Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run the tool tests individually, they succeed. So I looked into why they fail when running them in batch, and it turns out to be a database lock. I'm using the default sqllite database that run_tests.sh creates. Does this need to be tuned somehow?
galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched Error - <class 'sqlalchemy.exc.OperationalError'>: (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) URL: http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746... File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 159 in handle_request trans = self.transaction_factory( environ ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 71 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 102 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 194 in __init__ self.error_message = self._authenticate_api( session_cookie ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 283 in _authenticate_api provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( self.app.model.APIKeys.table.c.key == api_key ).one() File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184 in one File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227 in __iter__ File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242 in _execute_and_instances File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 in execute File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584 in _execute_clauseelement File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line 331 in do_execute OperationalError: (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',)
Hi Ryan, there is no know fix for this, apart from moving to PostgreSQL.
Cheers, Nicola
Il 12.06.2015 16:43 Ryan G ha scritto:
Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run the tool tests individually, they succeed. So I looked into why they fail when running them in batch, and it turns out to be a database lock. I'm using the default sqllite database that run_tests.sh creates. Does this need to be tuned somehow?
galaxy.jobs.handler INFO 2015-06-12
10:28:35,854 (14) Job dispatched
Error - : (OperationalError) database
is locked u'SELECT api_keys.id [1] AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key nFROM api_keys nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',)
URL:
http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746... [2]
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
app_iter = self.application(environ,
sr_checker)
File
'/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__
return self.application(environ,
start_response)
File
'/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__
return self.application(environ,
start_response)
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ,
start_response )
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 159 in handle_request
trans = self.transaction_factory( environ
)
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 71 in
self.set_transaction_factory( lambda e:
self.transaction_chooser( e, galaxy_app, session_cookie ) )
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 102 in transaction_chooser
return GalaxyWebTransaction( environ,
galaxy_app, self, session_cookie )
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 194 in __init__
self.error_message = self._authenticate_api(
session_cookie )
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 283 in _authenticate_api
provided_key = self.sa_session.query(
self.app.model.APIKeys ).filter( self.app.model.APIKeys.table.c.key == api_key ).one()
File
'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184 in one
File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line
2227 in __iter__
File
'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242 in _execute_and_instances
File
'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 in execute
File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py',
line 1584 in _execute_clauseelement
File
'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 in _execute_context
File
'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 in _execute_context
File
'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line 331 in do_execute
OperationalError: (OperationalError) database is locked
u'SELECT api_keys.id [3] AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key nFROM api_keys nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',)
Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/
Is there a known cause for this?
On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo nsoranzo@tiscali.it wrote:
Hi Ryan, there is no know fix for this, apart from moving to PostgreSQL.
Cheers, Nicola
Il 12.06.2015 16:43 Ryan G ha scritto:
Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run the tool tests individually, they succeed. So I looked into why they fail when running them in batch, and it turns out to be a database lock. I'm using the default sqllite database that run_tests.sh creates. Does this need to be tuned somehow?
galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched Error - : (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) URL: http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746... File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 159 in handle_request trans = self.transaction_factory( environ ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 71 in self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 102 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 194 in __init__ self.error_message = self._authenticate_api( session_cookie ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 283 in _authenticate_api provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( self.app.model.APIKeys.table.c.key == api_key ).one() File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184 in one File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227 in __iter__ File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242 in _execute_and_instances File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 in execute File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584 in _execute_clauseelement File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line 331 in do_execute OperationalError: (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',)
Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/
Not exactly - I feel like sqlite should be able to do the kinds of things Galaxy does without this occurring - it should just be inefficient. We are probably doing something across multiple threads that we should not be - presumably related to job handling. After a recent sqlalchemy upgrade - there is now a new error message in the logs that should help track down the problem:
sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception during reset or similar Traceback (most recent call last): File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 571, in _finalize_fairy fairy._reset(pool) File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 705, in _reset pool._dialect.do_rollback(self) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 412, in do_rollback dbapi_connection.rollback() ProgrammingError: SQLite objects created in a thread can only be used in that same thread.The object was created in thread id 140442561648384 and this is thread id 140442989479680
At any rate - we recommend using postgres in production for a reason - these sqlite errors are pretty common.
