Re: [galaxy-dev] Storing data in the user session

Thanks Bjoern, look forward to seeing this, happy to test it when it’s ready. Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy On 17 Oct. 2016, at 5:41 pm, Björn Grüning mailto:bjoern.gruen...@gmail.com>> wrote: Hi Steve and Katherine, we are workin

Re: [galaxy-dev] Storing data in the user session

Hi Steve and Katherine, we are working on this branch and it is working: https://github.com/bgruening/galaxy/tree/extra_user_preferences But are a little bit sidetracked by porting the user-preferences from mako to JS before we can include this into Main Galaxy, but the main idea should work for

Re: [galaxy-dev] Storing data in the user session

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 wrote: > Thanks Katherine, in my case I want to store the API key for an externa

Re: [galaxy-dev] Storing data in the user session

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

Re: [galaxy-dev] Storing data in the user session

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-K

Re: [galaxy-dev] Storing data in the user session

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

Re: [galaxy-dev] Storing data in the user session

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 : > Hi Steve & Mohammed, > > I'm working on a user-profile extension to get credentials for a user, > but this will take

Re: [galaxy-dev] Storing data in the user session

Hi Eric, I think they are. What you described is more the user-facing part. My current proof-of-concept does not have a tool-user-interface, it just stores the credentials in the framework and makes it accessible through the user-object. Which should be enough for dynamic job destinations. A dedic

Re: [galaxy-dev] Storing data in the user session

Hey Björn, I talked a bit about this with Katherine today, her group is quite interested in working on this as well. I know we had discussed this a bit at GCC, and I posted a message today, outlining my plans which were formulated when I was at PSU the other month. Were those suggestions compatib

Re: [galaxy-dev] Storing data in the user session

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

Re: [galaxy-dev] Storing data in the user session

Hi Steve so what you can do create a web authentification tool with Galaxy and bring back the information as it is done with the ucsc genopme browser. Maybe it should work, then you don't need to show the password in the history . Mohamed 2016-07-28 10:17 GMT+02:00 Steve Cassidy : > Hi Mohamed,

Re: [galaxy-dev] Storing data in the user session

Hi Mohamed, The problem with this solution is that the password again becomes part of the history since it is one of the inputs to the tool. If I want to publish this workflow then the password can’t be visible. For this reason password storage needs to be outside of workflows and handled som

Re: [galaxy-dev] Storing data in the user session

Hi Steve, there is another solution is that the user is giving his credential via the tool. The only thing is missing the tag password on the xml then you can encrypt the password. I tried to add the new paramter on the build.py but I have some errors, don't know if someone arrived to fixed it. Mo

Re: [galaxy-dev] Storing data in the user session

Hi Mohamed, In my case, the credentials on Galaxy are not generally the same as on the remote system so we need some way to store a second set of credentials in the galaxy session. So, for example, user Fred has an account on Galaxy (f...@here.com) and wants to get data

Re: [galaxy-dev] Storing data in the user session

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,

Re: [galaxy-dev] Storing data in the user session

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 a

Re: [galaxy-dev] Storing data in the user session

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

[galaxy-dev] Storing data in the user session

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.