Over next couple days, I'll take a look at what's in 
lib/galaxy/web/base/pluginframework.py and see if there is a way to refactor it 
with my stuff in order to get a general plugin framework 
(galaxy.pluginframework) as proposed by James. Sorry for the delay. Teaching a 
math class this semester is really eating up my time.



Sincerely,
Michael E. Cotterell

Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA & TA, University of Georgia
Department Liaison, CS Graduate Student Association, University of Georgia
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
mepc...@uga.edu (mailto:mepc...@uga.edu)
m...@cs.uga.edu (mailto:m...@cs.uga.edu)
http://michaelcotterell.com/


On Tuesday, September 3, 2013 at 12:45 PM, Carl Eberhard wrote:

> It is web-specific and only handles the mako/static serving cases. I think 
> the only areas we were generalizing at this point were the directory 
> structures and main configuration.
> 
> Agreed on more generalization and the hook system. Michael's stuff is a good 
> direction to move in.
> 
> I know John was looking to use it for dynamic job destinations and dynamic 
> toolbox filters. I'd like to see some lab/community discussion on (even broad 
> stroke) functional requirements and use cases. 
> 
> 
> On Tue, Sep 3, 2013 at 12:27 PM, James Taylor <ja...@jamestaylor.org 
> (mailto:ja...@jamestaylor.org)> wrote:
> > Carl, is what you have now totally web specific? It would be great to
> > have a general plugin framework (galaxy.pluginframework) which the web
> > stuff could perhaps extend?
> > 
> > 
> > On Tue, Sep 3, 2013 at 10:56 AM, Carl Eberhard <carlfeberh...@gmail.com 
> > (mailto:carlfeberh...@gmail.com)> wrote:
> > > Heya, Michael
> > > 
> > > Right now our only plugin code is located in
> > > lib/galaxy/web/base/pluginframework.py. It's only purpose so far is to:
> > > - allow locally modified/created code to serve mako templates and static
> > > pages/resources from paste.
> > > - serve as a super class for the visualization framework.
> > > 
> > > I think your git repo has some great ideas.
> > > 
> > > Carl
> > > 
> > > 
> > > On Fri, Aug 30, 2013 at 2:25 PM, Michael Cotterell 
> > > <mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)>
> > > wrote:
> > > > 
> > > > Is this plugin code hosted anywhere (like in central)?
> > > > 
> > > > 
> > > > On Monday, August 26, 2013, James Taylor wrote:
> > > > > 
> > > > > Michael,
> > > > > 
> > > > > Carl has been working on a plugin framework for Galaxy, and John
> > > > > Chilton has made some improvements. It would be great if you could
> > > > > look over what each other has done and come up with some suggestions.
> > > > > I personally am in favor of a very generic hook system where a hook
> > > > > can be defined anywhere in the code and then the user can provide any
> > > > > callable.
> > > > > 
> > > > > I'm fond of the way sup implemented hooks, see the use of HookManager
> > > > > here: 
> > > > > https://github.com/sup-heliotrope/sup/blob/develop/lib/sup/time.rb
> > > > > 
> > > > > Your approach is quite similar and I like it.
> > > > > 
> > > > > This makes it easy to have a script that can list all available hooks
> > > > > with their documentation.
> > > > > 
> > > > > 
> > > > > --
> > > > > James Taylor, Assistant Professor, Biology/CS, Emory University
> > > > > 
> > > > > 
> > > > > On Fri, Aug 23, 2013 at 10:29 AM, Michael E. Cotterell
> > > > > <mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)> wrote:
> > > > > > James,
> > > > > > 
> > > > > > Has there been any more talk about this? I'd be willing to work in 
> > > > > > my
> > > > > > reference implementation into central as a pull request, but I 
> > > > > > don't want to
> > > > > > do that unless there is an agreed upon roadmap or something.
> > > > > > 
> > > > > > Thanks!
> > > > > > 
> > > > > > Sincerely,
> > > > > > Michael E. Cotterell
> > > > > > 
> > > > > > Ph.D. Student in Computer Science, University of Georgia
> > > > > > Instructor of Record, Graduate RA & TA, University of Georgia
> > > > > > Department Liaison, CS Graduate Student Association, University of
