diff --git a/public/biopet-framework/pom.xml b/public/biopet-framework/pom.xml
index e2bf9afa18e0b58b7896ea4b6843026169f5d41e..905ae9fda5733ccb769a159669c6bfbfaa0a19b1 100644
--- a/public/biopet-framework/pom.xml
+++ b/public/biopet-framework/pom.xml
@@ -110,5 +110,10 @@
<artifactId>scopt_2.10</artifactId>
<version>3.3.0</version>
</dependency>
+ <dependency>
+ <groupId>org.yaml</groupId>
+ <artifactId>snakeyaml</artifactId>
+ <version>1.15</version>
+ </dependency>
</dependencies>
</project>
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 dbb390e521bdcf297940e74966ce4c801a857afd..8b7748a24fd77018092d65bb0a5366c1a58ac9d1 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
@@ -25,19 +25,19 @@ import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFun
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
import scala.collection.mutable.ListBuffer
-/**
- * Base for biopet pipeline
- */
+/** Base for biopet pipeline */
trait BiopetQScript extends Configurable with GatkLogging {
- @Argument(doc = "JSON config file(s)", fullName = "config_file", shortName = "config", required = false)
+ @Argument(doc = "JSON / YAML config file(s)", fullName = "config_file", shortName = "config", required = false)
val configfiles: List[File] = Nil
+ @Argument(doc = "Config values, value should be formatted like 'key=value' or 'path:path:key=value'", fullName = "config_value", shortName = "cv", required = false)
+ val configValues: List[String] = Nil
+
+ /** Output directory of pipeline */
var outputDir: File = {
- Config.getValueFromMap(globalConfig.map, ConfigValueIndex(this.configName, configPath, "output_dir")) match {
- case Some(value) => new File(value.asString).getAbsoluteFile
- case _ => new File(".")
- }
+ if (config.contains("output_dir", path = Nil)) config("output_dir", path = Nil).asFile
+ else new File(".")
}
@Argument(doc = "Disable all scatters", shortName = "DSC", required = false)
@@ -57,11 +57,10 @@ trait BiopetQScript extends Configurable with GatkLogging {
/** Pipeline itself */
def biopetScript
- /**
- * Script from queue itself, final to force some checks for each pipeline and write report
- */
+ /** Script from queue itself, final to force some checks for each pipeline and write report */
final def script() {
- outputDir = config("output_dir").asFile.getAbsoluteFile
+ outputDir = config("output_dir")
+ outputDir = outputDir.getAbsoluteFile
init
biopetScript
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
index 8a6d6657ab820aed7fcdff294b8c0f4c768cacb7..fde126135bcdbde225b61ee2cbf065aaa9d7963f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
@@ -20,9 +20,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Config
import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
-/**
- * Wrapper around executable from Queue
- */
+/** Wrapper around executable from Queue */
trait PipelineCommand extends MainCommand with GatkLogging {
/**
@@ -31,10 +29,7 @@ trait PipelineCommand extends MainCommand with GatkLogging {
*/
def pipeline = "/" + getClass.getName.stripSuffix("$").replaceAll("\\.", "/") + ".class"
- /**
- * Class can be used directly from java with -cp option
- * @param args
- */
+ /** Class can be used directly from java with -cp option */
def main(args: Array[String]): Unit = {
val argsSize = args.size
for (t <- 0 until argsSize) {
@@ -42,6 +37,17 @@ trait PipelineCommand extends MainCommand with GatkLogging {
if (t >= argsSize) throw new IllegalStateException("-config needs a value")
Config.global.loadConfigFile(new File(args(t + 1)))
}
+
+ if (args(t) == "-cv" || args(t) == "--config_value") {
+ val v = args(t + 1).split("=")
+ require(v.size == 2, "Value should be formatted like 'key=value' or 'path:path:key=value'")
+ val value = v(1)
+ val p = v(0).split(":")
+ val key = p.last
+ val path = p.dropRight(1).toList
+ Config.global.addValue(key, value, path)
+ }
+
if (args(t) == "--logging_level" || args(t) == "-l") {
args(t + 1).toLowerCase match {
case "debug" => Logging.logger.setLevel(org.apache.log4j.Level.DEBUG)
