From fdf136943612cc87d00393d11b32a59c2e747cba Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 6 Apr 2015 13:04:43 +0200
Subject: [PATCH] Added manual path set to config
---
.../lumc/sasc/biopet/core/config/Configurable.scala | 12 +++++++-----
1 file changed, 7 insertions(+), 5 deletions(-)
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 1a3df9eaf..2f33005c2 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
@@ -52,7 +52,7 @@ trait Configurable extends ImplicitConversions {
* @param submodule
* @return
*/
- def path(sample: String = null, library: String = null, submodule: String = null) = {
+ def getConfigPath(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) configPath ::: configName :: Nil else configPath)
@@ -91,11 +91,12 @@ trait Configurable extends ImplicitConversions {
submodule: String = null,
freeVar: Boolean = true,
sample: String = null,
- library: String = null): ConfigValue = {
+ library: String = null,
+ path: List[String] = null): ConfigValue = {
val s = if (sample != null || defaultSample.isEmpty) sample else defaultSample.get
val l = if (library != null || defaultLibrary.isEmpty) library else defaultLibrary.get
val m = if (submodule != null) submodule else configName
- val p = path(s, l, submodule)
+ val p = if (path == null) getConfigPath(s, l, submodule) else path
val d = {
val value = Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar))
if (value.isDefined) value.get.value else default
@@ -117,11 +118,12 @@ trait Configurable extends ImplicitConversions {
submodule: String = null,
freeVar: Boolean = true,
sample: String = null,
- library: String = null) = {
+ library: String = null,
+ path: List[String] = null) = {
val s = if (sample != null || defaultSample.isEmpty) sample else defaultSample.get
val l = if (library != null || defaultLibrary.isEmpty) library else defaultLibrary.get
val m = if (submodule != null) submodule else configName
- val p = path(s, l, submodule)
+ val p = if (path == null) getConfigPath(s, l, submodule) else path
globalConfig.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
}
--
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