[galaxy-dev] UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped
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, ... snip ... 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 'sqlalchemy.orm.exc.UnmappedClassError': 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 lambda 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 'string', 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 __call__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2788 in _event_on_first_init File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2684 in configure_mappers File
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 p.j.a.c...@googlemail.com 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 dannon.ba...@gmail.com 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 p.j.a.c...@googlemail.com 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, ... snip ... 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 'sqlalchemy.orm.exc.UnmappedClassError': 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 lambda 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 'string', 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
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 p.j.a.c...@googlemail.com 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, ... snip ... 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 'sqlalchemy.orm.exc.UnmappedClassError': 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 lambda 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 'string', 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 __call__ File
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 dannon.ba...@gmail.com 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 p.j.a.c...@googlemail.com 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, ... snip ... 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 'sqlalchemy.orm.exc.UnmappedClassError': 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 lambda 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 'string', 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
