Hi,
Tried to remove a trackster visualization in the latest galaxy-dist and got this error:
Error Traceback: View as: Interactive | Text | XML (full) ⇝ NameError: global name 'util' is not defined URL: http://srv151/visualization/list?f-sharing=All&sort=-update_time&f-t... Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
environ, self.app)
Module paste.wsgilib:539 in intercept_output view
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:91 in __call__ view
return self.app( environ, start_response )
Module paste.httpexceptions:632 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
body = method( trans, **kwargs )
Module galaxy.web.framework:94 in decorator view
return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.visualization:320 in list view
ids = util.listify( kwargs['id'] )
NameError: global name 'util' is not defined
Extra Features
Display the lines of code near each part of the traceback
Show a debug prompt to allow you to directly debug the code at the traceback Re-GET Page
This has been fixed in -central and will be available in the next Galaxy distribution.
Thanks, J.
On Jan 16, 2013, at 10:02 PM, Anthonius deBoer wrote:
Hi,
Tried to remove a trackster visualization in the latest galaxy-dist and got this error:
Error Traceback: View as: Interactive | Text | XML (full) ⇝ NameError: global name 'util' is not defined URL: http://srv151/visualization/list?f-sharing=All&sort=-update_time&f-t... Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
environ, self.app)
Module paste.wsgilib:539 in intercept_output view
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:91 in __call__ view
return self.app( environ, start_response )
Module paste.httpexceptions:632 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
body = method( trans, **kwargs )
Module galaxy.web.framework:94 in decorator view
return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.visualization:320 in list view
ids = util.listify( kwargs['id'] )
NameError: global name 'util' is not defined
Extra Features
Display the lines of code near each part of the traceback
Show a debug prompt to allow you to directly debug the code at the traceback Re-GET Page
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Not to be ungrateful for the hard work you guys are all doing and please don't get this the wrong way, but is there any QA that is being done on the galaxy-dist when it is being released? I have been a QA manager and I know how hard it is to test UI, but the last few releases on galaxy-dist have been rather broken in one way or another and for a production server this is scary...I am trying to get more people to use galaxy in my organization, but I am hesitant since there are so many simple things that are broken with every release...
I know I should do my own QA before I install galaxy-dist on a production server, but I was sorta hoping that the whole reason for galaxy-dev and galaxy-dist was to have a test bed for any fixed in galaxy-dev, so when it was time for a production version for galaxy-dist, it would at least been tested a few weeks...
Maybe its an idea to install galaxy-dist on the main galaxy server for a few weeks, before releasing it to the public so we know it has been running and stable...
Again...I know we are dealing with opensource and free software and it has been very valuable to me and my organization. I have been happily testing and reporting each release when I was just running it for my self, but since every release I got was broken in one way or another, I had to get the next galaxy-dist just to be able to run my tests, let alone be able to release it to a larger audience....
Maybe its time for a more formal release policy of galaxy-dist (other than me just waiting for bug reports before getting it)?
Thanks,
A very grateful Thon...
On Jan 17, 2013, at 05:23 AM, Jeremy Goecks jeremy.goecks@emory.edu wrote:
This has been fixed in -central and will be available in the next Galaxy distribution.
Thanks, J.
On Jan 16, 2013, at 10:02 PM, Anthonius deBoer wrote:
Hi,
Tried to remove a trackster visualization in the latest galaxy-dist and got this error:
Error Traceback: View as: Interactive | Text | XML (full) ⇝ NameError: global name 'util' is not defined URL: http://srv151/visualization/list?f-sharing=All&sort=-update_time&f-t... Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
environ, self.app)
Module paste.wsgilib:539 in intercept_output view
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:91 in __call__ view
return self.app( environ, start_response )
Module paste.httpexceptions:632 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
body = method( trans, **kwargs )
Module galaxy.web.framework:94 in decorator view
return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.visualization:320 in list view
ids = util.listify( kwargs['id'] )
NameError: global name 'util' is not defined
Extra Features
Display the lines of code near each part of the traceback
Show a debug prompt to allow you to directly debug the code at the traceback Re-GET Page
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Thu, Jan 17, 2013 at 1:16 PM, Anthonius deBoer thondeboer@me.com wrote:
Not to be ungrateful for the hard work you guys are all doing and please don't get this the wrong way, but is there any QA that is being done on the galaxy-dist when it is being released?
