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__
<http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> environ, self.app) Module paste.wsgilib:539 in intercept_output <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.dataset:496 in edit <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> all_roles = trans.app.security_agent.get_legitimate_roles( trans, data.dataset, 'root' ) Module galaxy.security:192 in get_legitimate_roles <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> return self.get_all_roles( trans, cntrller ) Module galaxy.security:168 in get_all_roles <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> return self.sort_by_attr( [ role for role in roles ], 'name' ) Module galaxy.security:137 in sort_by_attr <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq ) AttributeError: 'NoneType' object has no attribute 'name'
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__
<http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> environ, self.app) Module paste.wsgilib:539 in intercept_output <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.dataset:496 in edit <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> all_roles = trans.app.security_agent.get_legitimate_roles( trans, data.dataset, 'root' ) Module galaxy.security:192 in get_legitimate_roles <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> return self.get_all_roles( trans, cntrller ) Module galaxy.security:168 in get_all_roles <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> return self.sort_by_attr( [ role for role in roles ], 'name' ) Module galaxy.security:137 in sort_by_attr <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq ) AttributeError: 'NoneType' object has no attribute 'name'
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Bossers, Alex