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 d2fe78ec224c921896e51e04c2f51ad0435e201b..c41c8f3175463733e16611920b1968369d4c39c8 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
@@ -20,19 +20,16 @@ import nl.lumc.sasc.biopet.core.Logging
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.ConfigUtils._
-import scala.reflect.io.Directory
-
/**
* This class can store nested config values
* @param map Map with value for new config
* @constructor Load config with existing map
*/
-class Config(var map: Map[String, Any]) extends Logging {
+class Config(var map: Map[String, Any],
+ protected[core] var defaults: Map[String, Any] = Map()) extends Logging {
logger.debug("Init phase of config")
- /**
- * Default constructor
- */
+ /** Default constructor */
def this() = {
this(Map())
loadDefaultConfig()
@@ -41,15 +38,16 @@ class Config(var map: Map[String, Any]) extends Logging {
/**
* Loading a environmental variable as location of config files to merge into the config
* @param valueName Name of value
+ * @param default if true files are added to default instead of normal map
*/
- def loadConfigEnv(valueName: String) {
+ def loadConfigEnv(valueName: String, default: Boolean) {
sys.env.get(valueName) match {
case Some(globalFiles) => {
for (globalFile <- globalFiles.split(":")) {
val file: File = new File(globalFile)
if (file.exists) {
logger.info("Loading config file: " + file)
- loadConfigFile(file)
+ loadConfigFile(file, default)
} else logger.warn(valueName + " value found but file '" + file + "' does not exist, no global config is loaded")
}
}
@@ -57,23 +55,39 @@ class Config(var map: Map[String, Any]) extends Logging {
}
}
- /**
- * Loading default value for biopet
- */
+ /** Loading default value for biopet */
def loadDefaultConfig() {
- loadConfigEnv("BIOPET_CONFIG")
+ loadConfigEnv("BIOPET_CONFIG", true)
}
/**
* Merge a json file into the config
* @param configFile Location of file
*/
- def loadConfigFile(configFile: File) {
+ def loadConfigFile(configFile: File, default: Boolean = false) {
val configMap = fileToConfigMap(configFile)
+ if (default) {
+ if (defaults.isEmpty) defaults = configMap
+ 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)
+ /**
+ * Add a single vallue to the config
+ * @param key key of value
+ * @param value value itself
+ * @param path Path to value
+ * @param default if true value is put in default map
+ */
+ 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)
}
protected[config] var notFoundCache: List[ConfigValueIndex] = List()
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala
index bc3b5fc1394a3ae09169a138c39025788552858d..c95f4ddf8ff803521cf7edb2101df8c7bf28636a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala
@@ -19,64 +19,34 @@ import java.io.File
import nl.lumc.sasc.biopet.utils.ConfigUtils._
class ConfigValue(val requestIndex: ConfigValueIndex, val foundIndex: ConfigValueIndex, val value: Any, val default: Boolean) {
- /**
- * Get value as String
- * @return value as String
- */
+ /** Get value as String */
def asString = any2string(value)
- /**
- * Get value as File
- * @return value as File
- */
+ /** Get value as File */
def asFile = new File(any2string(value))
- /**
- * Get value as Int
- * @return value as Int
- */
+ /** Get value as Int */
def asInt = any2int(value)
- /**
- * Get value as Double
- * @return value as Double
- */
+ /** Get value as Double */
def asDouble = any2double(value)
- /**
- * Get value as List[Any]
- * @return value as List[Any]
- */
+ /** Get value as List[Any] */
def asList = any2list(value)
- /**
- * Get value as List[File]
- * @return value as List[File]
- */
+ /** Get value as List[File] */
def asFileList: List[File] = for (file <- any2stringList(value)) yield new File(file)
- /**
- * Get value as List[String]
- * @return value as List[String]
- */
+ /** Get value as List[String] */
def asStringList: List[String] = any2stringList(value)
- /**
- * Get value as Map
- * @return value as Map
- */
+ /** Get value as Map */
def asMap = any2map(value)
- /**
- * Get value as Boolean
- * @return value as Boolean
- */
+ /** Get value as Boolean */
def asBoolean = any2boolean(value)
- /**
- * Readable output of indexes and value, just for debug
