Non-admin users uploading from paths
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 labadorf@mit.edu
Adam Labadorf 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?
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
-- Adam Labadorf Computational Tech Fraenkel Lab, MIT labadorf@mit.edu <mailto:labadorf@mit.edu>
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From the documentation in universe_wsgi.ini, I don't think this option will 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
Hi Nate, 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 On Mon, Aug 9, 2010 at 10:57 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Adam Labadorf 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?
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
--
Adam Labadorf Computational Tech Fraenkel Lab, MIT labadorf@mit.edu <mailto:labadorf@mit.edu>
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On Tue, 2010-08-10 at 10:10 -0400, Adam Labadorf wrote:
Hi Nate,
From the documentation in universe_wsgi.ini, I don't think this option will 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.
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
- Adam
On Mon, Aug 9, 2010 at 10:57 PM, Nate Coraor <nate@bx.psu.edu> wrote: Adam Labadorf 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?
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
-- Adam Labadorf Computational Tech Fraenkel Lab, MIT
labadorf@mit.edu <mailto:labadorf@mit.edu>
------------------------------------------------------------------------
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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 On Wed, Aug 11, 2010 at 10:31 AM, Nate Coraor <nate@bx.psu.edu> wrote:
On Tue, 2010-08-10 at 10:10 -0400, Adam Labadorf wrote:
Hi Nate,
From the documentation in universe_wsgi.ini, I don't think this option will 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.
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
- Adam
On Mon, Aug 9, 2010 at 10:57 PM, Nate Coraor <nate@bx.psu.edu> wrote: Adam Labadorf 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?
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
-- Adam Labadorf Computational Tech Fraenkel Lab, MIT
labadorf@mit.edu <mailto:labadorf@mit.edu>
------------------------------------------------------------------------
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On Wed, 2010-08-11 at 10:38 -0400, Adam Labadorf wrote:
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.
Hi Adam, A simple workaround might be to symlink from the real location into user_library_import_dir. --nate
- Adam
On Wed, Aug 11, 2010 at 10:31 AM, Nate Coraor <nate@bx.psu.edu> wrote: On Tue, 2010-08-10 at 10:10 -0400, Adam Labadorf wrote: > Hi Nate, > > > From the documentation in universe_wsgi.ini, I don't think this option > will 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.
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
> > > - Adam > > > On Mon, Aug 9, 2010 at 10:57 PM, Nate Coraor <nate@bx.psu.edu> wrote: > Adam Labadorf 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? > > > 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 > > > -- > Adam Labadorf > Computational Tech > Fraenkel Lab, MIT > > labadorf@mit.edu <mailto:labadorf@mit.edu> > > > ------------------------------------------------------------------------ > > _______________________________________________ > galaxy-user mailing list > galaxy-user@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user > > >
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