diff --git a/build.xml b/build.xml index 47472d33e..16cfa9a61 100644 --- a/build.xml +++ b/build.xml @@ -538,7 +538,7 @@ Building Scala... - + @@ -1219,7 +1219,7 @@ - + diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala index 9cfd69247..79fc8589f 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala +++ b/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) } } diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala index 1140c4945..ead29bbf5 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala +++ b/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) } } diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala index 13b3c7cb3..e3528f54f 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala +++ b/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 => - logger.error("Unable to kill shell job: " + function.description) + case e: Exception => + logger.error("Unable to kill shell job: " + function.description, e) } } } diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala index 81c76dd29..abbb63271 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala +++ b/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. diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala b/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala index 6dcc69854..ddff95f21 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala +++ b/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)) diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala b/public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala index 4d3bf719c..96a5973be 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala +++ b/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) } } diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala b/public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala index 4acd27497..cb7b95b76 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala +++ b/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. */ diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala b/public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala index b112ed9a3..5b9e42a1e 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala +++ b/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) diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala b/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala index 8e8a87abe..ff99cb346 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala +++ b/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 diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala index e9a288117..251b1c511 100644 --- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala +++ b/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 */ }) } })