Re: Plugins

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Re: Plugins

Michael E. Cotterell
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
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
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 <[hidden email] (mailto:[hidden email])> 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 <[hidden email] (mailto:[hidden email])> 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 <[hidden email] (mailto:[hidden email])>
> > > 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
> > > > > <[hidden email] (mailto:[hidden email])> 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
> > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > 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
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > 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
> > > > > > > > <[hidden email] (mailto:[hidden email]) (mailto:[hidden email])> 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
> > > > [hidden email] (mailto:[hidden email])
> > > > [hidden email] (mailto:[hidden email])
> > > > [hidden email] (mailto:[hidden email])
> > > > http://michaelcotterell.com/
> > >
> >
>



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Re: Plugins

Carl Eberhard
Heya, Michael

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


Any feedback is appreciated.


On Mon, Sep 16, 2013 at 11:42 AM, Michael E. Cotterell <[hidden email]> 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
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
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 <[hidden email] (mailto:[hidden email])> 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 <[hidden email] (mailto:[hidden email])> 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 <[hidden email] (mailto:[hidden email])>
> > > 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
> > > > > <[hidden email] (mailto:[hidden email])> 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
> > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > 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
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > 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
> > > > > > > > <[hidden email] (mailto:[hidden email]) (mailto:[hidden email])> 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
> > > > [hidden email] (mailto:[hidden email])
> > > > [hidden email] (mailto:[hidden email])
> > > > [hidden email] (mailto:[hidden email])
> > > > http://michaelcotterell.com/
> > >
> >
>





___________________________________________________________
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:
  http://lists.bx.psu.edu/

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Re: Plugins

Carl Eberhard
I've factored out the plugin discovery from the (page serving) plugin framework and subclassed an initial stab at a hook plugin manager. The page serving responsibilities are now in a separate subclass and the visualization registry is based on that:

It should at least be easier modify. Have a look and let me know if you see any issues or have suggestions.



On Tue, Sep 17, 2013 at 11:19 AM, Carl Eberhard <[hidden email]> wrote:
Heya, Michael

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


Any feedback is appreciated.


On Mon, Sep 16, 2013 at 11:42 AM, Michael E. Cotterell <[hidden email]> 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
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
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 <[hidden email] (mailto:[hidden email])> 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 <[hidden email] (mailto:[hidden email])> 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 <[hidden email] (mailto:[hidden email])>
> > > 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
> > > > > <[hidden email] (mailto:[hidden email])> 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
> > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > 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
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > 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
> > > > > > > > <[hidden email] (mailto:[hidden email]) (mailto:[hidden email])> 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
> > > > [hidden email] (mailto:[hidden email])
> > > > [hidden email] (mailto:[hidden email])
> > > > [hidden email] (mailto:[hidden email])
> > > > http://michaelcotterell.com/
> > >
> >
>






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Re: Plugins

Michael E. Cotterell
Carl,

Is there a way for a tool_shed installed tool to provide a plugin? Also, have you actually added any hooks anywhere? If so, where are they documented?

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
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
[hidden email] (mailto:[hidden email])
http://michaelcotterell.com/


On Wednesday, September 18, 2013 at 11:00 AM, Carl Eberhard wrote:

> I've factored out the plugin discovery from the (page serving) plugin framework and subclassed an initial stab at a hook plugin manager. The page serving responsibilities are now in a separate subclass and the visualization registry is based on that:
> https://bitbucket.org/galaxy/galaxy-central/src/2d0bcb07596c4c688ed3908391d866831c65c042/lib/galaxy/web/base/pluginframework.py?at=default
>
> It should at least be easier modify. Have a look and let me know if you see any issues or have suggestions.
>
>
>
> On Tue, Sep 17, 2013 at 11:19 AM, Carl Eberhard <[hidden email] (mailto:[hidden email])> wrote:
> > 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 <[hidden email] (mailto:[hidden email])> 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
> > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > 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 <[hidden email] (mailto:[hidden email]) (mailto:[hidden email])> 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 <[hidden email] (mailto:[hidden email]) (mailto:[hidden email])> 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 <[hidden email] (mailto:[hidden email]) (mailto:[hidden email])>
> > > > > > 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
> > > > > > > > <[hidden email] (mailto:[hidden email]) (mailto:[hidden email])> 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
> > > > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > > > 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
> > > > > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > > > > 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
> > > > > > > > > > > <[hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])> 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
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > http://michaelcotterell.com/
> > > > > >
> > > > >
> > > >
> > >
> >
>



___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Plugins

Carl Eberhard
Hi, Michael

It was good meeting you in Athens. You guys are doing amazing things.

There currently is no mechanism to install a plugin (either hook or visualization) from the toolshed. I think it's certainly possible (and planned) in the future.

I haven't added any hooks for plugins. I would hope there would be some discussion as to the which places in the code would be the most useful and desired within the community. Hopefully, that discussion can be sparked soon.

As to the whether we can implement an admin link to reload the entire tool shed without restarting Galaxy: I talked a bit to Greg about it and it might be more possible and easier to reload entire tool sections (for example, 'Data sources'). Would that work for your use case?

Carl


On Thu, Mar 6, 2014 at 9:00 AM, Michael E. Cotterell <[hidden email]> wrote:
Carl,

Is there a way for a tool_shed installed tool to provide a plugin? Also, have you actually added any hooks anywhere? If so, where are they documented?

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
[hidden email] (mailto:[hidden email])
On Wednesday, September 18, 2013 at 11:00 AM, Carl Eberhard wrote:

> I've factored out the plugin discovery from the (page serving) plugin framework and subclassed an initial stab at a hook plugin manager. The page serving responsibilities are now in a separate subclass and the visualization registry is based on that:
> https://bitbucket.org/galaxy/galaxy-central/src/2d0bcb07596c4c688ed3908391d866831c65c042/lib/galaxy/web/base/pluginframework.py?at=default
>
> It should at least be easier modify. Have a look and let me know if you see any issues or have suggestions.
>
>
>
> On Tue, Sep 17, 2013 at 11:19 AM, Carl Eberhard <[hidden email] (mailto:[hidden email])> wrote:
> > 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 <[hidden email] (mailto:[hidden email])> 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
> > > 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 <[hidden email] (mailto:[hidden email]) (mailto:[hidden email])> 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 <[hidden email] (mailto:[hidden email]) (mailto:[hidden email])> 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 <[hidden email] (mailto:[hidden email]) (mailto:[hidden email])>
> > > > > > 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
> > > > > > > > <[hidden email] (mailto:[hidden email]) (mailto:[hidden email])> 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
> > > > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > > > 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
> > > > > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > > > > 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
> > > > > > > > > > > <[hidden email] (mailto:[hidden email]) (mailto:[hidden email]) (mailto:[hidden email])> 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
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > [hidden email] (mailto:[hidden email]) (mailto:[hidden email])
> > > > > > > http://michaelcotterell.com/
> > > > > >
> > > > >
> > > >
> > >
> >
>





___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/