Commit d2f9c54e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Made a global config

parent 5c3e9590
......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.core
import java.io.File
import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.config.{ Config, Configurable }
import org.broadinstitute.gatk.utils.commandline.Argument
import org.broadinstitute.gatk.queue.QSettings
import org.broadinstitute.gatk.queue.function.QFunction
......@@ -25,7 +25,7 @@ trait BiopetQScript extends Configurable {
var functions: Seq[QFunction]
final def script() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
for (file <- configfiles) Config.global.loadConfigFile(file)
if (!outputDir.endsWith("/")) outputDir += "/"
init
biopetScript
......@@ -33,7 +33,7 @@ trait BiopetQScript extends Configurable {
case f: BiopetCommandLineFunctionTrait => f.afterGraph
case _ =>
}
val configReport = globalConfig.getReport
val configReport = Config.global.getReport
val configReportFile = new File(outputDir + qSettings.runName + ".configreport.txt")
configReportFile.getParentFile.mkdir
val writer = new PrintWriter(configReportFile)
......
package nl.lumc.sasc.biopet.core
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.config.{ Config, Configurable }
trait MultiSampleQScript extends BiopetQScript {
type LibraryOutput <: AbstractLibraryOutput
......@@ -20,7 +20,7 @@ trait MultiSampleQScript extends BiopetQScript {
final def runSamplesJobs() {
samplesConfig = config("samples")
if (samplesConfig == null) samplesConfig = Map()
if (globalConfig.contains("samples")) for ((key, value) <- samplesConfig) {
if (Config.global.contains("samples")) for ((key, value) <- samplesConfig) {
var sample = Configurable.any2map(value)
if (!sample.contains("ID")) sample += ("ID" -> key)
if (sample("ID") == key) {
......
......@@ -105,6 +105,8 @@ class Config(var map: Map[String, Any]) extends Logging {
}
object Config {
val global = new Config
def valueToMap(input: Any): Map[String, Any] = {
input match {
case m: Map[_, _] => return m.asInstanceOf[Map[String, Any]]
......
......@@ -6,7 +6,7 @@ import scala.language.implicitConversions
trait Configurable extends Logging {
val root: Configurable
val globalConfig: Config = if (root != null) root.globalConfig else new Config()
//val globalConfig: Config = if (root != null) root.globalConfig else new Config()
def configPath: List[String] = if (root != null) root.configFullPath else List()
protected lazy val configName = getClass.getSimpleName.toLowerCase
protected lazy val configFullPath = configName :: configPath
......@@ -29,15 +29,15 @@ trait Configurable extends Logging {
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 globalConfig(m, p, key, freeVar)
else return globalConfig(m, p, key, d, freeVar)
if (d == null) return Config.global(m, p, key, freeVar)
else return Config.global(m, p, key, d, freeVar)
}
def contains(key: String, submodule: String = null, freeVar: Boolean = true) = {
val m = if (submodule != null) submodule else configName
val p = if (submodule != null) configName :: configPath else configPath
globalConfig.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
Config.global.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
}
}
......
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