Peter,
if you were just interested in having a dynamic refresh.... it was posted long
time ago and we have it operational. It comes as a tool in your tool list and
refreshes all from the tool_conf.xml. Not the loc filtes though! As far as i
remember it doesn't kill running jobs.
It requires two lines of code in galaxy source and the addition of a tool to
the tools section.
I pasted it from my archive below. But it is quite self explanatory.
Alex
Galaxy source adapt for tool refresh
> Changes to Galaxy to add refresh toolbox ability:
> 1. change the execute method of the class tool in
> lib/galaxy/tools/__init__.py to
>
> def execute( self, trans, incoming={}, set_output_hid=True ):
> """
> Execute the tool using parameter values in `incoming`. This just
> dispatches to the `ToolAction` instance specified by
> `self.tool_action`. In general this will create a `Job` that
> when run will build the tool's outputs, e.g. `DefaultToolAction`.
> """
>
> #############
> #add code to verify if user has administrative privileges
> #added by sumedha ganjoo, sganjoo at uga.edu: line 1104 to 1109 - to
> refresh toolbox
> if self.id == 'REFRESH_ID':
> self.app.refreshToolBox()
> #############
>
> return self.tool_action.execute( self, trans,
> incoming=incoming, set_output_hid=set_output_hid )
>
> 2. add refreshToolBox method (find below) to UniverseApplication class
> in lib/galaxy/app.py
>
> ###########
> # added by sumedha ganjoo,sganjoo at uga.edu, line 86-90
> def refreshToolBox( self):
> self.toolbox = tools.ToolBox( self.config.tool_config,
> self.config.tool_path, self )
> ###########
>
>
> 3. Add Refresh tool. Attached.
>
> Thanks,
> Sumedha
>
>
> <tool id="REFRESH_ID" name="Refresh" Version="1.0.0"> <description>
> :Refresh Galaxy</description> <command interpreter="python">
> refreshTool.py
> $input
> $output
> </command>
> <inputs>
> <param name="input" type="select" display="radio" size="250"
> label="Execute this tool by clicking on Execute button">
> <option value="refresh">Refresh Galaxy</option>
> </param>
>
> </inputs>
> <outputs>
> <data format="tabular" name="output" />
> </outputs>
> <tests>
> </tests>
> <help>
>
>
> **Click on "Galaxy" on the top left corner of this window to refresh
> the page.**
>
> </help>
> </tool>
>
________________________________________
Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
namens Peter Cock [p.j.a.c...@googlemail.com]
Verzonden: maandag 30 mei 2011 21:09
Aan: Vossen, Bodo
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] Implemented adding tools via admin console
On Mon, May 30, 2011 at 9:54 AM, Vossen, Bodo wrote:
> Hi Peter,
>
> thanks a lot for your comments.
Hi Bodo,
No problem :)
> I think it is more comfortable to be able to upload tools and xml via the
> webbrowser than to open a terminal and copy them, that was the idea
> behind my work. Especially for our institute this is very useful.
For me the command vs the web interface is not important.
What I was excited about was adding a tool to Galaxy without
having to restart Galaxy and interrupt any users.
> You're right about the check_argument methods. I wasn't sure to add this
> kind of functionality in the first place, because it can become very tricky.
> What I did should just be the very first step for someone who wants to
> continue the work (if this makes sense).
> That's why I added a checkbox that disable this check, so that you still
> can upload your tool/xml even the argument test would fail.
It might be useful then.
> Do you have some comments about the other parts ? Is this something
> you would be interested in using ?
I've not had a chance to try the code yet, but it could be useful.
Peter
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