- * @return
- */
+ /** Readable output of indexes and value, just for debug */
override def toString: String = {
var output = "key = " + requestIndex.key
output += ", value = " + value
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 df01a54371ee836acdfc93ac41a87d15d7fbce28..eb8f17bb423de90b923ab14fd058dc0996065baa 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
@@ -15,9 +15,7 @@
*/
package nl.lumc.sasc.biopet.core.config
-import nl.lumc.sasc.biopet.core.Logging
import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
-import scala.collection.JavaConversions._
trait Configurable extends ImplicitConversions {
/** Should be object of parant object */
@@ -39,7 +37,7 @@ trait Configurable extends ImplicitConversions {
/** Map to store defaults for config */
def defaults: Map[String, Any] = {
if (root != null) root.defaults
- else Map()
+ else globalConfig.defaults
}
val config = new ConfigFunctions
@@ -52,15 +50,13 @@ trait Configurable extends ImplicitConversions {
* @param submodule
* @return
*/
- def path(sample: String = null, library: String = null, submodule: String = null) = {
+ def getConfigPath(sample: String = null, library: String = null, submodule: String = null) = {
(if (sample != null) "samples" :: sample :: Nil else Nil) :::
(if (library != null) "libraries" :: library :: Nil else Nil) :::
(if (submodule != null) configPath ::: configName :: Nil else configPath)
}
- /**
- * Class is used for retrieval of config values
- */
+ /** Class is used for retrieval of config values */
protected class ConfigFunctions(val defaultSample: Option[String] = None, val defaultLibrary: Option[String] = None) {
def this(defaultSample: String, defaultLibrary: String) = {
this(defaultSample = Some(defaultSample), defaultLibrary = Some(defaultLibrary))
@@ -91,11 +87,12 @@ trait Configurable extends ImplicitConversions {
submodule: String = null,
freeVar: Boolean = true,
sample: String = null,
- library: String = null): ConfigValue = {
+ library: String = null,
+ path: List[String] = null): ConfigValue = {
val s = if (sample != null || defaultSample.isEmpty) sample else defaultSample.get
val l = if (library != null || defaultLibrary.isEmpty) library else defaultLibrary.get
val m = if (submodule != null) submodule else configName
- val p = path(s, l, submodule)
+ val p = if (path == null) getConfigPath(s, l, submodule) else path
val d = {
val value = Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar))
if (value.isDefined) value.get.value else default
@@ -117,11 +114,12 @@ trait Configurable extends ImplicitConversions {
submodule: String = null,
freeVar: Boolean = true,
sample: String = null,
- library: String = null) = {
+ library: String = null,
+ path: List[String] = null) = {
val s = if (sample != null || defaultSample.isEmpty) sample else defaultSample.get
val l = if (library != null || defaultLibrary.isEmpty) library else defaultLibrary.get
val m = if (submodule != null) submodule else configName
- val p = path(s, l, submodule)
+ val p = if (path == null) getConfigPath(s, l, submodule) else path
globalConfig.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
index eaea3ad41a20a8cf82af63d973a1a06a10ff42e2..b82f3da406ec4c2cd12ad6403ed574e6919e63a3 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
@@ -20,7 +20,9 @@ import nl.lumc.sasc.biopet.core.BiopetQScript
import nl.lumc.sasc.biopet.core.Logging
import nl.lumc.sasc.biopet.core.config.ConfigValue
import argonaut._, Argonaut._
+import org.yaml.snakeyaml.Yaml
import scalaz._, Scalaz._
+import scala.collection.JavaConversions._
/**
* This object contains general function for the config
@@ -78,16 +80,13 @@ object ConfigUtils extends Logging {
val value = map.get(path.head)
if (path.tail == Nil || value == None) value
else value.get match {
- case map: Map[_, _] => getValueFromPath(map.asInstanceOf[Map[String, Any]], path.tail)
- case _ => None
+ case map: Map[_, _] => getValueFromPath(map.asInstanceOf[Map[String, Any]], path.tail)
+ case map: java.util.LinkedHashMap[_, _] => getValueFromPath(map.toMap.asInstanceOf[Map[String, Any]], path.tail)
