From a4bacc878af4dc211dcdf388547a0ea4e8f72717 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 23 Jun 2014 12:54:00 +0200
Subject: [PATCH] Moved getThreads to BiopetCommandLineFunction
---
.../core/BiopetCommandLineFunction.scala | 23 +++++++++++--------
.../biopet/core/config/Configurable.scala | 15 ------------
2 files changed, 14 insertions(+), 24 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index a56ed05d8..bf8fe4d04 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -9,11 +9,7 @@ import scala.util.matching.Regex
import nl.lumc.sasc.biopet.core.config._
abstract class BiopetCommandLineFunction extends CommandLineFunction with Configurable {
-// val globalConfig: Config
analysisName = getClass.getSimpleName
-// protected var config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName.toLowerCase), globalConfig)
-// logger.debug("config passed for " + analysisName)
-// logger.debug("config for " + analysisName + ": " + config)
@Input(doc="deps", required=false)
var deps: List[File] = Nil
@@ -35,11 +31,6 @@ abstract class BiopetCommandLineFunction extends CommandLineFunction with Config
protected def afterGraph {
}
-// def setConfig(name:String) {
-// analysisName = name
-// config = Config.mergeConfigs(config.getAsConfig(analysisName.toLowerCase), config)
-// }
-
override def freezeFieldValues() {
checkExecuteble
afterGraph
@@ -115,4 +106,18 @@ abstract class BiopetCommandLineFunction extends CommandLineFunction with Config
logger.warn("Version command: '" + versionCommand + "' give a exit code 0 but no version was found, executeble oke?")
return "N/A"
}
+
+ def getThreads(default:Int) : Int = {
+ val maxThreads: Int = config("maxthreads", 8)
+ val threads: Int = config("threads", default)
+ if (maxThreads > threads) return threads
+ else return maxThreads
+ }
+
+ def getThreads(default:Int, module:String) : Int = {
+ val maxThreads: Int = config("maxthreads", 8, module)
+ val threads: Int = config("threads", default, module)
+ if (maxThreads > threads) return threads
+ else return maxThreads
+ }
}
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
index ecb93d81e..884d36b61 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
@@ -28,21 +28,6 @@ trait Configurable extends Logging {
implicit def configValue2stringList(value:ConfigValue) = Configurable.any2stringList(value.value)
implicit def configValue2stringSet(value:ConfigValue) = Configurable.any2stringList(value.value).toSet
implicit def configValue2map(value:ConfigValue) = Configurable.any2map(value.value)
-
-
- def getThreads(default:Int) : Int = {
- val maxThreads: Int = config("maxthreads", 8)
- val threads: Int = config("threads", default)
- if (maxThreads > threads) return threads
- else return maxThreads
- }
-
- def getThreads(default:Int, module:String) : Int = {
- val maxThreads: Int = config("maxthreads", 8, module)
- val threads: Int = config("threads", default, module)
- if (maxThreads > threads) return threads
- else return maxThreads
- }
}
object Configurable extends Logging {
--
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