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
Cheers,
Katherine

On Mon, Oct 17, 2016 at 5:17 PM, Steve Cassidy <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
>
> 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
>
> On 28 Jul. 2016, at 2:59 pm, Björn Grüning <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
>
> 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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