Moving all file cleanup to IOUtils for easier debugging.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4646 348d0f76-0448-11de-a6fe-93d51630548a

scala/src/org/broadinstitute/sting/queue/engine/LsfJobRunner.scala

@@ -139,11 +139,11 @@ class LsfJobRunner(val function: CommandLineFunction) extends DispatchJobRunner
    * Removes all temporary files used for this LSF job.
    */
   def removeTemporaryFiles() = {
-    FileUtils.deleteQuietly(exec)
-    FileUtils.deleteQuietly(preExec)
-    FileUtils.deleteQuietly(postExec)
-    FileUtils.deleteQuietly(jobDoneFile)
-    FileUtils.deleteQuietly(jobFailFile)
+    IOUtils.tryDelete(exec)
+    IOUtils.tryDelete(preExec)
+    IOUtils.tryDelete(postExec)
+    IOUtils.tryDelete(jobDoneFile)
+    IOUtils.tryDelete(jobFailFile)
   }
 
   /**

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

@@ -7,7 +7,6 @@ import org.broadinstitute.sting.queue.{QException, QSettings}
 import collection.JavaConversions._
 import org.broadinstitute.sting.queue.function.scattergather.{Gather, SimpleTextGatherFunction}
 import org.broadinstitute.sting.queue.util.{Logging, CollectionUtils, IOUtils, ReflectionUtils}
-import org.apache.commons.io.FileUtils
 
 /**
  * The base interface for all functions in Queue.
@@ -157,23 +156,18 @@ trait QFunction extends Logging {
    * Deletes the log files for this function.
    */
   def deleteLogs() = {
-    deleteOutput(jobOutputFile)
+    IOUtils.tryDelete(jobOutputFile)
     if (jobErrorFile != null)
-      deleteOutput(jobErrorFile)
+      IOUtils.tryDelete(jobErrorFile)
   }
 
   /**
    * Deletes the output files and all the status files for this function.
    */
   def deleteOutputs() = {
-    outputs.foreach(file => deleteOutput(file))
-    doneOutputs.foreach(file => deleteOutput(file))
-    failOutputs.foreach(file => deleteOutput(file))
-  }
-
-  private def deleteOutput(file: File) = {
-    if (FileUtils.deleteQuietly(file))
-      logger.debug("Deleted " + file)
+    outputs.foreach(file => IOUtils.tryDelete(file))
+    doneOutputs.foreach(file => IOUtils.tryDelete(file))
+    failOutputs.foreach(file => IOUtils.tryDelete(file))
   }
 
   /**

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

@@ -7,7 +7,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException
 /**
  * A collection of utilities for modifying java.io.
  */
-object IOUtils {
+object IOUtils extends Logging {
   /** The current directory "." */
   val CURRENT_DIR = new File(".")
 
@@ -89,7 +89,7 @@ object IOUtils {
 
   def writeContents(file: File, content: String) =  FileUtils.writeStringToFile(file, content)
 
-  def   writeTempFile(content: String, prefix: String, suffix: String = "", directory: File = null) = {
+  def writeTempFile(content: String, prefix: String, suffix: String = "", directory: File = null) = {
     val tempFile = absolute(File.createTempFile(prefix, suffix, directory))
     writeContents(tempFile, content)
     tempFile
@@ -181,4 +181,18 @@ object IOUtils {
     }
     tailLines
   }
+
+  /**
+   * Tries to delete a file.  Emits a warning if the file was unable to be deleted.
+   * @param file File to delete.
+   * @return true if the file was deleted.
+   */
+  def tryDelete(file: File) = {
+    val deleted = FileUtils.deleteQuietly(file)
+    if (deleted)
+      logger.debug("Deleted " + file)
+    else if (file.exists)
+      logger.warn("Unable to delete " + file)
+    deleted
+  }
 }

scala/test/org/broadinstitute/sting/queue/util/IOUtilsUnitTest.scala

@@ -71,7 +71,7 @@ class IOUtilsUnitTest extends BaseTest {
     Assert.assertTrue(tempDir.exists)
     Assert.assertFalse(tempDir.isFile)
     Assert.assertTrue(tempDir.isDirectory)
-    val deleted = tempDir.delete
+    val deleted = IOUtils.tryDelete(tempDir)
     Assert.assertTrue(deleted)
     Assert.assertFalse(tempDir.exists)
   }