+ case _ => None
}
}
- /**
- * Make json aboject from a file
- * @param configFile Input file
- * @return Json object
- */
+ /** Make json aboject from a file */
def fileToJson(configFile: File): Json = {
logger.debug("Jsonfile: " + configFile)
val jsonText = scala.io.Source.fromFile(configFile).mkString
@@ -99,22 +98,25 @@ object ConfigUtils extends Logging {
}
}
- /**
- * Convert config value to map
- * @param configFile
- * @return Config map
- */
+ /** Convert config value to map */
def fileToConfigMap(configFile: File): Map[String, Any] = {
- val configJson = jsonToMap(fileToJson(configFile))
- logger.debug("Contain: " + configJson)
- return configJson
+
+ val configMap = {
+ if (configFile.getName.endsWith(".yaml")) yamlToMap(configFile)
+ else jsonToMap(fileToJson(configFile))
+ }
+ logger.debug("Contain: " + configMap)
+ return configMap
}
- /**
- * Convert json to native scala map/values
- * @param json input json
- * @return
- */
+ /** Convert a yaml file to map[String, Any] */
+ def yamlToMap(file: File): Map[String, Any] = {
+ val yaml = new Yaml()
+ val a = yaml.load(scala.io.Source.fromFile(file).reader())
+ ConfigUtils.any2map(a)
+ }
+
+ /** Convert json to native scala map/values */
def jsonToMap(json: Json): Map[String, Any] = {
var output: Map[String, Any] = Map()
if (json.isObject) {
@@ -126,11 +128,7 @@ object ConfigUtils extends Logging {
return output
}
- /**
- * Convert json value to native scala value
- * @param json input json
- * @return
- */
+ /** Convert json value to native scala value */
def jsonToAny(json: Json): Any = {
if (json.isObject) return jsonToMap(json)
else if (json.isArray) {
@@ -147,11 +145,7 @@ object ConfigUtils extends Logging {
else throw new IllegalStateException("Config value type not supported, value: " + json)
}
- /**
- * Convert native scala map to json
- * @param map Input map
- * @return
- */
+ /** Convert native scala map to json */
def mapToJson(map: Map[String, Any]): Json = {
map.foldLeft(jEmptyObject)((acc, kv) => (kv._1 := {
kv._2 match {
@@ -161,11 +155,7 @@ object ConfigUtils extends Logging {
}) ->: acc)
}
- /**
- * Convert native scala value to json, fall back on .toString if type is not a native scala value
- * @param any Input Any value
- * @return
- */
+ /** Convert native scala value to json, fall back on .toString if type is not a native scala value */
def anyToJson(any: Any): Json = {
any match {
case j: Json => j
@@ -183,11 +173,7 @@ object ConfigUtils extends Logging {
}
}
- /**
- * Convert Any to String
- * @param any Input Any value
- * @return
- */
+ /** Convert Any to String */
def any2string(any: Any): String = {
if (any == null) return null
any match {
@@ -196,11 +182,7 @@ object ConfigUtils extends Logging {
}
}
- /**
- * Convert Any to Int
- * @param any Input Any value
- * @return
- */
+ /** Convert Any to Int */
def any2int(any: Any): Int = {
any match {
case i: Int => i
@@ -214,11 +196,7 @@ object ConfigUtils extends Logging {
}
}
- /**
- * Convert Any to Long
- * @param any Input Any value
- * @return
- */
+ /** Convert Any to Long */
def any2long(any: Any): Long = {
any match {
case l: Double => l.toLong
@@ -232,11 +210,7 @@ object ConfigUtils extends Logging {
}
}
- /**
- * Convert Any to Double
- * @param any Input Any value
- * @return
- */
+ /** Convert Any to Double */
def any2double(any: Any): Double = {
any match {
case d: Double => d
@@ -251,11 +225,7 @@ object ConfigUtils extends Logging {
}
}
- /**
- * Convert Any to Float
- * @param any Input Any value
- * @return
- */
+ /** Convert Any to Float */
def any2float(any: Any): Float = {
any match {
case f: Double => f.toFloat
@@ -270,11 +240,7 @@ object ConfigUtils extends Logging {
}
}
- /**
- * Convert Any to Boolean
- * @param any Input Any value
- * @return
- */
+ /** Convert Any to Boolean */
def any2boolean(any: Any): Boolean = {
any match {
case b: Boolean => b
@@ -290,11 +256,7 @@ object ConfigUtils extends Logging {
}
}
- /**
- * Convert Any to List[Any], fallback on list with 1 value
- * @param any Input Any value
- * @return
- */
+ /** Convert Any to List[Any], fallback on list with 1 value */