No worries Thon, we appreciate your feedback.
Maybe its an idea to install galaxy-dist on the main galaxy server for a few weeks, before releasing it to the public so we know it has been running and stable...
For what it is worth, this actually is our release process. The code that gets pulled from galaxy-central to galaxy-dist is a revision that has been running on Galaxy main for some period of time. We also have automated tests that run on every commit. However, neither of these techniques catches every bug.
We're never happy when bugs go out in dist. There are likely a few causes of the increase in this problem. One is the wide variety of functionality now available in Galaxy, with increasing contributions from a wide developer community, means there are many more corner cases to test.
This has been particularly exacerbated by increasing use of more interactive client side web technologies. These have enabled some powerful new features, but are also significantly more difficult to test well. We're currently working on a new framework for client side automated testing which will hopefully improve our ability to catch regressions.
Again...I know we are dealing with opensource and free software
True, but our goal is still to deliver a stable product (while still innovating quickly). We're always evolving and improving our QA process and would appreciate your suggestions.
Hi Thon, James and Dannon
I fully understand Thon's frustration. I have been running into similar situations during code upgrades of our production server.
Although the code is tested on 'Galaxy main', it is rather impossible to catch everything, since most local Galaxy servers have a different set-up and are used in a very different way than 'Galaxy main' (eg: I guess you can't test the functionalities of "Galaxy libraries" with your external users on 'Galaxy main' ?)
We go through a thorough testing phase whenever we upgrade our production server: First a fresh install, followed by the upgrade of our development server, and only if we are happy with the new code base, we upgrade our production server. And still, we sometimes catch problems only once the code is running for a few days on the production server.
We usually wait a few weeks before we work with a new release from galaxy-dist. This allows us to add individual fixes from galaxy-central. Hence, it would be great to get more information than just saying "This has been fixed in -central and will be available in the next Galaxy distribution".
Please don't misunderstand me, I fully appreciate the quick availability of the fixes. It would just be nice to get some details helping to merge the fix manually into our local code. - Maybe it is worth considering to branch the code with each release, allowing to fix certain bugs on galaxy-dist as well? I had a quick discussion about this last fall with Dannon.
Again, don't misunderstand me, I don't want to complain. Galaxy is a great software and it works. My job would not be do-able with out it.
Regards, Hans-Rudolf
On 01/17/2013 09:13 PM, James Taylor wrote:
On Thu, Jan 17, 2013 at 1:16 PM, Anthonius deBoer thondeboer@me.com wrote:
Not to be ungrateful for the hard work you guys are all doing and please don't get this the wrong way, but is there any QA that is being done on the galaxy-dist when it is being released?
No worries Thon, we appreciate your feedback.
Maybe its an idea to install galaxy-dist on the main galaxy server for a few weeks, before releasing it to the public so we know it has been running and stable...
For what it is worth, this actually is our release process. The code that gets pulled from galaxy-central to galaxy-dist is a revision that has been running on Galaxy main for some period of time. We also have automated tests that run on every commit. However, neither of these techniques catches every bug.
We're never happy when bugs go out in dist. There are likely a few causes of the increase in this problem. One is the wide variety of functionality now available in Galaxy, with increasing contributions from a wide developer community, means there are many more corner cases to test.
This has been particularly exacerbated by increasing use of more interactive client side web technologies. These have enabled some powerful new features, but are also significantly more difficult to test well. We're currently working on a new framework for client side automated testing which will hopefully improve our ability to catch regressions.
Again...I know we are dealing with opensource and free software
True, but our goal is still to deliver a stable product (while still innovating quickly). We're always evolving and improving our QA process and would appreciate your suggestions. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
galaxy-dev@lists.galaxyproject.org
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Anthonius deBoer -
Hans-Rudolf Hotz -
James Taylor -
Jeremy Goecks