From 8fc4872e795b0c9b757fa95c2f9552c414895311 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 6 Apr 2015 11:35:59 +0200
Subject: [PATCH] Switch defaults from BIOPET_CONFIG env to a defaults var
---
.../lumc/sasc/biopet/core/config/Config.scala | 24 ++++++++++++-------
.../biopet/core/config/Configurable.scala | 2 +-
2 files changed, 16 insertions(+), 10 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
index d2fe78ec2..21fa088ac 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
@@ -27,7 +27,8 @@ import scala.reflect.io.Directory
* @param map Map with value for new config
* @constructor Load config with existing map
*/
-class Config(var map: Map[String, Any]) extends Logging {
+class Config(var map: Map[String, Any],
+ protected[core] var defaults: Map[String, Any] = Map()) extends Logging {
logger.debug("Init phase of config")
/**
@@ -42,14 +43,14 @@ class Config(var map: Map[String, Any]) extends Logging {
* Loading a environmental variable as location of config files to merge into the config
* @param valueName Name of value
*/
- def loadConfigEnv(valueName: String) {
+ def loadConfigEnv(valueName: String, default: Boolean) {
sys.env.get(valueName) match {
case Some(globalFiles) => {
for (globalFile <- globalFiles.split(":")) {
val file: File = new File(globalFile)
if (file.exists) {
logger.info("Loading config file: " + file)
- loadConfigFile(file)
+ loadConfigFile(file, default)
} else logger.warn(valueName + " value found but file '" + file + "' does not exist, no global config is loaded")
}
}
@@ -61,19 +62,24 @@ class Config(var map: Map[String, Any]) extends Logging {
* Loading default value for biopet
*/
def loadDefaultConfig() {
- loadConfigEnv("BIOPET_CONFIG")
+ loadConfigEnv("BIOPET_CONFIG", true)
}
/**
* Merge a json file into the config
* @param configFile Location of file
*/
- def loadConfigFile(configFile: File) {
+ def loadConfigFile(configFile: File, default: Boolean = false) {
val configMap = fileToConfigMap(configFile)
-
- if (map.isEmpty) map = configMap
- else map = mergeMaps(configMap, map)
- logger.debug("New config: " + map)
+ if (default) {
+ if (defaults.isEmpty) defaults = configMap
+ else defaults = mergeMaps(configMap, defaults)
+ logger.debug("New defaults: " + defaults)
+ } else {
+ if (map.isEmpty) map = configMap
+ else map = mergeMaps(configMap, map)
+ logger.debug("New config: " + map)
+ }
}
protected[config] var notFoundCache: List[ConfigValueIndex] = List()
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
index df01a5437..1a3df9eaf 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
@@ -39,7 +39,7 @@ trait Configurable extends ImplicitConversions {
/** Map to store defaults for config */
def defaults: Map[String, Any] = {
if (root != null) root.defaults
- else Map()
+ else globalConfig.defaults
}
val config = new ConfigFunctions
--
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