UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped

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UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped

Peter Cock
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 '/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 1706 in _post_configure_properties
File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/interfaces.py',
line 183 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/relationships.py',
line 1616 in do_init
File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/relationships.py',
line 1673 in _process_dependent_arguments
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/relationships.py',
line 1595 in mapper
File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/base.py',
line 426 in class_mapper
UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped


CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT_ENCODING: 'identity'
  HTTP_HOST: 'localhost:9572'
  PATH_INFO: '/'
  REMOTE_ADDR: '127.0.0.1'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '9572'
  SERVER_PROTOCOL: 'HTTP/1.1'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0xa1a4e10>
  is_api_request: False
  paste.cookies: (<SimpleCookie: >, '')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
object at 0xa1a4a90>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
0xa720d50>
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: '6f5c7eaaee5411e4bea1473d5f4e3057'
  wsgi process: 'Multithreaded'
------------------------------------------------------------
Exception in thread Thread-1:
Traceback (most recent call last):
  File "/usr/lib/python2.7/threading.py", line 551, in __bootstrap_inner
    self.run()
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
line 170, in run
    for _ in self.consume(limit=None):  # pragma: no cover
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
line 187, in consume
    with self.consumer_context(**kwargs) as (conn, channel, consumers):
  File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
line 180, in consumer_context
    with self.Consumer() as (connection, channel, consumers):
  File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
line 229, in Consumer
    with self._consume_from(*self.get_consumers(cls, channel)) as c:
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/queue_worker.py",
line 53, in get_consumers
    callbacks=[self.process_task])]
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py",
line 359, in __init__
    self.revive(self.channel)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py",
line 371, in revive
    self.declare()
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py",
line 381, in declare
    queue.declare()
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/entity.py",
line 505, in declare
    self.queue_declare(nowait, passive=False)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/entity.py",
line 531, in queue_declare
    nowait=nowait)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/virtual/__init__.py",
line 446, in queue_declare
    self._new_queue(queue, **kwargs)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/sqlalchemy/__init__.py",
line 80, in _new_queue
    self._get_or_create(queue)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/sqlalchemy/__init__.py",
line 68, in _get_or_create
    obj = self.session.query(self.queue_cls) \
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 1249, in query
    return self._query_cls(entities, self, **kwargs)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 110, in __init__
    self._set_entities(entities)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 120, in _set_entities
    self._set_entity_selectables(self._entities)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 150, in _set_entity_selectables
    ent.setup_entity(*d[entity])
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 3184, in setup_entity
    self._with_polymorphic = ext_info.with_polymorphic_mappers
  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__
    obj.__dict__[self.__name__] = result = self.fget(obj)
  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 1889, in _with_polymorphic_mappers
    configure_mappers()
  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 2681, in configure_mappers
    raise e
InvalidRequestError: One or more mappers failed to initialize - can't
proceed with initialization of other mappers.  Original exception was:
Class 'kombu.transport.sqlalchemy.Message' is not mapped

Error - <class 'sqlalchemy.exc.InvalidRequestError'>: One or more
mappers failed to initialize - can't proceed with initialization of
other mappers.  Original exception was: 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__
  obj.__dict__[self.__name__] = result = self.fget(obj)
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
  configure_mappers()
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 2681 in configure_mappers
  raise e
InvalidRequestError: One or more mappers failed to initialize - can't
proceed with initialization of other mappers.  Original exception was:
Class 'kombu.transport.sqlalchemy.Message' is not mapped


CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT_ENCODING: 'identity'
  HTTP_HOST: 'localhost:9572'
  PATH_INFO: '/'
  REMOTE_ADDR: '127.0.0.1'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '9572'
  SERVER_PROTOCOL: 'HTTP/1.1'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0xa1a4e10>
  is_api_request: False
  paste.cookies: (<SimpleCookie: >, '')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
object at 0xa1a4a90>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
0xa720d50>
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: '6f72e654ee5411e490fc473d5f4e3057'
  wsgi process: 'Multithreaded'
------------------------------------------------------------
Error - <class 'sqlalchemy.exc.InvalidRequestError'>: One or more
mappers failed to initialize - can't proceed with initialization of
other mappers.  Original exception was: 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__
  obj.__dict__[self.__name__] = result = self.fget(obj)
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
  configure_mappers()
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 2681 in configure_mappers
  raise e
InvalidRequestError: One or more mappers failed to initialize - can't
proceed with initialization of other mappers.  Original exception was:
Class 'kombu.transport.sqlalchemy.Message' is not mapped


CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT_ENCODING: 'identity'
  HTTP_HOST: 'localhost:9572'
  PATH_INFO: '/'
  REMOTE_ADDR: '127.0.0.1'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '9572'
  SERVER_PROTOCOL: 'HTTP/1.1'


(etc, repeats this a lot)
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Re: UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped

Dannon Baker-2
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 <[hidden email]> 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 '/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 '/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 1706 in _post_configure_properties
File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/interfaces.py',
line 183 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/relationships.py',
line 1616 in do_init
File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/relationships.py',
line 1673 in _process_dependent_arguments
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/relationships.py',
line 1595 in mapper
File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/base.py',
line 426 in class_mapper
UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped


CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT_ENCODING: 'identity'
  HTTP_HOST: 'localhost:9572'
  PATH_INFO: '/'
  REMOTE_ADDR: '127.0.0.1'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '9572'
  SERVER_PROTOCOL: 'HTTP/1.1'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0xa1a4e10>
  is_api_request: False
  paste.cookies: (<SimpleCookie: >, '')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
object at 0xa1a4a90>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
0xa720d50>
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: '6f5c7eaaee5411e4bea1473d5f4e3057'
  wsgi process: 'Multithreaded'
------------------------------------------------------------
Exception in thread Thread-1:
Traceback (most recent call last):
  File "/usr/lib/python2.7/threading.py", line 551, in __bootstrap_inner
    self.run()
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
line 170, in run
    for _ in self.consume(limit=None):  # pragma: no cover
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
line 187, in consume
    with self.consumer_context(**kwargs) as (conn, channel, consumers):
  File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
line 180, in consumer_context
    with self.Consumer() as (connection, channel, consumers):
  File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
line 229, in Consumer
    with self._consume_from(*self.get_consumers(cls, channel)) as c:
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/queue_worker.py",
line 53, in get_consumers
    callbacks=[self.process_task])]
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py",
line 359, in __init__
    self.revive(self.channel)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py",
line 371, in revive
    self.declare()
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py",
line 381, in declare
    queue.declare()
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/entity.py",
line 505, in declare
    self.queue_declare(nowait, passive=False)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/entity.py",
line 531, in queue_declare
    nowait=nowait)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/virtual/__init__.py",
line 446, in queue_declare
    self._new_queue(queue, **kwargs)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/sqlalchemy/__init__.py",
line 80, in _new_queue
    self._get_or_create(queue)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/sqlalchemy/__init__.py",
line 68, in _get_or_create
    obj = self.session.query(self.queue_cls) \
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 1249, in query
    return self._query_cls(entities, self, **kwargs)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 110, in __init__
    self._set_entities(entities)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 120, in _set_entities
    self._set_entity_selectables(self._entities)
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 150, in _set_entity_selectables
    ent.setup_entity(*d[entity])
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 3184, in setup_entity
    self._with_polymorphic = ext_info.with_polymorphic_mappers
  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__
    obj.__dict__[self.__name__] = result = self.fget(obj)
  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 1889, in _with_polymorphic_mappers
    configure_mappers()
  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 2681, in configure_mappers
    raise e
InvalidRequestError: One or more mappers failed to initialize - can't
proceed with initialization of other mappers.  Original exception was:
Class 'kombu.transport.sqlalchemy.Message' is not mapped

Error - <class 'sqlalchemy.exc.InvalidRequestError'>: One or more
mappers failed to initialize - can't proceed with initialization of
other mappers.  Original exception was: 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__
  obj.__dict__[self.__name__] = result = self.fget(obj)
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
  configure_mappers()
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 2681 in configure_mappers
  raise e
InvalidRequestError: One or more mappers failed to initialize - can't
proceed with initialization of other mappers.  Original exception was:
Class 'kombu.transport.sqlalchemy.Message' is not mapped


CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT_ENCODING: 'identity'
  HTTP_HOST: 'localhost:9572'
  PATH_INFO: '/'
  REMOTE_ADDR: '127.0.0.1'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '9572'
  SERVER_PROTOCOL: 'HTTP/1.1'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0xa1a4e10>
  is_api_request: False
  paste.cookies: (<SimpleCookie: >, '')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
object at 0xa1a4a90>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
0xa720d50>
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: '6f72e654ee5411e490fc473d5f4e3057'
  wsgi process: 'Multithreaded'
------------------------------------------------------------
Error - <class 'sqlalchemy.exc.InvalidRequestError'>: One or more
mappers failed to initialize - can't proceed with initialization of
other mappers.  Original exception was: 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__
  obj.__dict__[self.__name__] = result = self.fget(obj)
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
  configure_mappers()
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 2681 in configure_mappers
  raise e
InvalidRequestError: One or more mappers failed to initialize - can't
proceed with initialization of other mappers.  Original exception was:
Class 'kombu.transport.sqlalchemy.Message' is not mapped


CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT_ENCODING: 'identity'
  HTTP_HOST: 'localhost:9572'
  PATH_INFO: '/'
  REMOTE_ADDR: '127.0.0.1'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '9572'
  SERVER_PROTOCOL: 'HTTP/1.1'


(etc, repeats this a lot)
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Re: UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped

