I dumped the DB structure to sql. When I diff the old version with the newly generated one I see quite some differences. Mostly are related to api or cloud tables.

I also see some diffs regarding table ENGINE which is InnoDB for the new while many tables were MyISAM previously (ie. Lines 40, 403, ... of the diff). I presume innoDB is ok though...

Enclosed both DB structures from old to the newly populated one.

Maybe that is of help.

Alex

Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Bossers, Alex
Verzonden: maandag 12 november 2012 13:37
Aan: galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] Error: change attributes generates error on fresh dist-release

Hi All,

Due to previous DB errors we decided to let galaxy-dist repopulate the database (MySQL). We purged all tables from the DB and when restarting galaxy it repopulates the DB on the fly while doing all migration steps. A nicely running galaxy as the result.

I encountered a strange error which might be linked to this... or not...

When changing the attribute of a dataset I get the error below; We never had this before so my guess is that the DB is not constructed properly.

We are at tip 7986:12fcd068b12e of the dist release.

Any pointer to fix this? There is currently no user-data or histories anymore so I can experiment... before I open it for running publicly again...

Thanks;

Alex

URL: http://galaxy.wur.nl:8080/galaxy/datasets/b4bd1d7d8ca50a82/edit
Module paste.exceptions.errormiddleware:143 in __call__
>>  app_iter = self.application(environ, start_response)
Module paste.debug.prints:98 in __call__
>>  environ, self.app)
Module paste.wsgilib:539 in intercept_output
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__
>>  return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__
>>  body = method( trans, **kwargs )
Module galaxy.webapps.galaxy.controllers.dataset:496 in edit
>>  all_roles = trans.app.security_agent.get_legitimate_roles( trans, data.dataset, 'root' )
Module galaxy.security:192 in get_legitimate_roles
>>  return self.get_all_roles( trans, cntrller )
Module galaxy.security:168 in get_all_roles
>>  return self.sort_by_attr( [ role for role in roles ], 'name' )
Module galaxy.security:137 in sort_by_attr
>>  intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq )
AttributeError: 'NoneType' object has no attribute 'name'