Re: [galaxy-dev] Implemented adding tools via admin console

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-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Peter Cock [p.j.a.cock@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 ___________________________________________________________ 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:

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