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
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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