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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>>
>>
>>
>



-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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