Dear Bjoern, I think it should work for me.
I will contatct you to see how it can work for my purpose.
Thank you in advance,
Mohamed
2016-07-28 20:59 GMT+02:00 Björn Grüning bjoern.gruening@gmail.com:
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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