3:44 p.m.
Using the run.sh script, and the default 'log_level = DEBUG'
universe_wsgi.ini file setting gives a huge amount of output.
Changing the ini to either log_level = INFO, WARNING or ERROR and i
get the same output, including the INFO messages every second.
I assumed that WARNING or ERROR would not give the INFO messages; is
there some way to not see these?
Cheers
m
--
Michael Pheasant
Software Engineer
Queensland Facility for Advanced Bioinformatics
Level 6, QBP
University of Queensland, QLD 4072
T: +61 (0)7 3346 2070
F: +61 (0)7 3346 2101
www.qfab.org
1:24 p.m.
Michael Pheasant wrote:
Using the run.sh script, and the default 'log_level = DEBUG'
universe_wsgi.ini file setting gives a huge amount of output.
Changing the ini to either log_level = INFO, WARNING or ERROR and i
get the same output, including the INFO messages every second.
I assumed that WARNING or ERROR would not give the INFO messages; is
there some way to not see these?
Hi Michael,
Can you provide an example of which INFO messages still appear? WARNING
is suppressing everything above the WARNING level for me.
--nate
Cheers
m
--
Michael Pheasant
Software Engineer
Queensland Facility for Advanced Bioinformatics
Level 6, QBP
University of Queensland, QLD 4072
T: +61 (0)7 3346 2070
F: +61 (0)7 3346 2101
www.qfab.org
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
11:53 p.m.
using run script with single web server/jobrunner:
universe_wsgi.ini:
log_level = WARNING
enable_job_running = True
*) During the startup sequence there is a bunch of INFO stuff;
2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
Created new connection <_mysql.connection open to 'localhost' at
1aab1730>
sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
Created new connection <_mysql.connection open to 'localhost' at
1aab1730>
2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
Connection <_mysql.connection open to 'localhost' at 1aab1730> checked
out from pool
sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
Connection <_mysql.connection open to 'localhost' at 1aab1730> checked
out from pool
2010-06-02 09:49:55,322 INFO sqlalchemy.engine.base.Engine.0x...85d0
SHOW VARIABLES LIKE 'character_set%%'
sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,322
SHOW VARIABLES LIKE 'character_set%%'
2010-06-02 09:49:55,322 INFO sqlalchemy.engine.base.Engine.0x...85d0 ()
sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,322 ()
2010-06-02 09:49:55,323 INFO sqlalchemy.engine.base.Engine.0x...85d0
SHOW VARIABLES LIKE 'sql_mode'
sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,323
SHOW VARIABLES LIKE 'sql_mode'
2010-06-02 09:49:55,323 INFO sqlalchemy.engine.base.Engine.0x...85d0 ()
sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,323 ()
2010-06-02 09:49:55,348 INFO sqlalchemy.engine.base.Engine.0x...85d0
SHOW CREATE TABLE dataset
sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,348
SHOW CREATE TABLE dataset
2010-06-02 09:49:55,348 INFO sqlalchemy.engine.base.Engine.0x...85d0 ()
Then every second there is the database ping for jobs;
sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,153
SELECT job.id AS job_id, job.create_time AS job_create_time,
job.update_time AS job_update_time, job.history_id AS job_history_id,
job.library_folder_id AS job_library_folder_id, job.tool_id AS
job_tool_id, job.tool_version AS job_tool_version, job.state AS
job_state, job.info AS job_info, job.command_line AS job_command_line,
job.param_filename AS job_param_filename, job.runner_name AS
job_runner_name_1, job.stdout AS job_stdout, job.stderr AS job_stderr,
job.traceback AS job_traceback, job.session_id AS job_session_id,
job.job_runner_name AS job_job_runner_name, job.job_runner_external_id
AS job_job_runner_external_id,
library_dataset_dataset_association_1.id AS
library_dataset_dataset_association_1_id,
library_dataset_dataset_association_1.library_dataset_id AS
library_dataset_dataset_association_1_library_dataset_id,
library_dataset_dataset_association_1.dataset_id AS
library_dataset_dataset_association_1_dataset_id,
library_dataset_dataset_association_1.create_time AS
library_dataset_dataset_association_1_create_time,
library_dataset_dataset_association_1.update_time AS
library_dataset_dataset_association_1_update_time,
library_dataset_dataset_association_1.copied_from_history_dataset_association_id
