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.cassidy@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
On 17 Oct. 2016, at 5:26 pm, Katherine Beaulieu < katherine.beaulieu014@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 Cheers, Katherine
On Mon, Oct 17, 2016 at 5:17 PM, Steve Cassidy <steve.cassidy@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.gruening@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_Des tination_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.gruening@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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