def any2list(any: Any): List[Any] = {
if (any == null) return null
any match {
@@ -303,42 +265,39 @@ object ConfigUtils extends Logging {
}
}
- /**
- * Convert Any to List[String]
- * @param any Input Any value
- * @return
- */
+ /** Convert Any to List[String] */
def any2stringList(any: Any): List[String] = {
if (any == null) return null
any2list(any).map(_.toString)
}
- /**
- * Convert Any to List[File]
- * @param any Input Any value
- * @return
- */
+ /** Convert Any to List[File] */
def any2fileList(any: Any): List[File] = {
if (any == null) return null
any2list(any).map(x => new File(x.toString))
}
- /**
- * Convert Any to Map[String, Any]
- * @param any Input Any value
- * @return
- */
+ /** Convert Any to Map[String, Any] */
def any2map(any: Any): Map[String, Any] = {
if (any == null) return null
any match {
- case m: Map[_, _] => m.map(x => x._1.toString -> x._2)
- case _ => throw new IllegalStateException("Value '" + any + "' is not an Map")
+ case m: Map[_, _] => m.map(x => x._1.toString -> x._2)
+ case m: java.util.LinkedHashMap[_, _] => nestedJavaHashMaptoScalaMap(m)
+ case _ => throw new IllegalStateException("Value '" + any + "' is not an Map")
}
}
- /**
- * Trait for implicit conversions for ConfigValue to native scala values
- */
+ /** Convert nested java hash map to scala hash map */
+ def nestedJavaHashMaptoScalaMap(input: java.util.LinkedHashMap[_, _]): Map[String, Any] = {
+ input.map(value => {
+ value._2 match {
+ case m: java.util.LinkedHashMap[_, _] => value._1.toString -> nestedJavaHashMaptoScalaMap(m)
+ case _ => value._1.toString -> value._2
+ }
+ }).toMap
+ }
+
+ /** Trait for implicit conversions for ConfigValue to native scala values */
trait ImplicitConversions {
import scala.language.implicitConversions
@@ -355,191 +314,115 @@ object ConfigUtils extends Logging {
value != null && value.value != null && value.value != None
}
- /**
- * Convert ConfigValue to File
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to File */
implicit def configValue2file(value: ConfigValue): File = {
if (requiredValue(value)) new File(any2string(value.value))
else new File("")
}
- /**
- * Convert ConfigValue to File
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to File */
implicit def configValue2optionFile(value: ConfigValue): Option[File] = {
if (valueExists(value)) Some(new File(any2string(value.value)))
else None
}
- /**
- * Convert ConfigValue to String
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to String */
implicit def configValue2string(value: ConfigValue): String = {
if (requiredValue(value)) any2string(value.value)
else ""
}
- /**
- * Convert ConfigValue to String
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to String */
implicit def configValue2optionString(value: ConfigValue): Option[String] = {
if (valueExists(value)) Some(any2string(value.value))
else None
}
- /**
- * Convert ConfigValue to Long
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to Long */
implicit def configValue2long(value: ConfigValue): Long = {
if (requiredValue(value)) any2long(value.value)
else 0L
}
- /**
- * Convert ConfigValue top Option[Long]
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue top Option[Long] */
implicit def configValue2optionLong(value: ConfigValue): Option[Long] = {
if (valueExists(value)) Option(any2long(value.value))
else None
}
- /**
- * Convert ConfigValue to Int
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to Int */
implicit def configValue2int(value: ConfigValue): Int = {
if (requiredValue(value)) any2int(value.value)
else 0
}
- /**
- * Convert ConfigValue to Option[Int]
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to Option[Int] */
implicit def configValue2optionInt(value: ConfigValue): Option[Int] = {
if (valueExists(value)) Option(any2int(value.value))
else None
}
- /**
- * Convert ConfigValue to Double
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to Double */
implicit def configValue2double(value: ConfigValue): Double = {
if (requiredValue(value)) any2double(value.value)
else 0.0
}
- /**
- * Convert ConfigValue to Option[Double]
