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.gruen...@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.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> > >>> > >>> > >>> > >>> ___________________________________________________________ > >>> Please keep all replies on the list by using "reply all" > >>> in your mail client. To manage your subscriptions to this > >>> and other Galaxy lists, please use the interface at: > >>> https://lists.galaxyproject.org/ > >>> > >>> To search Galaxy mailing lists use the unified search at: > >>> http://galaxyproject.org/search/mailinglists/ > > >
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