From 313b0c0493e758243c8d68d217b088656c62f8d3 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 11 Feb 2015 16:01:47 +0100
Subject: [PATCH] Make a val for globalConfig, test should now be able to
override it so unit test are not depending on a global var
---
.../nl/lumc/sasc/biopet/core/BiopetQScript.scala | 4 ++--
.../lumc/sasc/biopet/core/MultiSampleQScript.scala | 6 +++---
.../nl/lumc/sasc/biopet/core/config/Config.scala | 3 +--
.../sasc/biopet/core/config/Configurable.scala | 7 ++++---
.../sasc/biopet/core/config/ConfigurableTest.scala | 14 ++++++--------
5 files changed, 16 insertions(+), 18 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 9dd433ab5..062d725ba 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -32,7 +32,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
val configfiles: List[File] = Nil
var outputDir: String = {
- val temp = Config.getValueFromMap(Config.global.map, ConfigValueIndex(this.configName, configPath, "output_dir"))
+ val temp = Config.getValueFromMap(globalConfig.map, ConfigValueIndex(this.configName, configPath, "output_dir"))
if (temp.isEmpty) ""
else {
val t = temp.get.value.toString
@@ -71,7 +71,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
case _ =>
}
- if (new File(outputDir).canWrite) Config.global.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
+ if (new File(outputDir).canWrite) globalConfig.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
else BiopetQScript.addError("Output dir: '" + outputDir + "' is not writeable")
BiopetQScript.checkErrors
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index eb76502c8..4184f29af 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -28,7 +28,7 @@ trait MultiSampleQScript extends BiopetQScript {
@Argument(doc = "Only Sample", shortName = "sample", required = false)
private val onlySamples: List[String] = Nil
- require(Config.global.map.contains("samples"), "No Samples found in config")
+ require(globalConfig.map.contains("samples"), "No Samples found in config")
/**
* Sample class with basic functions build in
@@ -80,7 +80,7 @@ trait MultiSampleQScript extends BiopetQScript {
/** returns a set with library names */
protected def libIds: Set[String] = {
- ConfigUtils.getMapFromPath(Config.global.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
+ ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
}
/** Adds sample jobs */
@@ -125,7 +125,7 @@ trait MultiSampleQScript extends BiopetQScript {
val samples: Map[String, Sample] = sampleIds.map(id => id -> makeSample(id)).toMap
/** Returns a list of all sampleIDs */
- protected def sampleIds: Set[String] = ConfigUtils.any2map(Config.global.map("samples")).keySet
+ protected def sampleIds: Set[String] = ConfigUtils.any2map(globalConfig.map("samples")).keySet
/** Runs addAndTrackJobs method for each sample */
final def addSamplesJobs() {
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 0e404dd5c..e25e8ef50 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
@@ -138,7 +138,6 @@ class Config(var map: Map[String, Any]) extends Logging {
defaultCache += (requestedIndex -> ConfigValue(requestedIndex, null, default, freeVar))
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 = {
@@ -175,7 +174,7 @@ class Config(var map: Map[String, Any]) extends Logging {
val fullEffective = ConfigUtils.mergeMaps(effectiveFound, effectiveDefaultFound)
val fullEffectiveWithNotFound = ConfigUtils.mergeMaps(fullEffective, notFound)
- writeMapToJsonFile(Config.global.map, "input")
+ writeMapToJsonFile(this.map, "input")
writeMapToJsonFile(found, "found")
writeMapToJsonFile(effectiveFound, "effective.found")
writeMapToJsonFile(effectiveDefaultFound, "effective.defaults")
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 774b15d2d..51997ccb8 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
@@ -21,6 +21,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
trait Configurable extends ImplicitConversions {
/** Should be object of parant object */
val root: Configurable
+ val globalConfig: Config = if (root != null) root.globalConfig else Config.global
/** subfix to the path */
def subPath: List[String] = Nil
@@ -98,8 +99,8 @@ trait Configurable extends ImplicitConversions {
val value = Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar))
if (value.isDefined) value.get.value else default
}
- if (d == null) Config.global(m, p, key, freeVar = freeVar)
- else Config.global(m, p, key, d, freeVar)
+ if (d == null) globalConfig(m, p, key, freeVar = freeVar)
+ else globalConfig(m, p, key, d, freeVar)
}
/**
@@ -121,7 +122,7 @@ trait Configurable extends ImplicitConversions {
val m = if (submodule != null) submodule else configName
val p = path(s, l, submodule)
- Config.global.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
+ globalConfig.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
}
}
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
index 55f672cc1..ba0429fd3 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
@@ -11,10 +11,10 @@ import org.testng.annotations.Test
*/
class ConfigurableTest extends TestNGSuite with Matchers {
@Test def testConfigurable: Unit = {
- Config.global.map = Map()
- Config.global.loadConfigFile(ConfigurableTest.file)
-
- val classC = new ClassC
+ val classC = new ClassC {
+ override def configName = "classc"
+ override val globalConfig = new Config(ConfigurableTest.map)
+ }
classC.configPath shouldBe Nil
classC.configFullPath shouldBe List("classc")
@@ -53,12 +53,12 @@ abstract class Cfg extends Configurable {
class ClassA(val root: Configurable) extends Cfg
class ClassB(val root: Configurable) extends Cfg {
- val classA = new ClassA(this)
+ lazy val classA = new ClassA(this)
}
class ClassC(val root: Configurable) extends Cfg {
def this() = this(null)
- val classB = new ClassB(this)
+ lazy val classB = new ClassB(this)
}
object ConfigurableTest {
@@ -80,6 +80,4 @@ object ConfigurableTest {
)
)
)
-
- val file = ConfigUtilsTest.writeTemp(ConfigUtils.mapToJson(map).spaces2)
}
--
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