Peter Cock
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 <[hidden email]> 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 <[hidden email]>
> 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
>> '/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
>> '/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 1706 in _post_configure_properties
>> File
>> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/interfaces.py',
>> line 183 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/relationships.py',
>> line 1616 in do_init
>> File
>> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/relationships.py',
>> line 1673 in _process_dependent_arguments
>> 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/relationships.py',
>> line 1595 in mapper
>> File
>> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/base.py',
>> line 426 in class_mapper
>> UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not
>> mapped
>>
>>
>> CGI Variables
>> -------------
>>   CONTENT_LENGTH: '0'
>>   HTTP_ACCEPT_ENCODING: 'identity'
>>   HTTP_HOST: 'localhost:9572'
>>   PATH_INFO: '/'
>>   REMOTE_ADDR: '127.0.0.1'
>>   REQUEST_METHOD: 'GET'
>>   SERVER_NAME: '127.0.0.1'
>>   SERVER_PORT: '9572'
>>   SERVER_PROTOCOL: 'HTTP/1.1'
>>
>>
>> WSGI Variables
>> --------------
>>   application: <paste.recursive.RecursiveMiddleware object at 0xa1a4e10>
>>   is_api_request: False
>>   paste.cookies: (<SimpleCookie: >, '')
>>   paste.expected_exceptions: [<class
>> 'paste.httpexceptions.HTTPException'>]
>>   paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
>> object at 0xa1a4a90>
>>   paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
>> 0xa720d50>
>>   paste.recursive.forward: <paste.recursive.Forwarder from />
>>   paste.recursive.include: <paste.recursive.Includer from />
>>   paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from
>> />
>>   paste.recursive.script_name: ''
>>   paste.throw_errors: True
>>   request_id: '6f5c7eaaee5411e4bea1473d5f4e3057'
>>   wsgi process: 'Multithreaded'
>> ------------------------------------------------------------
>> Exception in thread Thread-1:
>> Traceback (most recent call last):
>>   File "/usr/lib/python2.7/threading.py", line 551, in __bootstrap_inner
>>     self.run()
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
>> line 170, in run
>>     for _ in self.consume(limit=None):  # pragma: no cover
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
>> line 187, in consume
>>     with self.consumer_context(**kwargs) as (conn, channel, consumers):
>>   File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
>>     return self.gen.next()
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
>> line 180, in consumer_context
>>     with self.Consumer() as (connection, channel, consumers):
>>   File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
>>     return self.gen.next()
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
>> line 229, in Consumer
>>     with self._consume_from(*self.get_consumers(cls, channel)) as c:
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/queue_worker.py",
>> line 53, in get_consumers
>>     callbacks=[self.process_task])]
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py",
>> line 359, in __init__
>>     self.revive(self.channel)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py",
>> line 371, in revive
>>     self.declare()
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py",
>> line 381, in declare
>>     queue.declare()
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/entity.py",
>> line 505, in declare
>>     self.queue_declare(nowait, passive=False)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/entity.py",
>> line 531, in queue_declare
>>     nowait=nowait)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/virtual/__init__.py",
>> line 446, in queue_declare
>>     self._new_queue(queue, **kwargs)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/sqlalchemy/__init__.py",
>> line 80, in _new_queue
>>     self._get_or_create(queue)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/sqlalchemy/__init__.py",
>> line 68, in _get_or_create
>>     obj = self.session.query(self.queue_cls) \