-John
On Fri, Jun 12, 2015 at 11:15 AM, Ryan G ngsbioinformatics@gmail.com wrote:
Is there a known cause for this?
On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo nsoranzo@tiscali.it wrote:
Hi Ryan, there is no know fix for this, apart from moving to PostgreSQL.
Cheers, Nicola
Il 12.06.2015 16:43 Ryan G ha scritto:
Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run the tool tests individually, they succeed. So I looked into why they fail when running them in batch, and it turns out to be a database lock. I'm using the default sqllite database that run_tests.sh creates. Does this need to be tuned somehow?
galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched Error - : (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) URL: http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746... File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 159 in handle_request trans = self.transaction_factory( environ ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 71 in self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 102 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 194 in __init__ self.error_message = self._authenticate_api( session_cookie ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 283 in _authenticate_api provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( self.app.model.APIKeys.table.c.key == api_key ).one() File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184 in one File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227 in __iter__ File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242 in _execute_and_instances File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 in execute File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584 in _execute_clauseelement File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line 331 in do_execute OperationalError: (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',)
Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/
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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I am using postgres in production but want to validate my staging instance before pushing it into production. I do this with the functional tests. I guess I'll have to set up a postgres database for the staging instance as well.
On Mon, Jun 15, 2015 at 10:32 AM, John Chilton jmchilton@gmail.com wrote:
Not exactly - I feel like sqlite should be able to do the kinds of things Galaxy does without this occurring - it should just be inefficient. We are probably doing something across multiple threads that we should not be - presumably related to job handling. After a recent sqlalchemy upgrade - there is now a new error message in the logs that should help track down the problem:
sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception during reset or similar Traceback (most recent call last): File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 571, in _finalize_fairy fairy._reset(pool) File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 705, in _reset pool._dialect.do_rollback(self) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 412, in do_rollback dbapi_connection.rollback() ProgrammingError: SQLite objects created in a thread can only be used in that same thread.The object was created in thread id 140442561648384 and this is thread id 140442989479680
At any rate - we recommend using postgres in production for a reason - these sqlite errors are pretty common.
-John
On Fri, Jun 12, 2015 at 11:15 AM, Ryan G ngsbioinformatics@gmail.com wrote:
Is there a known cause for this?
On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo nsoranzo@tiscali.it wrote:
Hi Ryan, there is no know fix for this, apart from moving to PostgreSQL.
Cheers, Nicola
Il 12.06.2015 16:43 Ryan G ha scritto:
Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and
run
the tool tests individually, they succeed. So I looked into why they
fail
when running them in batch, and it turns out to be a database lock. I'm using the default sqllite database that run_tests.sh creates. Does this need to be tuned somehow?
galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched Error - : (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time,
api_keys.user_id
AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys
\nWHERE
api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) URL:
http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746...
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__ app_iter = self.application(environ, sr_checker) File
'/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__ return self.application(environ, start_response) File
'/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__ return self.application(environ, start_response) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
line 132 in __call__ return self.handle_request( environ, start_response ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
line 159 in handle_request trans = self.transaction_factory( environ ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 71 in self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 102 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self,
session_cookie )
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 194 in __init__ self.error_message = self._authenticate_api( session_cookie ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 283 in _authenticate_api provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( self.app.model.APIKeys.table.c.key == api_key ).one() File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184
in
one File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227
in
__iter__ File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242
in
_execute_and_instances File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 in execute File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584 in _execute_clauseelement File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line
331
in do_execute OperationalError: (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS
api_keys_create_time,
api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key
\nFROM
api_keys \nWHERE api_keys."key" = ?'
(u'e4fe9bf787edb9ef746714beb6212bc8',)
Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
I've migrated my staging instance to use postgres and ran the functional tests. I see lots failing. I know this is known and perhaps expected, but it still bothers me. I would expect to see all the tests pass on a clean instance. If the tests aren't passing, to me, that indicates a problem somewhere. What's the point in having the tests if they always fail?
