Hi all,

This may or may not be an actual problem, it's just something we ran into on 
our Galaxy instance in the past few days.

The symptom was that when a user clicked the "Edit attributes" button on an 
item in their history, they would get an "Internal server error" message. After 
that their history would completely disappear from the interface. Any attempts 
to reload it with the "Refresh history" button would result in an error. The 
only way to get it back was to restart Galaxy. The error from uwsgi.log is 

After some digging in the database, I found that the "role_id" column on every 
entry in "dataset_permissions" had no value. Additionally, the two users who 
have datasets on the system had no private roles in the "roles" table.

I fixed the issue by creating new private roles for those users, then manually 
setting "role_id" in the "dataset_permissions" table.

Unfortunately my Postgres backups only go back a few days, so I can't tell if 
something happened to those tables somewhere along the line.

We're running the release_17.01 branch plus some customizations, nothing that 
affects those tables though.

Has anyone else seen anything like this?



galaxy.web.framework.decorators ERROR 2017-02-17 10:32:36,574 Uncaught 
exception in exposed API method:
Traceback (most recent call last):
  File "/software/galaxy/app/galaxy/lib/galaxy/web/framework/decorators.py", 
line 295, in decorator
    rval = func( self, trans, *args, **kwargs )
 line 72, in index
    return self.__index_v2( trans, history_id, **kwd )
 line 582, in __index_v2
    user=trans.user, trans=trans, view='detailed', **serialization_params ) )
  File "/software/galaxy/app/galaxy/lib/galaxy/managers/base.py", line 719, in 
    return self.serialize( item, all_keys, **context )
  File "/software/galaxy/app/galaxy/lib/galaxy/managers/hdas.py", line 362, in 
    return super( HDASerializer, self ).serialize( hda, keys, user=user, 
**context )
  File "/software/galaxy/app/galaxy/lib/galaxy/managers/datasets.py", line 534, 
in serialize
    serialized = super( DatasetAssociationSerializer, self ).serialize( 
dataset_assoc, keys, **context )
  File "/software/galaxy/app/galaxy/lib/galaxy/managers/base.py", line 632, in 
    returned[ key ] = self.serializers[ key ]( item, key, **context )
  File "/software/galaxy/app/galaxy/lib/galaxy/managers/datasets.py", line 438, 
in <lambda>
    return lambda i, k, **c: serializer( i.dataset, key or k, **c )
  File "/software/galaxy/app/galaxy/lib/galaxy/managers/datasets.py", line 213, 
in serialize_permissions
    'manage' : [ self.app.security.encode_id( perm.role.id ) for perm in 
management_permissions ],
AttributeError: 'NoneType' object has no attribute 'id'

Rob Lemley
Systems Administrator - CIRC
University of Rochester

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