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We don't have to overwrite system properties like this.\n     *\n+    * Also copies variables from config/system/environment/defaults over to the system properties.\n+    * Fixes issue where users are trying to specify Java properties as environment variables.\n+    *\n     * @param args The command line arguments.\n     */\n-  private def setupServerLogging(args: Array[String]): Unit = {\n-    getAction(args) match {\n-      case Some(Actions.Server) => sys.props.getOrElseUpdate(\"LOG_MODE\", \"STANDARD\")\n-      case _ =>\n+  private def initLogging(args: Array[String]): Unit = {\n+    val defaultLogMode = getAction(args) match {\n+      case Some(Actions.Server) => \"STANDARD\"\n+      case _ => \"PRETTY\"\n     }\n+\n+    val defaultProps = Map(\"LOG_MODE\" -> defaultLogMode, \"LOG_LEVEL\" -> \"INFO\")\n+\n+    val config = ConfigFactory.load\n+      .withFallback(ConfigFactory.systemEnvironment())\n+      .withFallback(ConfigFactory.parseMap(defaultProps.asJava, \"Defaults\"))\n+\n+    val props = sys.props\n+    defaultProps.keys foreach { key =>\n+      props += key -> config.getString(key)\n+    }\n+\n+    ConfigFactory.invalidateCaches()","path":"src/main/scala/cromwell/Main.scala","position":63,"original_position":63,"commit_id":"a2ebf3bd9db2add020385203c00eabb1dced8145","original_commit_id":"a2ebf3bd9db2add020385203c00eabb1dced8145","user":{"login":"mcovarr","id":10790523,"avatar_url":"https://avatars.githubusercontent.com/u/10790523?v=3","gravatar_id":"","url":"https://api.github.com/users/mcovarr","html_url":"https://github.com/mcovarr","followers_url":"https://api.github.com/users/mcovarr/followers","following_url":"https://api.github.com/users/mcovarr/following{/other_user}","gists_url":"https://api.github.com/users/mcovarr/gists{/gist_id}","starred_url":"https://api.github.com/users/mcovarr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcovarr/subscriptions","organizations_url":"https://api.github.com/users/mcovarr/orgs","repos_url":"https://api.github.com/users/mcovarr/repos","events_url":"https://api.github.com/users/mcovarr/events{/privacy}","received_events_url":"https://api.github.com/users/mcovarr/received_events","type":"User","site_admin":false},"body":"I'm 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