On Tue, Jun 16, 2015 at 1:12 PM, Ryan G ngsbioinformatics@gmail.com wrote:
I am using postgres in production but want to validate my staging instance before pushing it into production. I do this with the functional tests. I guess I'll have to set up a postgres database for the staging instance as well.
On Mon, Jun 15, 2015 at 10:32 AM, John Chilton jmchilton@gmail.com wrote:
Not exactly - I feel like sqlite should be able to do the kinds of things Galaxy does without this occurring - it should just be inefficient. We are probably doing something across multiple threads that we should not be - presumably related to job handling. After a recent sqlalchemy upgrade - there is now a new error message in the logs that should help track down the problem:
sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception during reset or similar Traceback (most recent call last): File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 571, in _finalize_fairy fairy._reset(pool) File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 705, in _reset pool._dialect.do_rollback(self) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 412, in do_rollback dbapi_connection.rollback() ProgrammingError: SQLite objects created in a thread can only be used in that same thread.The object was created in thread id 140442561648384 and this is thread id 140442989479680
At any rate - we recommend using postgres in production for a reason - these sqlite errors are pretty common.
-John
On Fri, Jun 12, 2015 at 11:15 AM, Ryan G ngsbioinformatics@gmail.com wrote:
Is there a known cause for this?
On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo nsoranzo@tiscali.it wrote:
Hi Ryan, there is no know fix for this, apart from moving to PostgreSQL.
Cheers, Nicola
Il 12.06.2015 16:43 Ryan G ha scritto:
Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and
run
the tool tests individually, they succeed. So I looked into why they
fail
when running them in batch, and it turns out to be a database lock.
I'm
using the default sqllite database that run_tests.sh creates. Does
this
need to be tuned somehow?
galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched Error - : (OperationalError) database is locked u'SELECT api_keys.id
AS
api_keys_id, api_keys.create_time AS api_keys_create_time,
api_keys.user_id
AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys
\nWHERE
api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) URL:
http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746...
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__ app_iter = self.application(environ, sr_checker) File
'/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__ return self.application(environ, start_response) File
'/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__ return self.application(environ, start_response) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
line 132 in __call__ return self.handle_request( environ, start_response ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
line 159 in handle_request trans = self.transaction_factory( environ ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 71 in self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 102 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self,
session_cookie )
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 194 in __init__ self.error_message = self._authenticate_api( session_cookie ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 283 in _authenticate_api provided_key = self.sa_session.query( self.app.model.APIKeys
).filter(
self.app.model.APIKeys.table.c.key == api_key ).one() File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184
in
one File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227
in
__iter__ File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242
in
_execute_and_instances File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1449
in execute File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1584
in _execute_clauseelement File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1698
in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1691
in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line
331
in do_execute OperationalError: (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS
api_keys_create_time,
api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key
\nFROM
api_keys \nWHERE api_keys."key" = ?'
(u'e4fe9bf787edb9ef746714beb6212bc8',)
Connetti gratis il mondo con la nuova indoona: hai la chat, le
chiamate,
le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Which tests are failing, specifically? Many tests will fail without the underlying tools installed.
On Wed, Jun 17, 2015 at 12:01 PM Ryan G ngsbioinformatics@gmail.com wrote:
I've migrated my staging instance to use postgres and ran the functional tests. I see lots failing. I know this is known and perhaps expected, but it still bothers me. I would expect to see all the tests pass on a clean instance. If the tests aren't passing, to me, that indicates a problem somewhere. What's the point in having the tests if they always fail?
On Tue, Jun 16, 2015 at 1:12 PM, Ryan G ngsbioinformatics@gmail.com wrote:
I am using postgres in production but want to validate my staging instance before pushing it into production. I do this with the functional tests. I guess I'll have to set up a postgres database for the staging instance as well.
