Merge pull request #397 from lbergelson/lb_scala_2.10.2

Update scala from 2.9 to 2.10.2

build.xml

@@ -526,6 +526,7 @@
             <fileset dir="${lib.dir}">
                 <include name="scala-compiler-*.jar"/>
                 <include name="scala-library-*.jar"/>
+                <include name="scala-reflect-*.jar"/>
             </fileset>
         </path>
         <taskdef resource="scala/tools/ant/antlib.xml">
@@ -537,7 +538,7 @@
     <target name="scala.compile" depends="init,resolve,gatk.compile,queue-extensions.generate,init.scala.compile" if="include.scala">
         <mkdir dir="${scala.classes}"/>
         <echo>Building Scala...</echo>
-        <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
+        <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes" addparams="-feature">
             <src refid="scala.source.path" />
             <src path="${queue-extensions.source.dir}" />
             <include name="**/*.scala" />
@@ -1218,7 +1219,7 @@
 
     <target name="test.scala.compile" depends="test.java.compile,scala.compile" if="include.scala">
         <echo message="Scala: Compiling test cases!"/>
-        <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes">
+        <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes" addparams="-feature">
 	        <src refid="scala.test.source.path" />
             <classpath>
                 <path refid="build.results"/>

ivy.xml

@@ -82,8 +82,8 @@
         <dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>
 
         <!-- Scala dependancies -->
-        <dependency org="org.scala-lang" name="scala-compiler" rev="2.9.2"/>
+        <dependency org="org.scala-lang" name="scala-compiler" rev="2.10.2"/>
-        <dependency org="org.scala-lang" name="scala-library" rev="2.9.2"/>
+        <dependency org="org.scala-lang" name="scala-library" rev="2.10.2"/>
 
         <!-- testing and evaluation dependencies -->
         <dependency org="org.testng" name="testng" rev="6.8"/>

public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala

@@ -33,10 +33,9 @@ import java.io.File
 import scala.tools.nsc.reporters.AbstractReporter
 import java.lang.String
 import org.apache.log4j.Level
-import scala.tools.nsc.util.{FakePos, NoPosition, Position}
 import org.broadinstitute.sting.queue.util.TextFormatUtils._
 import org.broadinstitute.sting.utils.classloader.JVMUtils
-import tools.util.StringOps
+import scala.reflect.internal.util.{FakePos, NoPosition, Position, StringOps}
 
 /**
  * Plugin manager for QScripts which loads QScripts into the current class loader.
@@ -53,7 +52,10 @@ class QScriptManager() extends Logging {
       settings.outdir.value = tempDir.getPath
 
       // Set the classpath to the current class path.
-      JVMUtils.getClasspathURLs.foreach(url => settings.classpath.append(url.getPath))
+      JVMUtils.getClasspathURLs.foreach(url => {
+          settings.bootclasspath.append(url.getPath)
+          settings.classpath.append(url.getPath)
+      })
 
       val reporter = new QScriptManager.Log4JReporter(settings)
 

public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala

@@ -160,7 +160,7 @@ class DrmaaJobRunner(val session: Session, val function: CommandLineFunction) ex
           // resource of the designated queue to SIGTERM
           session.control(jobId, Session.TERMINATE)
         } catch {
-          case e =>
+          case e: Exception =>
             logger.error("Unable to kill job " + jobId, e)
         }
       }

public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala

@@ -361,7 +361,7 @@ object Lsf706JobRunner extends Logging {
           if (LibBat.lsb_signaljob(runner.jobId, SIGTERM) < 0)
             logger.error(LibBat.lsb_sperror("Unable to kill job " + runner.jobId))
         } catch {
-          case e =>
+          case e: Exception=>
             logger.error("Unable to kill job " + runner.jobId, e)
         }
       }

public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala

@@ -83,8 +83,8 @@ class ShellJobRunner(val function: CommandLineFunction) extends CommandLineJobRu
       try {
         controller.tryDestroy()
       } catch {
-        case e =>
+        case e: Exception =>
-          logger.error("Unable to kill shell job: " + function.description)
+          logger.error("Unable to kill shell job: " + function.description, e)
       }
     }
   }

public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala

@@ -32,6 +32,7 @@ import org.broadinstitute.sting.queue.{QException, QSettings}
 import java.lang.IllegalStateException
 import org.broadinstitute.sting.queue.util._
 import org.broadinstitute.sting.utils.io.IOUtils
+import scala.language.reflectiveCalls
 
 /**
  * The base interface for all functions in Queue.

public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala

@@ -39,7 +39,7 @@ class VCFExtractSamples(inVCF: File, outVCF: File, samples: List[String]) extend
   @Argument(doc="The samples to extract from the VCF") var extractSamples : List[String] = samples
 
   var out : PrintWriter = _
-  var columns : List[Int] = 0 to 8 toList
+  var columns : List[Int] = (0 to 8).toList
 
   def run = {
     out = new PrintWriter(new PrintStream(outputVCF))

public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala

@@ -26,7 +26,7 @@
 package org.broadinstitute.sting.queue.util
 
 import org.apache.commons.mail.{MultiPartEmail, EmailAttachment}
-import java.io.{FileReader, File}
+import java.io.{IOException, FileReader, File}
 import javax.mail.internet.InternetAddress
 import scala.collection.JavaConversions._
 