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
>> line 1249, in query
>>     return self._query_cls(entities, self, **kwargs)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>> line 110, in __init__
>>     self._set_entities(entities)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>> line 120, in _set_entities
>>     self._set_entity_selectables(self._entities)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>> line 150, in _set_entity_selectables
>>     ent.setup_entity(*d[entity])
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>> line 3184, in setup_entity
>>     self._with_polymorphic = ext_info.with_polymorphic_mappers
>>   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__
>>     obj.__dict__[self.__name__] = result = self.fget(obj)
>>   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 1889, in _with_polymorphic_mappers
>>     configure_mappers()
>>   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 2681, in configure_mappers
>>     raise e
>> InvalidRequestError: One or more mappers failed to initialize - can't
>> proceed with initialization of other mappers.  Original exception was:
>> Class 'kombu.transport.sqlalchemy.Message' is not mapped
>>
>> Error - <class 'sqlalchemy.exc.InvalidRequestError'>: One or more
>> mappers failed to initialize - can't proceed with initialization of
>> other mappers.  Original exception was: 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__
>>   obj.__dict__[self.__name__] = result = self.fget(obj)
>> 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
>>   configure_mappers()
>> 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 2681 in configure_mappers
>>   raise e
>> InvalidRequestError: One or more mappers failed to initialize - can't
>> proceed with initialization of other mappers.  Original exception was:
>> Class 'kombu.transport.sqlalchemy.Message' is not mapped
>>
>>
>> CGI Variables
>> -------------
>>   CONTENT_LENGTH: '0'
>>   HTTP_ACCEPT_ENCODING: 'identity'
>>   HTTP_HOST: 'localhost:9572'
>>   PATH_INFO: '/'
>>   REMOTE_ADDR: '127.0.0.1'
>>   REQUEST_METHOD: 'GET'
>>   SERVER_NAME: '127.0.0.1'
>>   SERVER_PORT: '9572'
>>   SERVER_PROTOCOL: 'HTTP/1.1'
>>
>>
>> WSGI Variables
>> --------------
>>   application: <paste.recursive.RecursiveMiddleware object at 0xa1a4e10>
>>   is_api_request: False
>>   paste.cookies: (<SimpleCookie: >, '')
>>   paste.expected_exceptions: [<class
>> 'paste.httpexceptions.HTTPException'>]
>>   paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
>> object at 0xa1a4a90>
>>   paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
>> 0xa720d50>
>>   paste.recursive.forward: <paste.recursive.Forwarder from />
>>   paste.recursive.include: <paste.recursive.Includer from />
>>   paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from
>> />
>>   paste.recursive.script_name: ''
>>   paste.throw_errors: True
>>   request_id: '6f72e654ee5411e490fc473d5f4e3057'
>>   wsgi process: 'Multithreaded'
>> ------------------------------------------------------------
>> Error - <class 'sqlalchemy.exc.InvalidRequestError'>: One or more
>> mappers failed to initialize - can't proceed with initialization of
>> other mappers.  Original exception was: 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__
>>   obj.__dict__[self.__name__] = result = self.fget(obj)
>> 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
>>   configure_mappers()
>> 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 2681 in configure_mappers
>>   raise e
>> InvalidRequestError: One or more mappers failed to initialize - can't
>> proceed with initialization of other mappers.  Original exception was:
>> Class 'kombu.transport.sqlalchemy.Message' is not mapped
>>
>>
>> CGI Variables
>> -------------
>>   CONTENT_LENGTH: '0'
>>   HTTP_ACCEPT_ENCODING: 'identity'
>>   HTTP_HOST: 'localhost:9572'
>>   PATH_INFO: '/'
>>   REMOTE_ADDR: '127.0.0.1'
>>   REQUEST_METHOD: 'GET'
>>   SERVER_NAME: '127.0.0.1'
>>   SERVER_PORT: '9572'
>>   SERVER_PROTOCOL: 'HTTP/1.1'
>>
>>
>> (etc, repeats this a lot)
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
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Re: UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped

