From b7fe37de45991d958ca9eb9feff843b1fe039588 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 9 Feb 2015 10:41:34 +0100
Subject: [PATCH] Removed required argument for config, now handled by
conversions, not a option means required
---
.../nl/lumc/sasc/biopet/core/config/Config.scala | 7 ++++---
.../lumc/sasc/biopet/core/config/Configurable.scala | 12 ++----------
.../nl/lumc/sasc/biopet/utils/ConfigUtils.scala | 4 +++-
3 files changed, 9 insertions(+), 14 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 4ea65cb5a..0e404dd5c 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
@@ -133,11 +133,12 @@ class Config(var map: Map[String, Any]) extends Logging {
*/
protected[config] def apply(module: String, path: List[String], key: String, default: Any = null, freeVar: Boolean = true): ConfigValue = {
val requestedIndex = ConfigValueIndex(module, path, key, freeVar)
- if (contains(requestedIndex)) return foundCache(requestedIndex)
+ if (contains(requestedIndex)) foundCache(requestedIndex)
else if (default != null) {
defaultCache += (requestedIndex -> ConfigValue(requestedIndex, null, default, freeVar))
- return defaultCache(requestedIndex)
- } else throw new IllegalStateException("Value in config could not be found but it seems required, index: " + requestedIndex)
+ defaultCache(requestedIndex)
+ } else ConfigValue(requestedIndex, null, null, freeVar)
+ //else throw new IllegalStateException("Value in config could not be found but it seems required, index: " + requestedIndex)
}
def writeReport(id: String, directory: String): Unit = {
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 54e6dfd17..774b15d2d 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
@@ -79,7 +79,6 @@ trait Configurable extends ImplicitConversions {
* @param key Name of value
* @param default Default value if not found
* @param submodule Adds to the path
- * @param required Default false, if true and value is not found this function will raise an exception
* @param freeVar Default true, if set false value must exist in module
* @param sample Default null, when set path is prefixed with "samples" -> "sampleID"
* @param library Default null, when set path is prefixed with "libraries" -> "libraryID"
@@ -88,7 +87,6 @@ trait Configurable extends ImplicitConversions {
def apply(key: String,
default: Any = null,
submodule: String = null,
- required: Boolean = false,
freeVar: Boolean = true,
sample: String = null,
library: String = null): ConfigValue = {
@@ -100,14 +98,8 @@ trait Configurable extends ImplicitConversions {
val value = Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar))
if (value.isDefined) value.get.value else default
}
- if (!contains(key, submodule, freeVar, sample = s, library = l) && 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)
- } else return null
- }
- if (d == null) return Config.global(m, p, key, freeVar = freeVar)
- else return Config.global(m, p, key, d, freeVar)
+ if (d == null) Config.global(m, p, key, freeVar = freeVar)
+ else Config.global(m, p, key, d, freeVar)
}
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
index cef97ffaa..c3a79b24c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
@@ -332,7 +332,9 @@ object ConfigUtils extends Logging {
private def requiredValue(value: ConfigValue): Unit = {
if (!valueExists(value))
- throw new IllegalStateException("Value does not exist but is required, key: '" + value.requestIndex.key + "'")
+ throw new IllegalStateException("Value does not exist but is required, key: " + value.requestIndex.key +
+ " module: " + value.requestIndex.module +
+ (if (value.requestIndex.path != Nil) " path: " + value.requestIndex.path.mkString("->") else ""))
}
private def valueExists(value: ConfigValue): Boolean = {
--
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