@@ -105,7 +105,7 @@ class EmailMessage extends Logging {
     try {
       Retry.attempt(() => send(settings), .5)
     } catch {
-      case e => logger.error("Error sending message: %n%s".format(this.toString), e)
+      case e: RetryException=> logger.error("Error sending message: %n%s".format(this.toString), e)
     }
   }
 

public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala

@@ -25,6 +25,8 @@
 
 package org.broadinstitute.sting.queue.util
 
+import scala.language.implicitConversions
+
 /**
  * An importable object that provides automatic primitive to option conversion.
  */

public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala

@@ -49,7 +49,7 @@ object Retry extends Logging {
         result = f()
         success = true
       } catch {
-        case e => {
+        case e: Exception=> {
           count += 1
           if (count < tries) {
             val minutes = wait(count-1)

public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.queue.util
 
 import java.io.{Serializable, File}
+import scala.language.implicitConversions
 
 /**
  * Converts String to/from File
@@ -77,21 +78,6 @@ object StringFileConversions {
     })
   }
 
-  implicit def stringsAsFiles(x: Set[Comparable[_ >: File with String <: Comparable[_ >: File with String <: Comparable[_ >: File with String <: Serializable] with Serializable] with Serializable] with Serializable]): Set[File] = {
-    x.map(_ match {
-      case string: String => stringAsFile(string)
-      case file: File => file
-      case null => null
-    })
-  }
-
-  implicit def filesAsStrings(x: Set[Comparable[_ >: String with File <: Comparable[_ >: String with File <: Comparable[_ >: String with File <: Serializable] with Serializable] with Serializable] with Serializable]): Set[String] = {
-    x.map(_ match {
-      case file: File => fileAsString(file)
-      case string: String => string
-      case null => null
-    })
-  }
 }
 
 /**
@@ -124,11 +110,4 @@ trait StringFileConversions {
     StringFileConversions.filesAsStringsList(x)
   }
 
-  implicit def stringsAsFiles(x: Set[Comparable[_ >: File with String <: Comparable[_ >: File with String <: Comparable[_ >: File with String <: Serializable] with Serializable] with Serializable] with Serializable]): Set[File] = {
-    StringFileConversions.stringsAsFiles(x)
-  }
-
-  implicit def filesAsStrings(x: Set[Comparable[_ >: String with File <: Comparable[_ >: String with File <: Comparable[_ >: String with File <: Serializable] with Serializable] with Serializable] with Serializable]): Set[String] = {
-    StringFileConversions.filesAsStrings(x)
-  }
 }

public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala

@@ -182,7 +182,7 @@ object PipelineTest extends BaseTest with Logging {
       println("Executing test %s with Queue arguments: %s".format(name, Utils.join(" ",command)))
       CommandLineProgram.start(instance, command)
     } catch {
-      case e =>
+      case e: Exception =>
         gotAnException = true
         if (expectedException != null) {
           // we expect an exception
@@ -224,7 +224,7 @@ object PipelineTest extends BaseTest with Logging {
         try {
           commandLine.shutdown()
         } catch {
-          case _ => /* ignore */
+          case _: Throwable => /* ignore */
         })
     }
   })

public/scala/test/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala

@@ -87,44 +87,6 @@ class StringFileConversionsUnitTest {
     Assert.assertEquals(strings, Seq(null, null))
   }
 
-  @Test
-  def testStringToFileSet() {
-    var files = Set(new File("foo"))
-    files += "bar"
-    Assert.assertEquals(files, Set(new File("foo"), new File("bar")))
-
-    files = Set(new File("foo"))
-    files += null.asInstanceOf[String]
-    Assert.assertEquals(files, Set(new File("foo"), null))
-
-    files = Set[File](null)
-    files += "foo"
-    Assert.assertEquals(files, Set(new File("foo"), null))
-
-    files = Set[File](null)
-    files += null.asInstanceOf[String]
-    Assert.assertEquals(files, Set(null))
-  }
-
-  @Test
-  def testFileToStringSet() {
-    var strings = Set("foo")
-    strings += new File("bar")
-    Assert.assertEquals(strings, Set("foo", "bar"))
-
-    strings = Set("foo")
-    strings += null.asInstanceOf[File]
-    Assert.assertEquals(strings, Set("foo", null))
-
-    strings = Set[String](null)
-    strings += new File("foo")
-    Assert.assertEquals(strings, Set("foo", null))
-
-    strings = Set[String](null)
-    strings += null.asInstanceOf[File]
-    Assert.assertEquals(strings, Set(null))
-  }
-
   @Test
   def testStringListToFileList() {
     var files = Seq(new File("foo"))
@@ -163,41 +125,4 @@ class StringFileConversionsUnitTest {
     Assert.assertEquals(strings, Seq(null, null))
   }
 
-  @Test
-  def testStringSetToFileSet() {
-    var files = Set(new File("foo"))
-    files ++= Set("bar")
-    Assert.assertEquals(files, Set(new File("foo"), new File("bar")))
-
-    files = Set(new File("foo"))
-    files ++= Set[String](null)
-    Assert.assertEquals(files, Set(new File("foo"), null))
-
-    files = Set[File](null)
-    files ++= Set("foo")
-    Assert.assertEquals(files, Set(new File("foo"), null))
-
-    files = Set[File](null)
-    files ++= Set[String](null)
-    Assert.assertEquals(files, Set(null))
-  }
-
-  @Test
-  def testFileSetToStringSet() {
-    var strings = Set("foo")
-    strings ++= Set(new File("bar"))
-    Assert.assertEquals(strings, Set("foo", "bar"))
-
-    strings = Set("foo")
-    strings ++= Set[File](null)
-    Assert.assertEquals(strings, Set("foo", null))
-
-    strings = Set[String](null)
-    strings ++= Set(new File("foo"))
-    Assert.assertEquals(strings, Set("foo", null))
-
-    strings = Set[String](null)
-    strings ++= Set[File](null)
-    Assert.assertEquals(strings, Set(null))
-  }
 }