nglims, error pages and permissions
Hi, I am using nglims, and I am getting Internal Error pages sometimes. I am not sure if it is because of Galaxy itself or nglims though. The latest is when I create a new role and hit submit. It is repeatable if I fill in the name as "test", no description, I add in a single role (others are present but excluded from being associated), if I check "create a new group..." and then click "save." However, when I created a group and checked "create a new role ...," it did not create an error. Next, I tried associating data with this new user. However, her new roles (both the new role I created and her username-role) did not show up, and so I could not give the data to her. Is there any reason why a new user's roles would not show up? -- Lee Katz, Ph.D.
Lee;
Hi, I am using nglims, and I am getting Internal Error pages sometimes. I am not sure if it is because of Galaxy itself or nglims though.
I believe these are all Galaxy-specific things. I haven't changed anything purposefully in the groups/roles permissions so unless I messed up a merge during the life of this branch they should be replicable on a clean galaxy-central. It might be worth checking and submitting as bug reports if you can verify. As a help for debugging, you might want to set `debug = True` in your universe_wsgi.ini while testing.
The latest is when I create a new role and hit submit. It is repeatable if I fill in the name as "test", no description, I add in a single role (others are present but excluded from being associated), if I check "create a new group..." and then click "save."
I have seen this when there is no description set. Including a description avoids the problem. I know it's not really a fix but an easy workaround is almost as good.
Next, I tried associating data with this new user. However, her new roles (both the new role I created and her username-role) did not show up, and so I could not give the data to her. Is there any reason why a new user's roles would not show up?
I don't believe so but am not sure. Does the data already have sharing roles? If so it often won't let new roles be added since the roles are additive: so two roles means barely anyone can use it unless they have both of those role (as opposed to either role). The best way around this is to create groups, give them roles, then associate data files with groups. I find this the easier way to manage permissions. Hope this helps, Brad
Thanks Brad! But her group's role is not even showing up when I edit permissions on the files. More frustrating is that her role and her group-role shows up when I try to edit the folder's permissions, but I can't see how to leverage that information. Also, I found that I cannot purge the group... frustrating... Hopefully it's an option in the ini file that I missed. On Thu, Jul 18, 2013 at 3:26 PM, Brad Chapman <chapmanb@50mail.com> wrote:
Lee;
Hi, I am using nglims, and I am getting Internal Error pages sometimes. I am not sure if it is because of Galaxy itself or nglims though.
I believe these are all Galaxy-specific things. I haven't changed anything purposefully in the groups/roles permissions so unless I messed up a merge during the life of this branch they should be replicable on a clean galaxy-central. It might be worth checking and submitting as bug reports if you can verify.
As a help for debugging, you might want to set `debug = True` in your universe_wsgi.ini while testing.
The latest is when I create a new role and hit submit. It is repeatable if I fill in the name as "test", no description, I add in a single role (others are present but excluded from being associated), if I check "create a new group..." and then click "save."
I have seen this when there is no description set. Including a description avoids the problem. I know it's not really a fix but an easy workaround is almost as good.
Next, I tried associating data with this new user. However, her new roles (both the new role I created and her username-role) did not show up, and so I could not give the data to her. Is there any reason why a new user's roles would not show up?
I don't believe so but am not sure. Does the data already have sharing roles? If so it often won't let new roles be added since the roles are additive: so two roles means barely anyone can use it unless they have both of those role (as opposed to either role).
The best way around this is to create groups, give them roles, then associate data files with groups. I find this the easier way to manage permissions.
Hope this helps, Brad
-- Lee Katz, Ph.D.
Lee; I think all these issues are due to using roles over groups. You'll get confusing behavior like this if you have roles assigned to top level folders in the data libraries. It tries to avoid letting you set conflicting roles on the underlying files so will have less options in permissions editing. My approach is to use groups exclusively, and then assign these to data libraries and let the permissions cascade down to avoid these type of conflicts. Hope this helps, Brad
Thanks Brad! But her group's role is not even showing up when I edit permissions on the files. More frustrating is that her role and her group-role shows up when I try to edit the folder's permissions, but I can't see how to leverage that information.
Also, I found that I cannot purge the group... frustrating... Hopefully it's an option in the ini file that I missed.
On Thu, Jul 18, 2013 at 3:26 PM, Brad Chapman <chapmanb@50mail.com> wrote:
Lee;
Hi, I am using nglims, and I am getting Internal Error pages sometimes. I am not sure if it is because of Galaxy itself or nglims though.
I believe these are all Galaxy-specific things. I haven't changed anything purposefully in the groups/roles permissions so unless I messed up a merge during the life of this branch they should be replicable on a clean galaxy-central. It might be worth checking and submitting as bug reports if you can verify.
As a help for debugging, you might want to set `debug = True` in your universe_wsgi.ini while testing.
The latest is when I create a new role and hit submit. It is repeatable if I fill in the name as "test", no description, I add in a single role (others are present but excluded from being associated), if I check "create a new group..." and then click "save."
I have seen this when there is no description set. Including a description avoids the problem. I know it's not really a fix but an easy workaround is almost as good.
Next, I tried associating data with this new user. However, her new roles (both the new role I created and her username-role) did not show up, and so I could not give the data to her. Is there any reason why a new user's roles would not show up?
I don't believe so but am not sure. Does the data already have sharing roles? If so it often won't let new roles be added since the roles are additive: so two roles means barely anyone can use it unless they have both of those role (as opposed to either role).
The best way around this is to create groups, give them roles, then associate data files with groups. I find this the easier way to manage permissions.
Hope this helps, Brad
-- Lee Katz, Ph.D.
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Lee Katz