Re: [galaxy-dev] UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped
No need, unless it becomes particularly worse after the next attempt to fix it :) On Wed, Apr 29, 2015 at 8:30 AM Peter Cock wrote: > Thanks Dannon, > > Do you want me to send you any future TravisCI cases of this failure? > > Peter > > On Wed, Apr 29, 2015 at 1:14 PM, Dannon Baker > wrote: > > Hi Peter, > > > > No need to rerun for my benefit -- it's definitely a race condition that > I > > know about and think I have a fairly good understanding of now. We've > tried > > a few different ideas for fixing it, (obviously none of which have > worked, > > yet), and I've been poking at a new fix this week. > > > > -Dannon > > > > On Wed, Apr 29, 2015 at 6:53 AM Peter Cock > > wrote: > >> > >> Hi all, > >> > >> I think this is the second time I've have the following error on > >> TravisCI (last time I reran a similar failure, and it worked). I've > >> not yet re-run the test so that you can see the full error log: > >> > >> UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not > >> mapped > >> > >> https://travis-ci.org/peterjc/galaxy_blast/builds/60510547 > >> > >> My hunch is this is a race condition, perhaps with the SQLite database? > >> Should I ask TravisCI to re-run the test and confirm this? > >> > >> Peter > >> > >> -- > >> > >> Except from the full log, > >> > >> ... ... > >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,952 Enabling > >> 'httpexceptions' middleware > >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,957 Enabling > >> 'recursive' middleware > >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,000 Enabling > >> 'error' middleware > >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,001 Enabling > >> 'x-forwarded-host' middleware > >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,002 Enabling > >> 'Request ID' middleware > >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,046 added > >> url, path to static middleware: /plugins/visualizations/charts/static, > >> ./config/plugins/visualizations/charts/static > >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added > >> url, path to static middleware: > >> /plugins/visualizations/graphview/static, > >> ./config/plugins/visualizations/graphview/static > >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added > >> url, path to static middleware: > >> /plugins/visualizations/scatterplot/static, > >> ./config/plugins/visualizations/scatterplot/static > >> galaxy.queue_worker INFO 2015-04-29 09:45:14,057 Initalizing Galaxy > >> Queue Worker on > >> sqlalchemy+sqlite:tmp/tmpGyX8vL/tmpTRGC3O/database/universe.sqlite > >> functional_tests.py DEBUG 2015-04-29 09:45:14,089 Attempting to serve > >> app on randomly chosen port: 9572 > >> Error - : Class > >> 'kombu.transport.sqlalchemy.Message' is not mapped > >> URL: http://localhost:9572/ > >> File > >> > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', > >> line 149 in __call__ > >> app_iter = self.application(environ, sr_checker) > >> File > >> > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', > >> line 84 in __call__ > >> return self.application(environ, start_response) > >> File > >> > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', > >> line 633 in __call__ > >> return self.application(environ, start_response) > >> File > >> > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', > >> line 133 in __call__ > >> return self.handle_request( environ, start_response ) > >> File > >> > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', > >> line 160 in handle_request > >> trans = self.transaction_factory( environ ) > >> File > >> > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', > >> line 73 in > >> self.set_transaction_factory( lambda e: self.transaction_chooser( e, > >> galaxy_app, session_cookie ) ) > >> File > >> > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', > >> line 104 in transaction_chooser > >> return GalaxyWebTransaction( environ, galaxy_app, self, > session_cookie ) > >> File > >> > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', > >> line 205 in __init__ > >> self._ensure_valid_session( session_cookie ) > >> File > >> > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', > >> line 430 in _ensure_valid_session > >> galaxy_session = self.__create_new_session( prev_galaxy_session, > >> user_for_new_session ) > >> File > >> > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', > >> line 510 in __create_new_session > >> referer=self.request.headers.get( 'Referer', None ) ) > >> File '', line 2 in __init__ > >> File > >> > '/home/travis
Re: [galaxy-dev] UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped
Thanks Dannon, Do you want me to send you any future TravisCI cases of this failure? Peter On Wed, Apr 29, 2015 at 1:14 PM, Dannon Baker wrote: > Hi Peter, > > No need to rerun for my benefit -- it's definitely a race condition that I > know about and think I have a fairly good understanding of now. We've tried > a few different ideas for fixing it, (obviously none of which have worked, > yet), and I've been poking at a new fix this week. > > -Dannon > > On Wed, Apr 29, 2015 at 6:53 AM Peter Cock > wrote: >> >> Hi all, >> >> I think this is the second time I've have the following error on >> TravisCI (last time I reran a similar failure, and it worked). I've >> not yet re-run the test so that you can see the full error log: >> >> UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not >> mapped >> >> https://travis-ci.org/peterjc/galaxy_blast/builds/60510547 >> >> My hunch is this is a race condition, perhaps with the SQLite database? >> Should I ask TravisCI to re-run the test and confirm this? >> >> Peter >> >> -- >> >> Except from the full log, >> >> ... ... >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,952 Enabling >> 'httpexceptions' middleware >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,957 Enabling >> 'recursive' middleware >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,000 Enabling >> 'error' middleware >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,001 Enabling >> 'x-forwarded-host' middleware >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,002 Enabling >> 'Request ID' middleware >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,046 added >> url, path to static middleware: /plugins/visualizations/charts/static, >> ./config/plugins/visualizations/charts/static >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added >> url, path to static middleware: >> /plugins/visualizations/graphview/static, >> ./config/plugins/visualizations/graphview/static >> galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added >> url, path to static middleware: >> /plugins/visualizations/scatterplot/static, >> ./config/plugins/visualizations/scatterplot/static >> galaxy.queue_worker INFO 2015-04-29 09:45:14,057 Initalizing Galaxy >> Queue Worker on >> sqlalchemy+sqlite:tmp/tmpGyX8vL/tmpTRGC3O/database/universe.sqlite >> functional_tests.py DEBUG 2015-04-29 09:45:14,089 Attempting to serve >> app on randomly chosen port: 9572 >> Error - : Class >> 'kombu.transport.sqlalchemy.Message' is not mapped >> URL: http://localhost:9572/ >> File >> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', >> line 149 in __call__ >> app_iter = self.application(environ, sr_checker) >> File >> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', >> line 84 in __call__ >> return self.application(environ, start_response) >> File >> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', >> line 633 in __call__ >> return self.application(environ, start_response) >> File >> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', >> line 133 in __call__ >> return self.handle_request( environ, start_response ) >> File >> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', >> line 160 in handle_request >> trans = self.transaction_factory( environ ) >> File >> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', >> line 73 in >> self.set_transaction_factory( lambda e: self.transaction_chooser( e, >> galaxy_app, session_cookie ) ) >> File >> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', >> line 104 in transaction_chooser >> return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) >> File >> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', >> line 205 in __init__ >> self._ensure_valid_session( session_cookie ) >> File >> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', >> line 430 in _ensure_valid_session >> galaxy_session = self.__create_new_session( prev_galaxy_session, >> user_for_new_session ) >> File >> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', >> line 510 in __create_new_session >> referer=self.request.headers.get( 'Referer', None ) ) >> File '', line 2 in __init__ >> File >> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', >> line 347 in _new_state_if_none >> File >> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py', >> line 747 in __get__ >> File >> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/e
Re: [galaxy-dev] UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped
Hi Peter, No need to rerun for my benefit -- it's definitely a race condition that I know about and think I have a fairly good understanding of now. We've tried a few different ideas for fixing it, (obviously none of which have worked, yet), and I've been poking at a new fix this week. -Dannon On Wed, Apr 29, 2015 at 6:53 AM Peter Cock wrote: > Hi all, > > I think this is the second time I've have the following error on > TravisCI (last time I reran a similar failure, and it worked). I've > not yet re-run the test so that you can see the full error log: > > UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not > mapped > > https://travis-ci.org/peterjc/galaxy_blast/builds/60510547 > > My hunch is this is a race condition, perhaps with the SQLite database? > Should I ask TravisCI to re-run the test and confirm this? > > Peter > > -- > > Except from the full log, > > ... ... > galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,952 Enabling > 'httpexceptions' middleware > galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,957 Enabling > 'recursive' middleware > galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,000 Enabling > 'error' middleware > galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,001 Enabling > 'x-forwarded-host' middleware > galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,002 Enabling > 'Request ID' middleware > galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,046 added > url, path to static middleware: /plugins/visualizations/charts/static, > ./config/plugins/visualizations/charts/static > galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added > url, path to static middleware: > /plugins/visualizations/graphview/static, > ./config/plugins/visualizations/graphview/static > galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added > url, path to static middleware: > /plugins/visualizations/scatterplot/static, > ./config/plugins/visualizations/scatterplot/static > galaxy.queue_worker INFO 2015-04-29 09:45:14,057 Initalizing Galaxy > Queue Worker on > sqlalchemy+sqlite:tmp/tmpGyX8vL/tmpTRGC3O/database/universe.sqlite > functional_tests.py DEBUG 2015-04-29 09:45:14,089 Attempting to serve > app on randomly chosen port: 9572 > Error - : Class > 'kombu.transport.sqlalchemy.Message' is not mapped > URL: http://localhost:9572/ > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', > line 149 in __call__ > app_iter = self.application(environ, sr_checker) > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', > line 84 in __call__ > return self.application(environ, start_response) > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', > line 633 in __call__ > return self.application(environ, start_response) > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', > line 133 in __call__ > return self.handle_request( environ, start_response ) > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', > line 160 in handle_request > trans = self.transaction_factory( environ ) > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', > line 73 in > self.set_transaction_factory( lambda e: self.transaction_chooser( e, > galaxy_app, session_cookie ) ) > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', > line 104 in transaction_chooser > return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', > line 205 in __init__ > self._ensure_valid_session( session_cookie ) > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', > line 430 in _ensure_valid_session > galaxy_session = self.__create_new_session( prev_galaxy_session, > user_for_new_session ) > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', > line 510 in __create_new_session > referer=self.request.headers.get( 'Referer', None ) ) > File '', line 2 in __init__ > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', > line 347 in _new_state_if_none > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py', > line 747 in __get__ > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', > line 177 in _state_constructor > File > '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/event/attr.py', > line 258 in
