Hello Cassidy,
I have the same problem like you because I need the user credential to
access to an external tools.
I tried the user session variables available in the tool
 xml file: __user__, __user_email__, __user_name__ and __user_id__. I t
works perfectly I don't know if you need the password, because this is the
only information is missing.

Mohamed

2016-07-28 9:42 GMT+02:00 Steve Cassidy <steve.cass...@mq.edu.au>:

> 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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