From 7d27887a4b649d1baa12f63d6dc16e7bcc9c86cb Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 26 Jun 2014 10:28:29 +0200
Subject: [PATCH] Added config report
---
.../lumc/sasc/biopet/core/config/Config.scala | 116 +++++-------------
1 file changed, 31 insertions(+), 85 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
index 3d648648d..58b28113d 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
@@ -4,6 +4,7 @@ import nl.lumc.sasc.biopet.core._
import scala.util.parsing.json._
import java.io.File
import org.broadinstitute.sting.queue.util.Logging
+import argonaut._, Argonaut._
class Config(var map: Map[String,Any]) extends Logging {
logger.debug("Init phase of config")
@@ -19,8 +20,7 @@ class Config(var map: Map[String,Any]) extends Logging {
if (file.exists()) {
logger.info("Loading config file: " + file)
loadConfigFile(file)
- }
- else logger.warn("BIOPET_CONFIG value found but file does not exist, no global config is loaded")
+ } else logger.warn("BIOPET_CONFIG value found but file does not exist, no global config is loaded")
} else logger.info("BIOPET_CONFIG value not found, no global config is loaded")
}
@@ -48,6 +48,7 @@ class Config(var map: Map[String,Any]) extends Logging {
var notFoundCache: List[ConfigValueIndex] = List()
var foundCache: Map[ConfigValueIndex,ConfigValue] = Map()
+ var defaultCache: Map[ConfigValueIndex,ConfigValue] = Map()
def contains(s:String) : Boolean = map.contains(s)
def contains(requestedIndex:ConfigValueIndex) : Boolean = contains(requestedIndex.module, requestedIndex.path, requestedIndex.key)
@@ -98,8 +99,8 @@ class Config(var map: Map[String,Any]) extends Logging {
val requestedIndex = ConfigValueIndex(module,path,key)
if (contains(requestedIndex)) return foundCache(requestedIndex)
else {
- foundCache += (requestedIndex -> ConfigValue.apply(requestedIndex, null, default))
- return foundCache(requestedIndex)
+ defaultCache += (requestedIndex -> ConfigValue.apply(requestedIndex, null, default, true))
+ return defaultCache(requestedIndex)
}
}
@@ -121,88 +122,33 @@ class Config(var map: Map[String,Any]) extends Logging {
return returnMap
}
- private def check(module:String, path: List[String], key:String) {
-
+ def getReport: String = {
+ var output:StringBuilder = new StringBuilder
+ output.append("Config report, sorted on module:\n")
+ var modules:Map[String,StringBuilder] = Map()
+ for ((key,value) <- foundCache) {
+ val module = key.module
+ if (!modules.contains(module)) modules += (module -> new StringBuilder)
+ modules(module).append("Found: " + value.toString + "\n")
+ }
+ for ((key,value) <- defaultCache) {
+ val module = key.module
+ if (!modules.contains(module)) modules += (module -> new StringBuilder)
+ modules(module).append("Default used: " + value.toString + "\n")
+ }
+ for (value <- notFoundCache) {
+ val module = value.module
+ if (!modules.contains(module)) modules += (module -> new StringBuilder)
+ if (!defaultCache.contains(value)) modules(module).append("Not Found: " + value.toString + "\n")
+ }
+ for ((key,value) <- modules) {
+ output.append("Config options for module: " + key + "\n")
+ output.append(value.toString)
+ output.append("\n")
+ }
+ return output.toString
}
-
-// def getAsString(key:String) : String = map(key).toString
-// def getAsString(key:String, default:String) : String = if (contains(key)) getAsString(key) else default
-//
-// def getAsInt(key:String) : Int = {
-// map(key) match {
-// case i:Double => return i.toInt
-// case i:Int => return i
-// case i:String => {
-// logger.warn("Value '" + key + "' is a string insteadof int in json file, trying auto convert")
-// return i.toInt
-// }
-// case _ => throw new IllegalStateException("Value '" + key + "' is not an int")
-// }
-// }
-// def getAsInt(s:String, default:Int) : Int = if (contains(s)) getAsInt(s) else default
-//
-// def getAsDouble(key:String) : Double = {
-// map(key) match {
-// case d:Double => return d
-// case d:Int => return d.toDouble
-// case d:String => {
-// logger.warn("Value '" + key + "' is a string insteadof int in json file, trying auto convert")
-// return d.toDouble
-// }
-// case _ => throw new IllegalStateException("Value '" + key + "' is not an int")
-// }
-// }
-// def getAsDouble(key:String, default:Double) : Double = if (contains(key)) getAsDouble(key) else default
-//
-// def getAsBoolean(key:String) : Boolean = {
-// map(key) match {
-// case b:Boolean => b
-// case b:String => {
-// logger.warn("Value '" + key + "' is a string insteadof boolean in json file, trying auto convert")
-// return b.contains("true")
-// }
-// case b:Int => {
-// logger.warn("Value '" + key + "' is a int insteadof boolean in json file, trying auto convert")
-// (b > 0)
-// }
-// case _ => throw new IllegalStateException("Value '" + key + "' is not an boolean")
-// }
-// }
-// def getAsBoolean(key:String, default:Boolean) : Boolean = if (contains(key)) getAsBoolean(key) else default
-//
-// def getAsList(key:String) : List[Any] = {
-// map(key) match {
-// case l:List[_] => return l
-// case s:String => return List(s)
-// case _ => throw new IllegalStateException("Value '" + key + "' is not an List")
-// }
-// }
-// def getAsList(key:String, default:List[Any]) : List[Any] = if (contains(key)) getAsList(key) else default
-// def getAsListOfStrings(key:String) : List[String] = {
-// var l: List[String] = Nil
-// for (v <- getAsList(key)) l :+= v.toString
-// return l
-// }
-// def getAsListOfStrings(key:String, default:List[String]) : List[String] = if (contains(key)) getAsListOfStrings(key) else default
-//
-// def getAsMap(key:String) : Map[String,Any] = Config.valueToMap(map(key))
-// def getAsMap(key:String, default:Map[String,Any]) : Map[String,Any] = if (contains(key)) getAsMap(key) else default
-//
-// def getAsConfig(key:String, default:Map[String,Any]) : Config = if (contains(key)) new Config(getAsMap(key)) else new Config(default)
-// def getAsConfig(key:String, default:Config) : Config = if (contains(key)) Config.mergeConfigs(getAsConfig(key), default) else default
-// def getAsConfig(key:String, default:Config, subDefault:String) : Config = {
-// if (contains(key)) Config.mergeConfigs(getAsConfig(key), default.getAsConfig(subDefault))
-// else default
-// }
-// def getAsConfig(s:String) : Config = if (contains(s)) new Config(getAsMap(s)) else new Config(Map())
-//
-// def getThreads(default:Int) : Int = {
-// val maxThreads = this.getAsInt("maxthreads", 8)
-// val threads = this.getAsInt("threads", default)
-// if (maxThreads > threads) return threads
-// else return maxThreads
-// }
-
+
override def toString() : String = map.toString
}
--
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