On Mon, Jun 15, 2015 at 10:32 AM, John Chilton jmchilton@gmail.com wrote:
Not exactly - I feel like sqlite should be able to do the kinds of things Galaxy does without this occurring - it should just be inefficient. We are probably doing something across multiple threads that we should not be - presumably related to job handling. After a recent sqlalchemy upgrade - there is now a new error message in the logs that should help track down the problem:
sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception during reset or similar Traceback (most recent call last): File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 571, in _finalize_fairy fairy._reset(pool) File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 705, in _reset pool._dialect.do_rollback(self) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 412, in do_rollback dbapi_connection.rollback() ProgrammingError: SQLite objects created in a thread can only be used in that same thread.The object was created in thread id 140442561648384 and this is thread id 140442989479680
At any rate - we recommend using postgres in production for a reason - these sqlite errors are pretty common.
-John
On Fri, Jun 12, 2015 at 11:15 AM, Ryan G ngsbioinformatics@gmail.com wrote:
Is there a known cause for this?
On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo nsoranzo@tiscali.it wrote:
Hi Ryan, there is no know fix for this, apart from moving to PostgreSQL.
Cheers, Nicola
Il 12.06.2015 16:43 Ryan G ha scritto:
Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back
and run
the tool tests individually, they succeed. So I looked into why they
fail
when running them in batch, and it turns out to be a database lock.
I'm
using the default sqllite database that run_tests.sh creates. Does
this
need to be tuned somehow?
galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched Error - : (OperationalError) database is locked u'SELECT api_keys.id
AS
api_keys_id, api_keys.create_time AS api_keys_create_time,
api_keys.user_id
AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys
\nWHERE
api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) URL:
http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746...
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__ app_iter = self.application(environ, sr_checker) File
'/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__ return self.application(environ, start_response) File
'/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__ return self.application(environ, start_response) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
line 132 in __call__ return self.handle_request( environ, start_response ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
line 159 in handle_request trans = self.transaction_factory( environ ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 71 in self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 102 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self,
session_cookie )
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 194 in __init__ self.error_message = self._authenticate_api( session_cookie ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 283 in _authenticate_api provided_key = self.sa_session.query( self.app.model.APIKeys
).filter(
self.app.model.APIKeys.table.c.key == api_key ).one() File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line
2184 in
one File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line
2227 in
__iter__ File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line
2242 in
_execute_and_instances File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1449
in execute File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1584
in _execute_clauseelement File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1698
in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1691
in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py',
line 331
in do_execute OperationalError: (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS
api_keys_create_time,
api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key
\nFROM
api_keys \nWHERE api_keys."key" = ?'
(u'e4fe9bf787edb9ef746714beb6212bc8',)
Connetti gratis il mondo con la nuova indoona: hai la chat, le
chiamate,
le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
All the functional.test_admin_features Most of the functional.test_data_security functional.test_history_functions
I'm attaching a PDF printout of the run_functional_tests.html
On Wed, Jun 17, 2015 at 12:01 PM, Dannon Baker dannon.baker@gmail.com wrote:
Which tests are failing, specifically? Many tests will fail without the underlying tools installed.
On Wed, Jun 17, 2015 at 12:01 PM Ryan G ngsbioinformatics@gmail.com wrote:
I've migrated my staging instance to use postgres and ran the functional tests. I see lots failing. I know this is known and perhaps expected, but it still bothers me. I would expect to see all the tests pass on a clean instance. If the tests aren't passing, to me, that indicates a problem somewhere. What's the point in having the tests if they always fail?
On Tue, Jun 16, 2015 at 1:12 PM, Ryan G ngsbioinformatics@gmail.com wrote:
I am using postgres in production but want to validate my staging instance before pushing it into production. I do this with the functional tests. I guess I'll have to set up a postgres database for the staging instance as well.
On Mon, Jun 15, 2015 at 10:32 AM, John Chilton jmchilton@gmail.com wrote:
Not exactly - I feel like sqlite should be able to do the kinds of things Galaxy does without this occurring - it should just be inefficient. We are probably doing something across multiple threads that we should not be - presumably related to job handling. After a recent sqlalchemy upgrade - there is now a new error message in the logs that should help track down the problem:
sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception during reset or similar Traceback (most recent call last): File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 571, in _finalize_fairy fairy._reset(pool) File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 705, in _reset pool._dialect.do_rollback(self) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 412, in do_rollback dbapi_connection.rollback() ProgrammingError: SQLite objects created in a thread can only be used in that same thread.The object was created in thread id 140442561648384 and this is thread id 140442989479680
At any rate - we recommend using postgres in production for a reason - these sqlite errors are pretty common.
