Hi Eric,

I think they are. What you described is more the user-facing part.
My current proof-of-concept does not have a tool-user-interface, it just
stores the credentials in the framework and makes it accessible through
the user-object. Which should be enough for dynamic job destinations.
A dedicated user-interface for tools is a nice idea and we can put this
ontop I think very easily!

Thanks for sharing!
Bjoern

Am 28.07.2016 um 21:09 schrieb Eric Rasche:
> Hey Björn,
> 
> I talked a bit about this with Katherine today, her group is quite
> interested in working on this as well.
> 
> I know we had discussed this a bit at GCC, and I posted a message today,
> outlining my plans which were formulated when I was at PSU the other
> month. Were those suggestions compatible with the existing work you'd
> done on generic KV store stuff?
> 
> Cheers,
> Eric
> 
> On 28. juli 2016 18:59, Björn Grüning wrote:
>> Hi Steve & Mohammed,
>>
>> I'm working on a user-profile extension to get credentials for a user,
>> but this will take a few more weeks sorry.
>>
>> In the meantime can you look at the following idea:
>>
>> my_programm.py --credentials $USER_CREDENTIALS --arguments
>>
>> The variable $USER_CREDENTIALS is set during job execution with dynamic
>> destination mappings
>> https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping
>>
>> What do you think, would this work for you?
>> This assumes you as admin can pass along the user credentials if you
>> know the username.
>>
>> If not please get in touch and I will tell you about my plans to extend
>> the user-preferences maybe you can help me with this to speed things up.
>>
>> Ciao,
>> Bjoern
>>
>>
>>> Hi Bjorn,
>>>  sure, I don’t want to have the credentials stored in the tool but the tool 
>>> needs to act on behalf of the user to retrieve data from the repository, so
>>> it needs access to credentials.  This could for example be a token generated
>>> via an OAuth2 exchange - basically something that is sent along with every 
>>> http request to the remote resource to authenticate the user.  
>>>
>>> My thought is that this could be stored in the user profile if this can be 
>>> made
>>> available to the tool in the same way that __user_email__ is now. 
>>>
>>> When you say ‘on the framework level’ do you mean by Galaxy? 
>>>
>>> Steve
>>> —
>>> Department of Computing, Macquarie University
>>> http://web.science.mq.edu.au/~cassidy
>>>
>>>> On 28 Jul 2016, at 5:23 PM, Björn Grüning <bjoern.gruen...@gmail.com> 
>>>> wrote:
>>>>
>>>> Hi Steve,
>>>>
>>>> can you explain the larger use-case behind it. Imho you should not
>>>> populate a tool with credentials, this should be handled on the
>>>> framework level.
>>>>
>>>> Hope you are fine,
>>>> Bjoern
>>>>
>>>> Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
>>>>> Hi again,
>>>>>   I’m looking for the right way to store some user credentials in the
>>>>> galaxy session so that tools can work on behalf of the user with our
>>>>> repository. 
>>>>>
>>>>> Currently users have an API key and they need to upload it as a data
>>>>> item to that is then passed to each tool that needs it as input.  This
>>>>> doesn’t seem like the right solution since the API key becomes part of
>>>>> the history and so would be shared if the history were shared.  
>>>>>
>>>>> What would be better would be a way of storing the API key in the user
>>>>> session and then being able to pass that into a tool.
>>>>>
>>>>> I note that there are a few user session variables available in the tool
>>>>> xml file: __user__, __user_email__, __user_name__ and __user_id__.
>>>>> There is also a user preferences page where they can fill out a few
>>>>> details.  However, I can’t see a mechanism to extend this in any way and
>>>>> have extra properties in the preferences pane that would then be
>>>>> available to tools via the template file.  
>>>>>
>>>>> I can see that the standard practice for the data sources on
>>>>> usegalaxy.org <http://usegalaxy.org> is to send the user off to a
>>>>> repository website to find data that is then posted back to the galaxy
>>>>> server.  This isn’t appropriate for us since the interaction with the
>>>>> repository is not just for downloading a single dataset - tools will
>>>>> query the repository, download various kinds of data and possibly upload
>>>>> new data, so we need to store user credentials in some way. 
>>>>>
>>>>> Is there already a good way to achieve this or is this an enhancement to
>>>>> Galaxy? 
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Steve
>>>>>
>>>>>
>>>>> —
>>>>> Department of Computing, Macquarie University
>>>>> http://web.science.mq.edu.au/~cassidy
>>>>> <http://web.science.mq.edu.au/%7Ecassidy>
>>>>>
>>>>>
>>>>>
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> 
> -- 
> 
> Eric Rasche
> Programmer II
> 
> Center for Phage Technology
> Rm 312A, BioBio
> Texas A&M University
> College Station, TX 77843
> 404-692-2048 <tel:404-692-2048>
> e...@tamu.edu <mailto:e...@tamu.edu>
> Not responding quickly enough?
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