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biopet.biopet
Commit 11c99934 authored by Peter van 't Hof's avatar Peter van 't Hof
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Changed scala docs

parent 1c158133
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Showing with 53 additions and 244 deletions
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @ 11c99934
......@@ -25,9 +25,7 @@ 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 / YAML config file(s)", fullName = "config_file", shortName = "config", required = false)
......@@ -36,6 +34,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
@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 = {
if (config.contains("output_dir", path = Nil)) config("output_dir", path = Nil).asFile
else new File(".")
......@@ -58,9 +57,7 @@ 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")
outputDir = outputDir.getAbsoluteFile
......
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
View file @ 11c99934
......@@ -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) {
......
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
View file @ 11c99934
......@@ -20,8 +20,6 @@ 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
......
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala
View file @ 11c99934
......@@ -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
......
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
View file @ 11c99934
......@@ -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 */
......@@ -58,9 +56,7 @@ trait Configurable extends ImplicitConversions {
(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))
......
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
View file @ 11c99934
......@@ -21,7 +21,6 @@ import nl.lumc.sasc.biopet.core.Logging
import nl.lumc.sasc.biopet.core.config.ConfigValue
import argonaut._, Argonaut._
import org.yaml.snakeyaml.Yaml
import scala.collection.mutable
import scalaz._, Scalaz._
import scala.collection.JavaConversions._
......@@ -87,11 +86,7 @@ object ConfigUtils extends Logging {
}
}
/**
* 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
......@@ -103,11 +98,7 @@ 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 configMap = {
......@@ -118,22 +109,14 @@ object ConfigUtils extends Logging {
return configMap
}
/**
* Convert a yaml file to map[String, Any]
* @param file Input file
* @return config map
*/
/** 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
* @param json input json
* @return
*/
/** Convert json to native scala map/values */
def jsonToMap(json: Json): Map[String, Any] = {
var output: Map[String, Any] = Map()
if (json.isObject) {
......@@ -145,11 +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) {
......@@ -166,11 +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 {
......@@ -180,11 +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
......@@ -202,11 +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 {
......@@ -215,11 +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
......@@ -233,11 +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
......@@ -251,11 +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
......@@ -270,11 +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
......@@ -289,11 +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
......@@ -309,11 +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 {
......@@ -322,31 +265,19 @@ 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 {
......@@ -366,9 +297,7 @@ object ConfigUtils extends Logging {
}).toMap
}
/**
* Trait for implicit conversions for ConfigValue to native scala values
*/
/** Trait for implicit conversions for ConfigValue to native scala values */
trait ImplicitConversions {
import scala.language.implicitConversions
......@@ -385,191 +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] = {