Heya, Michael

I'm currently working in this area as well now - so no worries if your
schedule doesn't permit.

The card is here: https://trello.com/c/c2AzV3Xf

Any feedback is appreciated.


On Mon, Sep 16, 2013 at 11:42 AM, Michael E. Cotterell <
mepcotter...@gmail.com> wrote:

> 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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