Hi Steve and Katherine,

we are working on this branch and it is working:
https://github.com/bgruening/galaxy/tree/extra_user_preferences

But are a little bit sidetracked by porting the user-preferences from
mako to JS before we can include this into Main Galaxy, but the main
idea should work for tools and all other features we have in mind.

Cheers,
Bjoern

Am 17.10.2016 um 23:31 schrieb Katherine Beaulieu:
> Ah I see, we had a similar problem except our service used a password
> and username so we ended up implementing a password parameter that
> didn't persist in the database.
> 
> On Mon, Oct 17, 2016 at 5:29 PM, Steve Cassidy <steve.cass...@mq.edu.au
> <mailto:steve.cass...@mq.edu.au>> wrote:
> 
>     Thanks Katherine, in my case I want to store the API key for an
>     external service (not Galaxy) and get access to that from a tool so
>     that the tool can act on behalf of the user. 
> 
>     Steve
> 
>     —
>     Department of Computing, Macquarie University
>     http://web.science.mq.edu.au/~cassidy
>     <http://web.science.mq.edu.au/%7Ecassidy>
> 
>>     On 17 Oct. 2016, at 5:26 pm, Katherine Beaulieu
>>     <katherine.beaulieu...@gmail.com
>>     <mailto:katherine.beaulieu...@gmail.com>> wrote:
>>
>>     Hi Steve, 
>>     In terms of accessing the user's api key within a tool definition
>>     file, have a look at this thread I had started. John had suggested
>>     something but I haven't gotten it to work but maybe you will have
>>     more luck than me.
>>     
>> http://dev.list.galaxyproject.org/Workflow-ID-Galaxy-Instance-URL-API-Key-in-Galaxy-Tool-Config-td4669906.html#a4670104
>>     
>> <http://dev.list.galaxyproject.org/Workflow-ID-Galaxy-Instance-URL-API-Key-in-Galaxy-Tool-Config-td4669906.html#a4670104>
>>     Cheers,
>>     Katherine
>>
>>     On Mon, Oct 17, 2016 at 5:17 PM, Steve Cassidy
>>     <steve.cass...@mq.edu.au <mailto:steve.cass...@mq.edu.au>> wrote:
>>
>>         Hi Bjoern, 
>>          just wanting to revisit this question and perhaps get an
>>         update on what you were doing for extending the user profile. 
>>
>>         I just noticed in the galaxy sources the option to add ‘forms’
>>         to be filled out at registration time. The admin interface
>>         seems to allow me to create  a form but it doesn’t appear when
>>         I try to register.  The code for this seems to be 2-5 years
>>         old so perhaps it’s a forgotten corner? 
>>
>>         
>> https://github.com/galaxyproject/galaxy/tree/dev/templates/admin/forms
>>         
>> <https://github.com/galaxyproject/galaxy/tree/dev/templates/admin/forms>
>>
>>         Anyway, if you have made any progress on this I’d be happy to
>>         hear about it.  I’d like to be able to store the user’s API
>>         key in the profile and access it from a tool definition file. 
>>
>>         Cheers,
>>
>>         Steve
>>         —
>>         Department of Computing, Macquarie University
>>         http://web.science.mq.edu.au/~cassidy
>>         <http://web.science.mq.edu.au/%7Ecassidy>
>>
>>>         On 28 Jul. 2016, at 2:59 pm, Björn Grüning
>>>         <bjoern.gruen...@gmail.com
>>>         <mailto:bjoern.gruen...@gmail.com>> 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
>>>         
>>> <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
>>>>         <http://web.science.mq.edu.au/%7Ecassidy>
>>>>
>>>>>         On 28 Jul 2016, at 5:23 PM, Björn Grüning
>>>>>         <bjoern.gruen...@gmail.com
>>>>>         <mailto: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/>
>>>>>>         <http://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>
>>>>>>         <http://web.science.mq.edu.au/%7Ecassidy
>>>>>>         <http://web.science.mq.edu.au/%7Ecassidy>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>         ___________________________________________________________
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>>>>>>
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>>>>
>>
>>
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> 
> 
> 
> 
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