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to Option[Double] */
implicit def configValue2optionDouble(value: ConfigValue): Option[Double] = {
if (valueExists(value)) Option(any2double(value.value))
else None
}
- /**
- * Convert ConfigValue to Float
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to Float */
implicit def configValue2float(value: ConfigValue): Float = {
if (requiredValue(value)) any2float(value.value)
else 0f
}
- /**
- * Convert ConfigValue to Option[Float]
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to Option[Float] */
implicit def configValue2optionFloat(value: ConfigValue): Option[Float] = {
if (valueExists(value)) Option(any2float(value.value))
else None
}
- /**
- * Convert ConfigValue to Boolean
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to Boolean */
implicit def configValue2boolean(value: ConfigValue): Boolean = {
if (requiredValue(value)) any2boolean(value.value)
else false
}
- /**
- * Convert ConfigValue to Option[Boolean]
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to Option[Boolean] */
implicit def configValue2optionBoolean(value: ConfigValue): Option[Boolean] = {
if (valueExists(value)) Option(any2boolean(value.value))
else None
}
- /**
- * Convert ConfigValue to List[Any]
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to List[Any] */
implicit def configValue2list(value: ConfigValue): List[Any] = {
if (requiredValue(value)) any2list(value.value)
else Nil
}
- /**
- * Convert ConfigValue to List[String]
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to List[String] */
implicit def configValue2stringList(value: ConfigValue): List[String] = {
if (requiredValue(value)) any2stringList(value.value)
else Nil
}
- /**
- * Convert ConfigValue to List[File]
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to List[File] */
implicit def configValue2fileList(value: ConfigValue): List[File] = {
if (requiredValue(value)) any2fileList(value.value)
else Nil
}
- /**
- * Convert ConfigValue to Set[String]
- * @param value Input ConfigValue
- * @return
- */
+ /** Convert ConfigValue to Set[String] */
implicit def configValue2stringSet(value: ConfigValue): Set[String] = {
if (requiredValue(value)) any2stringList(value.value).toSet
else Set()
}
- /**
- * Config config value to Map[String, Any]
- * @param value Input ConfigValue
- * @return
- */
+ /** Config config value to Map[String, Any] */
implicit def configValue2map(value: ConfigValue): Map[String, Any] = {
if (requiredValue(value)) any2map(value.value)
else Map()
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
index 125579d13b78ee78ceab5547e986026e624be086..0878ae43ef0f8dd624c0210d4b0c8313f8f75cf0 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
@@ -141,7 +141,7 @@ object ConfigTest {
)
)
- val file = ConfigUtilsTest.writeTemp(ConfigUtils.mapToJson(map).spaces2)
+ val file = ConfigUtilsTest.writeTemp(ConfigUtils.mapToJson(map).spaces2, "json")
val config = new Config
config.loadConfigFile(file)
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
index b6c21092c9dd1acb375bce4964b230e8aca11806..e945da32c3f2679de81193f60ce37ad1c7af4783 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
@@ -205,8 +205,8 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
}
}
object ConfigUtilsTest {
- def writeTemp(text: String): File = {
- val file = File.createTempFile("TestConfigUtils.", ".json")
+ def writeTemp(text: String, extension: String): File = {
+ val file = File.createTempFile("TestConfigUtils.", extension)
val w = new PrintWriter(file)
w.write(text)
w.close()
@@ -229,7 +229,7 @@ object ConfigUtilsTest {
|}
""".stripMargin
- val file1 = writeTemp(jsonText1)
+ val file1 = writeTemp(jsonText1, ".json")
val json1 = {
("int" := 1337) ->:
@@ -262,7 +262,7 @@ object ConfigUtilsTest {
|}
""".stripMargin
- val file2 = writeTemp(jsonText2)
+ val file2 = writeTemp(jsonText2, ".yaml")
val json2 = {
("int" := 7331) ->:
@@ -283,5 +283,5 @@ object ConfigUtilsTest {
|}
""".stripMargin
- val corruptFile = writeTemp(corruptJson)
+ val corruptFile = writeTemp(corruptJson, ".json")
}
\ No newline at end of file