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gatk-3.8
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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()
This commit is contained in:
Mark DePristo 2011-09-12 22:02:42 -04:00
parent 72536e5d6d
commit 2316b6aad3
1 changed files with 4 additions and 4 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
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@ -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();
}
}
}