I am seeing some odd behavior with BAM file import from FTP staging directory 
where ownership of imported file is retained instead of being changed to galaxy 
system user account. 

I should note that our site is not using galaxy specific FTP server 
configuration, but instead we have configured a directory namespace where 
cluster users can drop-off files using scp, sftp or even fetch using wget. The 
galaxy system account can access these files and hence it can import them into 
it's datasets staging directory using 'FTP' upload mechanism. We have been 
using this configuration for about a year now with ~ 15,000 files deposited 
using it.  

There have been few instances (22) where file ownership didn't change to galaxy 
system account after a file was imported into the galaxy. Normally when a file 
is imported from FTP directory to Galaxy's datasets staging directory, it's 
inode entry and ownership is changed. In these twenty-two cases, which appear 
to be specific with BAM files, the inode entry and ownership didn't change, but 
the file name is in galaxy's datase_nnnnn.dat format and file contents/size are 
legit. So it seems for 'successful' import operations the file is copied to 
galaxy space (ownership and inode changed) and for 'unsuccessful'  import 
operations file is moved to galaxy space. 

I was wondering if someone could help me in understanding the upload tool 
operation, so that I can get better sense of underlying file ownership issues. 
I have seen it happening for a file where it had exactly same permissions/ACLs, 
as the file which was successfully imported. So are there any other factors 
that might be preventing file ownership/inode changes? Does galaxy have a 
different import mechanisms according to file type?

We are using galaxy-dist revision 40f1816d6857 (will be updated soon!). This 
issue has happened even before this dist version was in place. Any pointers for 
debugging will be really helpful. 

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