From 2316b6aad3e81cc0cd88980acd73d716fd4cdb2d Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 12 Sep 2011 22:02:42 -0400
Subject: [PATCH] Trying to fix problems with S3 uploading behind firewalls

-- Cannot reproduce the very long waits reported by some users.
-- Fixed problem that exception might result in an undeleted file, which is now fixed with deleteOnExit()
---
 .../sting/gatk/phonehome/GATKRunReport.java               | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
index 4d94130a8..70307380b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
@@ -293,15 +293,16 @@ public class GATKRunReport {
      * That is, postReport() is guarenteed not to fail for any reason.
      */
     private File postReportToLocalDisk(File rootDir) {
+        String filename = getID() + ".report.xml.gz";
+        File file = new File(rootDir, filename);
         try {
-            String filename = getID() + ".report.xml.gz";
-            File file = new File(rootDir, filename);
             postReportToFile(file);
             logger.debug("Wrote report to " + file);
             return file;
         } catch ( Exception e ) {
             // we catch everything, and no matter what eat the error
             exceptDuringRunReport("Couldn't read report file", e);
+            file.delete();
             return null;
         }
     }
@@ -312,6 +313,7 @@ public class GATKRunReport {
         File localFile = postReportToLocalDisk(new File("./"));
         logger.debug("Generating GATK report to AWS S3 based on local file " + localFile);
         if ( localFile != null ) { // we succeeded in creating the local file
+            localFile.deleteOnExit();
             try {
                 // stop us from printing the annoying, and meaningless, mime types warning
                 Logger mimeTypeLogger = Logger.getLogger(org.jets3t.service.utils.Mimetypes.class);
@@ -342,8 +344,6 @@ public class GATKRunReport {
                 exceptDuringRunReport("Couldn't calculate MD5", e);
             } catch ( IOException e ) {
                 exceptDuringRunReport("Couldn't read report file", e);
-            } finally {
-                localFile.delete();
             }
         }
     }