Question: Non-Admin Users Uploading From Paths
gravatar for Adam Labadorf
7.6 years ago by
Adam Labadorf30 wrote:
Hello, I'm trying to configure a non-admin user to upload data to our local galaxy instance. We manage our NGS data separately from galaxy and add access to them using the Import from system paths functionality. The non-admin user I have configured can upload from a local file or import from history but does not have the menu item to add files from systems paths like my admin user does. Is there a way to enable non-admin users to add datasets from system paths? -- Adam Labadorf Computational Tech Fraenkel Lab, MIT
galaxy • 811 views
ADD COMMENTlink modified 7.6 years ago by Nate Coraor3.1k • written 7.6 years ago by Adam Labadorf30
gravatar for Nate Coraor
7.6 years ago by
Nate Coraor3.1k
United States
Nate Coraor3.1k wrote:
Hi Adam, This can be done with the user_library_import_dir option in universe_wsgi.ini. Regular users are not given access to the regular import directory for security reasons (since it's not assumed that they should have access to all of its contents). --nate
ADD COMMENTlink written 7.6 years ago by Nate Coraor3.1k
Hi Nate, do what I want and I think I didn't explain clearly enough what I'm trying to do. I have a directory in a data library configured to allow a non-admin user to add datasets. I have the allow_library_path_paste option set in our init script and, when logged in as the admin, I see the "Upload files from filesystem paths" option in the "Create new data library datasets" dropdown list in addition to the two usual methods. When I log in as my non- admin user, only the "Upload files" and "Import datasets from current history" options exist in the dropdown for the same folder. I can upload and import files into this directory as non-admin, but the filesystem paths option is not there. Is it difficult to enable this option for non-admin users? Our local instance will be private to our lab, so security is less of an issue for us and, in any case, I will configure individual folders so only the users who should have the ability to add datasets can do so. Thanks. - Adam
ADD REPLYlink written 7.5 years ago by Adam Labadorf30
Hi Adam, Unfortunately allowing this option to regular users would give them full access to the filesystem, which is not a safe thing to do in most environments. It should be possible to enable it for non-admin users, but you'd need to change it in the code - both in the templates to allow the option and form to show up, and in the backend (which prevents non-admin users from accessing it). If this is a frequently necessary task, we could create an action which could be associated with a role that would allow for this. --nate
ADD REPLYlink written 7.5 years ago by Nate Coraor3.1k
Hi Nate, I understand and appreciate the security concerns of enabling this feature, and see why you left it out. In our case, all of our users have access to the underlying filesystem as it is and I'm trying to encourage them to migrate off of the command line and to galaxy. It's not a necessary use case, though - I was just trying to see if I could create a user that had 'data manager' type rights without full admin access. Since we manage our NGS data separately, uploading from systems paths is necessary for us but I can just upload everything as the admin. Thanks for your input. - Adam
ADD REPLYlink written 7.5 years ago by Adam Labadorf30
Hi Adam, A simple workaround might be to symlink from the real location into user_library_import_dir. --nate
ADD REPLYlink written 7.5 years ago by Nate Coraor3.1k
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