More dataset permissions issues / Missing role / datasets without any permissions

[hexylena]

I recently had some workflows that failed to schedule. I believe it's because the workflows lack proper access/manage permissions:

Attempting to run a tool returns:

The server could not complete the request. Please contact the Galaxy Team if this error persists. Error executing tool: User does not have permission to use a dataset (10798939) provided for input.

Attempting to run a workflow fails (silently)

I was curious how widespread the issue was. 1.48% of the datasets on our server lack any form of permissions:

galaxy=> select (select count(dataset.id) FROM dataset LEFT JOIN dataset_permissions ON dataset.id = dataset_permissions.id where dataset_permissions.id is null)::float * 100 / (select count(*) from dataset) as datasets_lacking_permissions;
┌──────────────────────────────┐
│ datasets_lacking_permissions │
├──────────────────────────────┤
│             1.48219320654745 │
└──────────────────────────────┘

Tools and workflows cannot be run on these datasets rendering them quite useless.

Permissions can also not be changed on these datasets (even as an admin), the boxes are rendered uneditable:

In my specific case, looking at the response a role was present in both access + manage lists, but it was not rendered in the UI:

That role is valid

galaxy=> select * from role where id = 7825;
┌──────┬────────────────────────────┬────────────────────────────┬─────────────────────┬──────────────────────────────────────┬─────────┬─────────┐
│  id  │        create_time         │        update_time         │        name         │             description              │  type   │ deleted │
├──────┼────────────────────────────┼────────────────────────────┼─────────────────────┼──────────────────────────────────────┼─────────┼─────────┤
│ 7825 │ 2019-07-15 17:36:33.313378 │ 2019-07-15 17:36:33.313403 │ redacted            │ Private Role for redacted            │ private  │ f       │
└──────┴────────────────────────────┴────────────────────────────┴─────────────────────┴──────────────────────────────────────┴─────────┴─────────┘

but it isn't displayed

So the bugs are:

1. Role isn't displayed
2. I as an admin have imported this history but cannot run tools on it or try and test/fix anything about it
3. Workflow invocations do not show errors (but I guess this is being fixed?)

And I guess that datasets without permissions really aren't an issue? It feels unexpected to me, but it looks like it auto-fixes whenever you attempt to edit permissions on a dataset that's completely lacking them.