-John
On Fri, Jun 12, 2015 at 11:15 AM, Ryan G ngsbioinformatics@gmail.com wrote:
Is there a known cause for this?
On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo <nsoranzo@tiscali.it
wrote:
Hi Ryan, there is no know fix for this, apart from moving to PostgreSQL.
Cheers, Nicola
Il 12.06.2015 16:43 Ryan G ha scritto:
Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back
and run
the tool tests individually, they succeed. So I looked into why
they fail
when running them in batch, and it turns out to be a database lock.
I'm
using the default sqllite database that run_tests.sh creates. Does
this
need to be tuned somehow?
galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched Error - : (OperationalError) database is locked u'SELECT api_keys.id
AS
api_keys_id, api_keys.create_time AS api_keys_create_time,
api_keys.user_id
AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys
\nWHERE
api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) URL:
http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746...
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__ app_iter = self.application(environ, sr_checker) File
'/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__ return self.application(environ, start_response) File
'/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__ return self.application(environ, start_response) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
line 132 in __call__ return self.handle_request( environ, start_response ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
line 159 in handle_request trans = self.transaction_factory( environ ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 71 in self.set_transaction_factory( lambda e: self.transaction_chooser(
e,
galaxy_app, session_cookie ) ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 102 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self,
session_cookie )
File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 194 in __init__ self.error_message = self._authenticate_api( session_cookie ) File
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
line 283 in _authenticate_api provided_key = self.sa_session.query( self.app.model.APIKeys
).filter(
self.app.model.APIKeys.table.c.key == api_key ).one() File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line
2184 in
one File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line
2227 in
__iter__ File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line
2242 in
_execute_and_instances File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1449
in execute File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1584
in _execute_clauseelement File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1698
in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1691
in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py',
line 331
in do_execute OperationalError: (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS
api_keys_create_time,
api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key
\nFROM
api_keys \nWHERE api_keys."key" = ?'
(u'e4fe9bf787edb9ef746714beb6212bc8',)
Connetti gratis il mondo con la nuova indoona: hai la chat, le
chiamate,
le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Thanks, I'll take a look. Non-tool-based functional tests should *not* fail out of the box, and we'll fix them :)
On Wed, Jun 17, 2015 at 12:04 PM Ryan G ngsbioinformatics@gmail.com wrote:
All the functional.test_admin_features Most of the functional.test_data_security functional.test_history_functions
I'm attaching a PDF printout of the run_functional_tests.html
On Wed, Jun 17, 2015 at 12:01 PM, Dannon Baker dannon.baker@gmail.com wrote:
Which tests are failing, specifically? Many tests will fail without the underlying tools installed.
On Wed, Jun 17, 2015 at 12:01 PM Ryan G ngsbioinformatics@gmail.com wrote:
I've migrated my staging instance to use postgres and ran the functional tests. I see lots failing. I know this is known and perhaps expected, but it still bothers me. I would expect to see all the tests pass on a clean instance. If the tests aren't passing, to me, that indicates a problem somewhere. What's the point in having the tests if they always fail?
On Tue, Jun 16, 2015 at 1:12 PM, Ryan G ngsbioinformatics@gmail.com wrote:
I am using postgres in production but want to validate my staging instance before pushing it into production. I do this with the functional tests. I guess I'll have to set up a postgres database for the staging instance as well.
On Mon, Jun 15, 2015 at 10:32 AM, John Chilton jmchilton@gmail.com wrote:
Not exactly - I feel like sqlite should be able to do the kinds of things Galaxy does without this occurring - it should just be inefficient. We are probably doing something across multiple threads that we should not be - presumably related to job handling. After a recent sqlalchemy upgrade - there is now a new error message in the logs that should help track down the problem:
sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception during reset or similar Traceback (most recent call last): File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 571, in _finalize_fairy fairy._reset(pool) File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 705, in _reset pool._dialect.do_rollback(self) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 412, in do_rollback dbapi_connection.rollback() ProgrammingError: SQLite objects created in a thread can only be used in that same thread.The object was created in thread id 140442561648384 and this is thread id 140442989479680
At any rate - we recommend using postgres in production for a reason - these sqlite errors are pretty common.
