[EMBOSS] Jemboss unable to delete job directories if results.home is on NFS

[Mahmut Uludag]

Hi Daniel,

Thanks for the patch. I will apply your changes to the latest CVS 
version of the file.

If I don't misread your email, problem may have stayed because we have 
more streams not closed in other jemboss classes. The ones in 
JembossFileServer get/put_file methods would be the main reason for the 
.nfs files you reported. I remember seeing this problem long time ago 
but didn't manage to find out its reason, i think i probably blamed nfs 
and didn't spend time to check whether we might have anything wrong in 
jemboss.

Mahmut

> the part of the previous email where I described the modifications we made that appear to have helped resolve this problem was completely incorrect. I'm attaching a version of JembossServer.java (originally from the 6.4.0 distribution) with our modifications preceded with comments starting with "// Biocceleration: " . To reiterate, these modifications were mostly guesswork - trying to identify possible places where an explicit close() could have helped resolve the issue.