Workaround for scala trait erasing parameterized types:

- Requiring explicit @ClassType on parameterized fields in traits.
- Scatter / Gather functions are now abstract classes since @ClassType can't be used on parameterized fields with type parameters.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3726 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/commandline/ClassType.java

@@ -0,0 +1,39 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.commandline;
+
+import java.lang.annotation.*;
+
+/**
+ * Annotates generic fields where the parameterized type is not specified or erased.
+ * Primarily used for Queue traits.  Defined in java since scala does not support RetentionPolicy.RUNTIME.
+ */
+@Documented
+@Inherited
+@Retention(RetentionPolicy.RUNTIME)
+@Target({ElementType.FIELD})
+public @interface ClassType {
+    Class value();
+}

scala/qscript/unifiedgenotyper_example.properties

@@ -3,3 +3,4 @@ referenceFile = /path/to/reference.fasta
 dbsnp = /path/to/dbsnp
 intervals = /path/to/my.interval_list
 jobNamePrefix = Q
+memoryLimit = 2

scala/src/org/broadinstitute/sting/queue/function/DispatchFunction.scala

@@ -2,14 +2,15 @@ package org.broadinstitute.sting.queue.function
 
 import java.io.File
 import java.lang.management.ManagementFactory
-import org.broadinstitute.sting.commandline.{Output, Input}
 import org.broadinstitute.sting.queue.function.scattergather.{Gather, SimpleTextGatherFunction}
 import org.broadinstitute.sting.queue.util.IOUtils
+import org.broadinstitute.sting.commandline.{ClassType, Output, Input}
 
 trait DispatchFunction extends InputOutputFunction {
   def commandLine: String
 
   @Input(doc="Upper memory limit", required=false)
+  @ClassType(classOf[Int])
   var memoryLimit: Option[Int] = None
 
   /**

scala/src/org/broadinstitute/sting/queue/function/gatk/GatkFunction.scala

@@ -3,7 +3,7 @@ package org.broadinstitute.sting.queue.function.gatk
 import java.io.File
 import org.broadinstitute.sting.queue.function.IntervalFunction
 import org.broadinstitute.sting.queue.function.scattergather.{Scatter, ScatterGatherableFunction, IntervalScatterFunction}
-import org.broadinstitute.sting.commandline.Input
+import org.broadinstitute.sting.commandline.{ClassType, Input}
 
 trait GatkFunction extends ScatterGatherableFunction with IntervalFunction {
   @Input(doc="Temporary directory to write any files", required=false)
@@ -16,6 +16,7 @@ trait GatkFunction extends ScatterGatherableFunction with IntervalFunction {
   var referenceFile: File = _
 
   @Input(doc="Bam files", required=false)
+  @ClassType(classOf[File])
   var bamFiles: List[File] = Nil
 
   @Input(doc="Intervals", required=false)

scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala

@@ -3,7 +3,11 @@ package org.broadinstitute.sting.queue.function.scattergather
 import org.broadinstitute.sting.queue.function.{CommandLineFunction}
 import org.broadinstitute.sting.commandline.{Input, Output}
 
-trait GatherFunction extends CommandLineFunction {
+/**
+ * Base class for Gather command line functions.
+ * NOTE: Using an abstract class instead of a trait due to scala parameterized type erasure on traits.
+ */
+abstract class GatherFunction extends CommandLineFunction {
   type GatherType
 
   @Input(doc="Parts to gather back into the original output")

scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala

@@ -1,10 +1,14 @@
 package org.broadinstitute.sting.queue.function.scattergather
 
 import org.broadinstitute.sting.queue.function.CommandLineFunction
-import org.broadinstitute.sting.commandline.{Input, Output}
 import java.io.File
+import org.broadinstitute.sting.commandline.{Input, Output}
 
-trait ScatterFunction extends CommandLineFunction {
+/**
+ * Base class for Scatter command line functions.
+ * NOTE: Using an abstract class instead of a trait due to scala parameterized type erasure on traits.
+ */
+abstract class ScatterFunction extends CommandLineFunction {
   type ScatterType
 
   @Input(doc="Original input to scatter")

scala/src/org/broadinstitute/sting/queue/util/ReflectionUtils.scala

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.queue.QException
 import java.lang.annotation.Annotation
 import scala.concurrent.JavaConversions._
 import java.lang.reflect.{ParameterizedType, Field}
+import org.broadinstitute.sting.commandline.ClassType
 
 object ReflectionUtils {
   def hasAnnotation(field: Field, annotation: Class[_ <: Annotation]) = field.getAnnotation(annotation) != null
@@ -73,12 +74,14 @@ object ReflectionUtils {
     }
   }
 
-  private def getGenericTypes(field: Field) = {
+  private def getGenericTypes(field: Field): Option[Array[Class[_]]] = {
     // TODO: Refactor: based on java code in org.broadinstitute.sting.commandline.ArgumentTypeDescriptor
     // If this is a parameterized collection, find the contained type.  If blow up if only one type exists.
     if (field.getGenericType.isInstanceOf[ParameterizedType]) {
       val parameterizedType = field.getGenericType.asInstanceOf[ParameterizedType]
       Some(parameterizedType.getActualTypeArguments.map(_.asInstanceOf[Class[_]]))
+    } else if (hasAnnotation(field, classOf[ClassType])) {
+      Some(Array(getAnnotation(field, classOf[ClassType]).value))
     }
     else None
   }