Thanks very much for reporting this problem. This issue has been fixed in
change set 8649:34404f848979 which will be available in the next Galaxy
The update manager is responsible for determining if any updates are available
from the tool shed for any repositories you may have installed into your local
Galaxy instance. The missing import resulted in the update manager not
discovering if updates for your installed repositories are available from the
tool shed, but the behavior will not result in any instability in your local
Galaxy instance. The only result of this is that your installed repositories
that have updates available were not displayed in yellow highlighted boxes when
you click the Manage installed tool shed repositories page from the Admin menu.
We have been developing a functional test framework for all tool shed related
features over the past 2 months, and we will make sure to add coverage for this
particular feature as soon as possible. This tool shed functional test
framework provides significant coverage already, but it's not quite 100% yet.
Again, any instability you are experiencing in your local Galaxy instance will
not be a result of this particular issue however.
Greg Von Kuster
On Jan 19, 2013, at 3:25 PM, Anthonius deBoer wrote:
> I am seeing this in the log files when I start up...
> It seems to identify a name error in the file update_manager.py
> I am not sure if it is related, but some of my manager processes are just
> dying without any errors in the log...The processes are just killed (The PID
> is just gone, so run.sh --stop_daemon tells me they are not valid)....
> I did notice that python library is /usr/lib64/python2.6/threading.py, but I
> am using a virtual_env installation so I would have assumed it would have
> been using the lib64 stuff in my virtual_env environment, but then again,
> there is no file threading.py in that library so I guess it is not making a
> complete copy of all the files...
> In any case, my galaxy system is very unstable, so any help would be
> galaxy.tool_shed.update_manager INFO 2013-01-19 12:19:02,167 Update manager
> restarter starting up...
> Exception in thread Thread-1:
> Traceback (most recent call last):
> File "/usr/lib64/python2.6/threading.py", line 532, in __bootstrap_inner
> File "/usr/lib64/python2.6/threading.py", line 484, in run
> self.__target(*self.__args, **self.__kwargs)
> line 25, in __restarter
> .filter( and_( self.app.model.ToolShedRepository.table.c.update_available
> == False,
> NameError: global name 'and_' is not defined
> galaxy.datatypes.registry DEBUG 2013-01-19 12:19:02,175 Loaded display
> application 'ucsc_bam' for datatype 'bam', i
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