Dannon Baker-2
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]>
> 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
>> '/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
>> '/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 1706 in _post_configure_properties
>> File
>> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/interfaces.py',
>> line 183 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/relationships.py',
>> line 1616 in do_init
>> File
>> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/relationships.py',
>> line 1673 in _process_dependent_arguments
>> 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/relationships.py',
>> line 1595 in mapper
>> File
>> '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/base.py',
>> line 426 in class_mapper
>> UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not
>> mapped
>>
>>
>> CGI Variables
>> -------------
>>   CONTENT_LENGTH: '0'
>>   HTTP_ACCEPT_ENCODING: 'identity'
>>   HTTP_HOST: 'localhost:9572'
>>   PATH_INFO: '/'
>>   REMOTE_ADDR: '127.0.0.1'
>>   REQUEST_METHOD: 'GET'
>>   SERVER_NAME: '127.0.0.1'
>>   SERVER_PORT: '9572'
>>   SERVER_PROTOCOL: 'HTTP/1.1'
>>
>>
>> WSGI Variables
>> --------------
>>   application: <paste.recursive.RecursiveMiddleware object at 0xa1a4e10>
>>   is_api_request: False
>>   paste.cookies: (<SimpleCookie: >, '')
>>   paste.expected_exceptions: [<class
>> 'paste.httpexceptions.HTTPException'>]
>>   paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
>> object at 0xa1a4a90>
>>   paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
>> 0xa720d50>
>>   paste.recursive.forward: <paste.recursive.Forwarder from />
>>   paste.recursive.include: <paste.recursive.Includer from />
>>   paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from
>> />
>>   paste.recursive.script_name: ''
>>   paste.throw_errors: True
>>   request_id: '6f5c7eaaee5411e4bea1473d5f4e3057'
>>   wsgi process: 'Multithreaded'
>> ------------------------------------------------------------
>> Exception in thread Thread-1:
>> Traceback (most recent call last):
>>   File "/usr/lib/python2.7/threading.py", line 551, in __bootstrap_inner
>>     self.run()
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
>> line 170, in run
>>     for _ in self.consume(limit=None):  # pragma: no cover
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
>> line 187, in consume
>>     with self.consumer_context(**kwargs) as (conn, channel, consumers):
>>   File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
>>     return self.gen.next()
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
>> line 180, in consumer_context
>>     with self.Consumer() as (connection, channel, consumers):
>>   File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
>>     return self.gen.next()
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/mixins.py",
>> line 229, in Consumer
>>     with self._consume_from(*self.get_consumers(cls, channel)) as c:
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/queue_worker.py",
>> line 53, in get_consumers
>>     callbacks=[self.process_task])]
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py",
>> line 359, in __init__
>>     self.revive(self.channel)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py",
>> line 371, in revive
>>     self.declare()
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/messaging.py",
>> line 381, in declare
>>     queue.declare()
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/entity.py",
>> line 505, in declare
>>     self.queue_declare(nowait, passive=False)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/entity.py",
>> line 531, in queue_declare
>>     nowait=nowait)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/virtual/__init__.py",
>> line 446, in queue_declare
>>     self._new_queue(queue, **kwargs)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/sqlalchemy/__init__.py",
>> line 80, in _new_queue
>>     self._get_or_create(queue)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/transport/sqlalchemy/__init__.py",
>> line 68, in _get_or_create
>>     obj = self.session.query(self.queue_cls) \
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
>> line 1249, in query
>>     return self._query_cls(entities, self, **kwargs)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>> line 110, in __init__
>>     self._set_entities(entities)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>> line 120, in _set_entities
>>     self._set_entity_selectables(self._entities)
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>> line 150, in _set_entity_selectables
>>     ent.setup_entity(*d[entity])
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>> line 3184, in setup_entity
>>     self._with_polymorphic = ext_info.with_polymorphic_mappers
>>   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__
>>     obj.__dict__[self.__name__] = result = self.fget(obj)
>>   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 1889, in _with_polymorphic_mappers
>>     configure_mappers()
>>   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 2681, in configure_mappers
>>     raise e
>> InvalidRequestError: One or more mappers failed to initialize - can't
>> proceed with initialization of other mappers.  Original exception was:
>> Class 'kombu.transport.sqlalchemy.Message' is not mapped
>>
>> Error - <class 'sqlalchemy.exc.InvalidRequestError'>: One or more
>> mappers failed to initialize - can't proceed with initialization of
>> other mappers.  Original exception was: 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__
>>   obj.__dict__[self.__name__] = result = self.fget(obj)
>> 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
>>   configure_mappers()
>> 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 2681 in configure_mappers
>>   raise e
>> InvalidRequestError: One or more mappers failed to initialize - can't
>> proceed with initialization of other mappers.  Original exception was:
>> Class 'kombu.transport.sqlalchemy.Message' is not mapped
>>
>>
>> CGI Variables
>> -------------
>>   CONTENT_LENGTH: '0'
>>   HTTP_ACCEPT_ENCODING: 'identity'
>>   HTTP_HOST: 'localhost:9572'
>>   PATH_INFO: '/'
>>   REMOTE_ADDR: '127.0.0.1'
>>   REQUEST_METHOD: 'GET'
>>   SERVER_NAME: '127.0.0.1'
>>   SERVER_PORT: '9572'
>>   SERVER_PROTOCOL: 'HTTP/1.1'
>>
>>
>> WSGI Variables
>> --------------
>>   application: <paste.recursive.RecursiveMiddleware object at 0xa1a4e10>
>>   is_api_request: False
>>   paste.cookies: (<SimpleCookie: >, '')
>>   paste.expected_exceptions: [<class
>> 'paste.httpexceptions.HTTPException'>]
>>   paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
>> object at 0xa1a4a90>
>>   paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
>> 0xa720d50>
>>   paste.recursive.forward: <paste.recursive.Forwarder from />
>>   paste.recursive.include: <paste.recursive.Includer from />
>>   paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from
>> />
>>   paste.recursive.script_name: ''
>>   paste.throw_errors: True
>>   request_id: '6f72e654ee5411e490fc473d5f4e3057'
>>   wsgi process: 'Multithreaded'
>> ------------------------------------------------------------
>> Error - <class 'sqlalchemy.exc.InvalidRequestError'>: One or more
>> mappers failed to initialize - can't proceed with initialization of
>> other mappers.  Original exception was: 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__
>>   obj.__dict__[self.__name__] = result = self.fget(obj)
>> 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
>>   configure_mappers()
>> 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 2681 in configure_mappers
>>   raise e
>> InvalidRequestError: One or more mappers failed to initialize - can't
>> proceed with initialization of other mappers.  Original exception was:
>> Class 'kombu.transport.sqlalchemy.Message' is not mapped
>>
>>
>> CGI Variables
>> -------------
>>   CONTENT_LENGTH: '0'
>>   HTTP_ACCEPT_ENCODING: 'identity'
>>   HTTP_HOST: 'localhost:9572'
>>   PATH_INFO: '/'
>>   REMOTE_ADDR: '127.0.0.1'
>>   REQUEST_METHOD: 'GET'
>>   SERVER_NAME: '127.0.0.1'
>>   SERVER_PORT: '9572'
>>   SERVER_PROTOCOL: 'HTTP/1.1'
>>
>>
>> (etc, repeats this a lot)
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
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___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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