-John
On Fri, Jun 12, 2015 at 11:15 AM, Ryan G ngsbioinformatics@gmail.com wrote:
Is there a known cause for this?
On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo <
nsoranzo@tiscali.it>
wrote: > > Hi Ryan, > there is no know fix for this, apart from moving to PostgreSQL. > > Cheers, > Nicola > > Il 12.06.2015 16:43 Ryan G ha scritto: > > Hi all - I'm running functional tests on a set of tools using > 'run_tests.sh -sid ...'. A few of the tests fail. When I go back
and run
> the tool tests individually, they succeed. So I looked into why
they fail
> when running them in batch, and it turns out to be a database
lock. I'm
> using the default sqllite database that run_tests.sh creates. Does
this
> need to be tuned somehow? > > > galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched > Error - : (OperationalError) database is locked u'SELECT
api_keys.id AS
> api_keys_id, api_keys.create_time AS api_keys_create_time,
api_keys.user_id
> AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys
\nWHERE
> api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) > URL: >
http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746...
> File >
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py',
> line 149 in __call__ > app_iter = self.application(environ, sr_checker) > File >
'/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
> line 84 in __call__ > return self.application(environ, start_response) > File >
'/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
> line 633 in __call__ > return self.application(environ, start_response) > File >
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
> line 132 in __call__ > return self.handle_request( environ, start_response ) > File >
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
> line 159 in handle_request > trans = self.transaction_factory( environ ) > File >
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
> line 71 in > self.set_transaction_factory( lambda e: self.transaction_chooser(
e,
> galaxy_app, session_cookie ) ) > File >
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
> line 102 in transaction_chooser > return GalaxyWebTransaction( environ, galaxy_app, self,
session_cookie )
> File >
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
> line 194 in __init__ > self.error_message = self._authenticate_api( session_cookie ) > File >
'/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
> line 283 in _authenticate_api > provided_key = self.sa_session.query( self.app.model.APIKeys
).filter(
> self.app.model.APIKeys.table.c.key == api_key ).one() > File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line
2184 in
> one > File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line
2227 in
> __iter__ > File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line
2242 in
> _execute_and_instances > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1449
> in execute > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1584
> in _execute_clauseelement > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1698
> in _execute_context > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line
1691
> in _execute_context > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py',
line 331
> in do_execute > OperationalError: (OperationalError) database is locked u'SELECT > api_keys.id AS api_keys_id, api_keys.create_time AS
api_keys_create_time,
> api_keys.user_id AS api_keys_user_id, api_keys."key" AS
api_keys_key \nFROM
> api_keys \nWHERE api_keys."key" = ?'
(u'e4fe9bf787edb9ef746714beb6212bc8',)
> > > > > > Connetti gratis il mondo con la nuova indoona: hai la chat, le
chiamate,
> le video chiamate e persino le chiamate di gruppo. > E chiami gratis anche i numeri fissi e mobili nel mondo! > Scarica subito l’app Vai su https://www.indoona.com/ >
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Thanks. Let me know how I can help.
On Wed, Jun 17, 2015 at 12:08 PM, Dannon Baker dannon.baker@gmail.com wrote:
Thanks, I'll take a look. Non-tool-based functional tests should *not* fail out of the box, and we'll fix them :)
On Wed, Jun 17, 2015 at 12:04 PM Ryan G ngsbioinformatics@gmail.com wrote:
All the functional.test_admin_features Most of the functional.test_data_security functional.test_history_functions
I'm attaching a PDF printout of the run_functional_tests.html
On Wed, Jun 17, 2015 at 12:01 PM, Dannon Baker dannon.baker@gmail.com wrote:
Which tests are failing, specifically? Many tests will fail without the underlying tools installed.
