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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