Hi Ross,

Yeah, it was probably a merging issue. I confess I didn't double-check in Bitbucket. *slaps hand*


Actually hg behaved strangely this time, and didn't report all failed merges so I had to look for the conflicting files manually. Hopefully there will be no remaining error.

Sorry for insisting but when do you think the fix will be pushed in galaxy-dist? Just to have a rough idea :)

Thanks for all the help!

Best,
L-A


Le 19/01/2012 11:32, Ross a écrit :
Hi, L-A,

2012/1/19 Louise-Amélie Schmitt<louise-amelie.schm...@embl.de>:
Hi Ross

Thanks a million, I hg-pull'ed it solved the problem!! Please push it to
galaxy-dist? ;)
Glad to hear it works - thanks for reporting back.

I ran in another little bug though, but nothing serious, you might even have
already spotted it by now:
In lib/galaxy/web/framework/__init__.py the line 873 made the whole thing
crash due to a wrong arguments number, so I changed it from:
            self._ensure_logged_in_user( environ )
to:
            self._ensure_logged_in_user( environ, session_cookie )
and it works fine now!
No, I hadn't encountered that - AFAIK, the function definition and
call are correct in the current tip of galaxy-central @
https://bitbucket.org/galaxy/galaxy-central/src/ab1a5ab063ce/lib/galaxy/web/framework/__init__.py
The tip of galaxy-dist on bitbucket currently looks consistent -
neither definition nor call have the session_cookie parameter - so I'm
not sure where the error you saw at line 873 comes from - in
https://bitbucket.org/galaxy/galaxy-dist/src/b258de1e6cea/lib/galaxy/web/framework/__init__.py
the call is at line 860...perhaps you were working with an older
revision or one that's been merged with central at some stage?


Best,
L-A


Le 19/01/2012 02:13, Ross a écrit :

Hi, L-A

Thanks for reporting this - I just pushed a fix in galaxy-central
6556:ab1a5ab063ce
Please let us know if that resolves the problem?


2012/1/19 Louise-Amélie Schmitt<louise-amelie.schm...@embl.de>:
Hello!

I'm running into an error when trying to download a composite dataset
from
the history with the floppy disk icon. Here is the error message in the
logs:


galaxy.web.controllers.dataset ERROR 2012-01-18 16:32:10,324 Unable to
remove temporary library download archive and directory
Traceback (most recent call last):
  File "/g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py", line
285, in archive_composite_dataset
    os.rmdir( tmpd )
OSError: [Errno 39] Directory not empty: './database/tmp/tmpkRv28I'


Then I tried replacing the os.rmdir by a shutil.rmtree to see if it would
solve the issue, and here is what I got:


galaxy.web.controllers.dataset ERROR 2012-01-18 16:34:30,239 Unable to
remove temporary library download archive and directory
Traceback (most recent call last):
  File "/g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py", line
286, in archive_composite_dataset
    shutil.rmtree( tmpd )
  File

"/g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py",
line 221, in rmtree
    onerror(os.remove, fullname, sys.exc_info())
  File

"/g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py",
line 219, in rmtree
    os.remove(fullname)
OSError: [Errno 16] Device or resource busy:
'./database/tmp/tmpwpsShD/.nfs000000000289ccea00000138'


But when I check the contents of the direcory, there is no hidden
.nfs-something file.

Does anyone have an idea why this could occur? Both our testing instance
and
our production instance have the same issue, the first being on
galaxy-central and the second on galaxy-dist.

Thanks,
L-A

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