> > > > > > Georgia
> > > > > > mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) 
> > > > > > (mailto:mepcotter...@gmail.com)
> > > > > > mepc...@uga.edu (mailto:mepc...@uga.edu) (mailto:mepc...@uga.edu)
> > > > > > m...@cs.uga.edu (mailto:m...@cs.uga.edu) (mailto:m...@cs.uga.edu)
> > > > > > http://michaelcotterell.com/
> > > > > > 
> > > > > > 
> > > > > > On Tuesday, July 16, 2013 at 2:08 PM, Michael E. Cotterell wrote:
> > > > > > 
> > > > > > > James,
> > > > > > > 
> > > > > > > That's exactly what I was thinking. In my opinion, hooks are the 
> > > > > > > way
> > > > > > > to go (as seen in my example), but if there's a better way then 
> > > > > > > I'm game for
> > > > > > > that to. I just want to be able to extend Galaxy without 
> > > > > > > modifying Galaxy
> > > > > > > itself.
> > > > > > > 
> > > > > > > Thanks!
> > > > > > > 
> > > > > > > Sincerely,
> > > > > > > Michael E. Cotterell
> > > > > > > 
> > > > > > > Ph.D. Student in Computer Science, University of Georgia
> > > > > > > Instructor of Record, Graduate RA & TA, University of Georgia
> > > > > > > Faculty Liaison, CS Graduate Student Association, University of
> > > > > > > Georgia
> > > > > > > mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) 
> > > > > > > (mailto:mepcotter...@gmail.com)
> > > > > > > mepc...@uga.edu (mailto:mepc...@uga.edu) (mailto:mepc...@uga.edu)
> > > > > > > m...@cs.uga.edu (mailto:m...@cs.uga.edu) (mailto:m...@cs.uga.edu)
> > > > > > > http://michaelcotterell.com/
> > > > > > > 
> > > > > > > 
> > > > > > > On Tuesday, July 16, 2013 at 2:05 PM, James Taylor wrote:
> > > > > > > 
> > > > > > > > Michael,
> > > > > > > > 
> > > > > > > > Galaxy is all about plugins! Tools, datatypes, batch systems,
> > > > > > > > visualizations, et cetera.
> > > > > > > > 
> > > > > > > > Additional ways to extend Galaxy through plugins are very 
> > > > > > > > welcome.
> > > > > > > > We
> > > > > > > > just need to make sure that whatever solution is chosen is 
> > > > > > > > extremely
> > > > > > > > general.
> > > > > > > > 
> > > > > > > > --
> > > > > > > > James Taylor, Assistant Professor, Biology/CS, Emory University
> > > > > > > > 
> > > > > > > > 
> > > > > > > > On Tue, Jul 16, 2013 at 1:57 PM, Michael E. Cotterell
> > > > > > > > <mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) 
> > > > > > > > (mailto:mepcotter...@gmail.com)> wrote:
> > > > > > > > > Are there any plans in the works to support plugins within 
> > > > > > > > > Galaxy?
> > > > > > > > > One of the tools I'm working on is actually more of an 
> > > > > > > > > extension of the
> > > > > > > > > workflow canvas/editor's user interface. Right now, I've 
> > > > > > > > > minimized the
> > > > > > > > > modifications required to the editor.mako file to simply 
> > > > > > > > > adding a mako
> > > > > > > > > include near the bottom of the file. However, like I just 
> > > > > > > > > said, this
> > > > > > > > > requires editing a Galaxy file. It would be a lot better if 
> > > > > > > > > Galaxy supported
> > > > > > > > > plugins with hooks, thus allowing me to extend the user 
> > > > > > > > > interface (or any
> > > > > > > > > other part of the application) by registering hooks in a 
> > > > > > > > > plugin.
> > > > > > > > > 
> > > > > > > > > To demonstrate how easy it would be to integrate plugins into 
> > > > > > > > > a
> > > > > > > > > python application, I've written up a simple plugin manager 
> > > > > > > > > script (~100
> > > > > > > > > loc) an placed it in a gist: https://gist.git
> > > > > > > > 
> > > > > > > 
> > > > > > 
> > > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > --
> > > > Sincerely,
> > > > Michael E. Cotterell
> > > > 
> > > > Ph.D. Student in Computer Science, University of Georgia
> > > > Graduate RA & TA, University of Georgia
> > > > mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
> > > > mepc...@uga.edu (mailto:mepc...@uga.edu)
> > > > m...@cs.uga.edu (mailto:m...@cs.uga.edu)
> > > > http://michaelcotterell.com/
> > > 
> > 
> 



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