S3 upload now directly creates the XML report in memory and puts that in S3

-- This is a partial fix for the problem with uploading S3 logs reported by Mauricio.  There the problem is that the java.io.tmpdir is not accessible (network just hangs).  Because of that the s3 upload fails because the underlying system uses tmpdir for caching, etc.  As far as I can tell there's no way around this bug -- you cannot overload the java.io.tmpdir programmatically and even if I could what value would we use?  The only solution seems to me is to detect that tmpdir is hanging (how?!) and fail with a meaningful error.

ivy.xml

@@ -72,7 +72,7 @@
     <dependency org="net.java.dev.jna" name="jna" rev="3.2.7"/>
 
     <!-- Dependencies for amazon.com S3 support -->
-    <dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.0"/>
+    <dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.1"/>
 
     <!-- Dependencies for GridEngine -->
     <dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>

public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java

@@ -264,22 +264,8 @@ public class GATKRunReport {
         }
     }
 
-    /**
+    private final String getKey() {
-     * Opens the destination file and writes a gzipped version of the XML report there.
+        return getID() + ".report.xml.gz";
-     *
-     * @param destination
-     * @throws IOException
-     */
-    private void postReportToFile(File destination) throws IOException {
-        BufferedOutputStream out =
-                new BufferedOutputStream(
-                        new GZIPOutputStream(
-                                new FileOutputStream(destination)));
-        try {
-            postReportToStream(out);
-        } finally {
-            out.close();
-        }
     }
 
     /**
@@ -288,16 +274,21 @@ 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";
+        final String filename = getKey();
-        File file = new File(rootDir, filename);
+        final File destination = new File(rootDir, filename);
+
         try {
-            postReportToFile(file);
+            final BufferedOutputStream out = new BufferedOutputStream(
-            logger.debug("Wrote report to " + file);
+                    new GZIPOutputStream(
-            return file;
+                            new FileOutputStream(destination)));
+            postReportToStream(out);
+            out.close();
+            logger.debug("Wrote report to " + destination);
+            return destination;
         } catch ( Exception e ) {
             // we catch everything, and no matter what eat the error
             exceptDuringRunReport("Couldn't read report file", e);
-            file.delete();
+            destination.delete();
             return null;
         }
     }
@@ -305,11 +296,16 @@ public class GATKRunReport {
     private void postReportToAWSS3() {
         // modifying example code from http://jets3t.s3.amazonaws.com/toolkit/code-samples.html
         this.hostName = Utils.resolveHostname(); // we want to fill in the host name
-        File localFile = postReportToLocalDisk(new File("./"));
+        final String key = getKey();
-        logger.debug("Generating GATK report to AWS S3 based on local file " + localFile);
+        logger.debug("Generating GATK report to AWS S3 with key " + key);
-        if ( localFile != null ) { // we succeeded in creating the local file
-            localFile.deleteOnExit();
         try {
+            // create an byte output stream so we can capture the output as a byte[]
+            final ByteArrayOutputStream byteStream = new ByteArrayOutputStream(8096);
+            final OutputStream outputStream = new GZIPOutputStream(byteStream);
+            postReportToStream(outputStream);
+            outputStream.close();
+            final byte[] report = byteStream.toByteArray();
+
             // stop us from printing the annoying, and meaningless, mime types warning
             Logger mimeTypeLogger = Logger.getLogger(org.jets3t.service.utils.Mimetypes.class);
             mimeTypeLogger.setLevel(Level.FATAL);
@@ -328,7 +324,7 @@ public class GATKRunReport {
 
             // Create an S3Object based on a file, with Content-Length set automatically and
             // Content-Type set based on the file's extension (using the Mimetypes utility class)
-                S3Object fileObject = new S3Object(localFile);
+            S3Object fileObject = new S3Object(key, report);
             //logger.info("Created S3Object" + fileObject);
             //logger.info("Uploading " + localFile + " to AWS bucket");
             S3Object s3Object = s3Service.putObject(REPORT_BUCKET_NAME, fileObject);
@@ -342,7 +338,6 @@ public class GATKRunReport {
             exceptDuringRunReport("Couldn't read report file", e);
         }
     }
-    }
 
     private void exceptDuringRunReport(String msg, Throwable e) {
         logger.debug("A problem occurred during GATK run reporting [*** everything is fine, but no report could be generated; please do not post this to the support forum ***].  Message is: " + msg + ".  Error message is: " + e.getMessage());