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.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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