On Wed, Jun 17, 2015 at 12:01 PM Ryan G ngsbioinformatics@gmail.com wrote:
I've migrated my staging instance to use postgres and ran the functional tests. I see lots failing. I know this is known and perhaps expected, but it still bothers me. I would expect to see all the tests pass on a clean instance. If the tests aren't passing, to me, that indicates a problem somewhere. What's the point in having the tests if they always fail?
On Tue, Jun 16, 2015 at 1:12 PM, Ryan G ngsbioinformatics@gmail.com wrote:
I am using postgres in production but want to validate my staging instance before pushing it into production. I do this with the functional tests. I guess I'll have to set up a postgres database for the staging instance as well.
On Mon, Jun 15, 2015 at 10:32 AM, John Chilton jmchilton@gmail.com wrote:
Not exactly - I feel like sqlite should be able to do the kinds of things Galaxy does without this occurring - it should just be inefficient. We are probably doing something across multiple threads that we should not be - presumably related to job handling. After a recent sqlalchemy upgrade - there is now a new error message in the logs that should help track down the problem:
sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception during reset or similar Traceback (most recent call last): File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 571, in _finalize_fairy fairy._reset(pool) File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 705, in _reset pool._dialect.do_rollback(self) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 412, in do_rollback dbapi_connection.rollback() ProgrammingError: SQLite objects created in a thread can only be used in that same thread.The object was created in thread id 140442561648384 and this is thread id 140442989479680
At any rate - we recommend using postgres in production for a reason - these sqlite errors are pretty common.
-John
On Fri, Jun 12, 2015 at 11:15 AM, Ryan G ngsbioinformatics@gmail.com wrote: > Is there a known cause for this? > > On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo < nsoranzo@tiscali.it> > wrote: >> >> Hi Ryan, >> there is no know fix for this, apart from moving to PostgreSQL. >> >> Cheers, >> Nicola >> >> Il 12.06.2015 16:43 Ryan G ha scritto: >> >> Hi all - I'm running functional tests on a set of tools using >> 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run >> the tool tests individually, they succeed. So I looked into why they fail >> when running them in batch, and it turns out to be a database lock. I'm >> using the default sqllite database that run_tests.sh creates. Does this >> need to be tuned somehow? >> >> >> galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched >> Error - : (OperationalError) database is locked u'SELECT api_keys.id AS >> api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id >> AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE >> api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) >> URL: >> http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746... >> File >> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', >> line 149 in __call__ >> app_iter = self.application(environ, sr_checker) >> File >> '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', >> line 84 in __call__ >> return self.application(environ, start_response) >> File >> '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', >> line 633 in __call__ >> return self.application(environ, start_response) >> File >> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', >> line 132 in __call__ >> return self.handle_request( environ, start_response ) >> File >> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', >> line 159 in handle_request >> trans = self.transaction_factory( environ ) >> File >> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', >> line 71 in >> self.set_transaction_factory( lambda e: self.transaction_chooser( e, >> galaxy_app, session_cookie ) ) >> File >> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', >> line 102 in transaction_chooser >> return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) >> File >> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', >> line 194 in __init__ >> self.error_message = self._authenticate_api( session_cookie ) >> File >> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', >> line 283 in _authenticate_api >> provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( >> self.app.model.APIKeys.table.c.key == api_key ).one() >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184 in >> one >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227 in >> __iter__ >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242 in >> _execute_and_instances >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 >> in execute >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584 >> in _execute_clauseelement >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 >> in _execute_context >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 >> in _execute_context >> File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line 331 >> in do_execute >> OperationalError: (OperationalError) database is locked u'SELECT >> api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, >> api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM >> api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) >> >> >> >> >> >> Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, >> le video chiamate e persino le chiamate di gruppo. >> E chiami gratis anche i numeri fissi e mobili nel mondo! >> Scarica subito l’app Vai su https://www.indoona.com/ >> > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
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galaxy-dev@lists.galaxyproject.org
-
Dannon Baker -
John Chilton -
Nicola Soranzo -
Ryan G