUtilsTest {