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

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

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
    >
    >
    >