From 37def774504467df8b5d61227ff1fe7894595e21 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 4 Sep 2015 21:15:39 +0200
Subject: [PATCH] Make config map immutable from outside the class
---
.../lumc/sasc/biopet/core/config/Config.scala | 24 ++++++++++---------
.../sasc/biopet/extensions/GsnapTest.scala | 20 +++++-----------
2 files changed, 19 insertions(+), 25 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 c477a4aaa..d9f0f650e 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
@@ -23,10 +23,10 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils._
/**
* This class can store nested config values
- * @param map Map with value for new config
+ * @param _map Map with value for new config
* @constructor Load config with existing map
*/
-class Config(var map: Map[String, Any],
+class Config(protected var _map: Map[String, Any],
protected[core] var defaults: Map[String, Any] = Map()) extends Logging {
logger.debug("Init phase of config")
@@ -36,6 +36,8 @@ class Config(var map: Map[String, Any],
loadDefaultConfig()
}
+ def map = _map
+
/**
* Loading a environmental variable as location of config files to merge into the config
* @param valueName Name of value
@@ -71,9 +73,9 @@ class Config(var map: Map[String, Any],
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)
+ if (_map.isEmpty) _map = configMap
+ else _map = mergeMaps(configMap, _map)
+ logger.debug("New config: " + _map)
}
}
@@ -87,7 +89,7 @@ class Config(var map: Map[String, Any],
def addValue(key: String, value: Any, path: List[String] = Nil, default: Boolean = false): Unit = {
val valueMap = path.foldRight(Map(key -> value))((a, b) => Map(a -> b))
if (default) defaults = mergeMaps(valueMap, defaults)
- else map = mergeMaps(valueMap, map)
+ else _map = mergeMaps(valueMap, _map)
}
protected[config] var notFoundCache: List[ConfigValueIndex] = List()
@@ -106,7 +108,7 @@ class Config(var map: Map[String, Any],
* @param s key
* @return True if exist
*/
- def contains(s: String): Boolean = map.contains(s)
+ def contains(s: String): Boolean = _map.contains(s)
/**
* Checks if value exist in config
@@ -131,7 +133,7 @@ class Config(var map: Map[String, Any],
fixedCache += (requestedIndex -> fixedValue.get)
true
} else {
- val value = Config.getValueFromMap(map, requestedIndex)
+ val value = Config.getValueFromMap(_map, requestedIndex)
if (value.isDefined && value.get.value != None) {
foundCache += (requestedIndex -> value.get)
true
@@ -215,7 +217,7 @@ class Config(var map: Map[String, Any],
val fullEffective = ConfigUtils.mergeMaps(effectiveFound, effectiveDefaultFound)
val fullEffectiveWithNotFound = ConfigUtils.mergeMaps(fullEffective, notFound)
- writeMapToJsonFile(this.map, "input")
+ writeMapToJsonFile(this._map, "input")
writeMapToJsonFile(found, "found")
writeMapToJsonFile(effectiveFound, "effective.found")
writeMapToJsonFile(effectiveDefaultFound, "effective.defaults")
@@ -224,7 +226,7 @@ class Config(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 {
@@ -236,7 +238,7 @@ object Config extends Logging {
* @param config2 Low prio map
* @return Merged config
*/
- def mergeConfigs(config1: Config, config2: Config): Config = new Config(mergeMaps(config1.map, config2.map))
+ def mergeConfigs(config1: Config, config2: Config): Config = new Config(mergeMaps(config1._map, config2._map))
/**
* Search for value in index position in a map
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
index 1ffd257e0..d155e9744 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
@@ -25,17 +25,10 @@ import scala.sys.process.{ Process, ProcessLogger }
class GsnapTest extends TestNGSuite with Matchers {
- private def setConfig(key: String, value: String): Map[String, Any] = {
- val oldMap: Map[String, Any] = Config.global.map
- Config.global.map += (key -> value)
- oldMap
- }
-
- private def restoreConfig(oldMap: Map[String, Any]): Unit = Config.global.map = oldMap
-
@BeforeClass def checkExecutable() = {
- val oldMap = setConfig("db", "mock")
- val wrapper = new Gsnap(null)
+ val wrapper = new Gsnap(null) {
+ override def globalConfig = new Config(Map("db" -> "mock"))
+ }
val proc = Process(wrapper.versionCommand)
val exitCode =
try {
@@ -47,13 +40,12 @@ class GsnapTest extends TestNGSuite with Matchers {
}
if (exitCode != 0)
throw new SkipException("Skipping GSNAP test because the executable can not be found")
- restoreConfig(oldMap)
}
@Test(description = "GSNAP version number capture from executable")
def testVersion() = {
- val oldMap = setConfig("db", "mock")
- new Gsnap(null).getVersion should not be "N/A"
- restoreConfig(oldMap)
+ new Gsnap(null) {
+ override def globalConfig = new Config(Map("db" -> "mock"))
+ }.getVersion should not be "N/A"
}
}
--
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