AS library_dataset_dataset_association_1_copied_from_history_dataset_association_id,
library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id
AS
library_dataset_dataset_association_1_copied_from_library_dataset_dataset_association_id,
library_dataset_dataset_association_1.name AS
library_dataset_dataset_association_1_name,
library_dataset_dataset_association_1.info AS
library_dataset_dataset_association_1_info,
library_dataset_dataset_association_1.blurb AS
library_dataset_dataset_association_1_blurb,
library_dataset_dataset_association_1.peek AS
library_dataset_dataset_association_1_peek,
library_dataset_dataset_association_1.extension AS
library_dataset_dataset_association_1_extension,
library_dataset_dataset_association_1.metadata AS
library_dataset_dataset_association_1_metadata,
library_dataset_dataset_association_1.parent_id AS
library_dataset_dataset_association_1_parent_id,
library_dataset_dataset_association_1.designation AS
library_dataset_dataset_association_1_designation,
library_dataset_dataset_association_1.deleted AS
library_dataset_dataset_association_1_deleted,
library_dataset_dataset_association_1.visible AS
library_dataset_dataset_association_1_visible,
library_dataset_dataset_association_1.user_id AS
library_dataset_dataset_association_1_user_id,
library_dataset_dataset_association_1.message AS
library_dataset_dataset_association_1_message,
job_to_output_library_dataset_1.id AS
job_to_output_library_dataset_1_id,
job_to_output_library_dataset_1.job_id AS
job_to_output_library_dataset_1_job_id,
job_to_output_library_dataset_1.ldda_id AS
job_to_output_library_dataset_1_ldda_id,
job_to_output_library_dataset_1.name AS
job_to_output_library_dataset_1_name, dataset_1.id AS dataset_1_id,
dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time
AS dataset_1_update_time, dataset_1.state AS dataset_1_state,
dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS
dataset_1_purged, dataset_1.purgable AS dataset_1_purgable,
dataset_1.external_filename AS dataset_1_external_filename,
dataset_1._extra_files_path AS dataset_1__extra_files_path,
dataset_1.file_size AS dataset_1_file_size,
history_dataset_association_1.id AS history_dataset_association_1_id,
history_dataset_association_1.history_id AS
history_dataset_association_1_history_id,
history_dataset_association_1.dataset_id AS
history_dataset_association_1_dataset_id,
history_dataset_association_1.create_time AS
history_dataset_association_1_create_time,
history_dataset_association_1.update_time AS
history_dataset_association_1_update_time,
history_dataset_association_1.copied_from_history_dataset_association_id
AS history_dataset_association_1_copied_from_history_dataset_association_id,
history_dataset_association_1.copied_from_library_dataset_dataset_association_id
AS history_dataset_association_1_copied_from_library_dataset_dataset_association_id,
history_dataset_association_1.hid AS
history_dataset_association_1_hid, history_dataset_association_1.name
AS history_dataset_association_1_name,
history_dataset_association_1.info AS
history_dataset_association_1_info,
history_dataset_association_1.blurb AS
history_dataset_association_1_blurb,
history_dataset_association_1.peek AS
history_dataset_association_1_peek,
history_dataset_association_1.extension AS
history_dataset_association_1_extension,
history_dataset_association_1.metadata AS
history_dataset_association_1_metadata,
history_dataset_association_1.parent_id AS
history_dataset_association_1_parent_id,
history_dataset_association_1.designation AS
history_dataset_association_1_designation,
history_dataset_association_1.deleted AS
history_dataset_association_1_deleted,
history_dataset_association_1.visible AS
history_dataset_association_1_visible, job_to_input_dataset_1.id AS
job_to_input_dataset_1_id, job_to_input_dataset_1.job_id AS
job_to_input_dataset_1_job_id, job_to_input_dataset_1.dataset_id AS
job_to_input_dataset_1_dataset_id, job_to_input_dataset_1.name AS
job_to_input_dataset_1_name, dataset_2.id AS dataset_2_id,
dataset_2.create_time AS dataset_2_create_time, dataset_2.update_time
AS dataset_2_update_time, dataset_2.state AS dataset_2_state,
dataset_2.deleted AS dataset_2_deleted, dataset_2.purged AS
dataset_2_purged, dataset_2.purgable AS dataset_2_purgable,
dataset_2.external_filename AS dataset_2_external_filename,
dataset_2._extra_files_path AS dataset_2__extra_files_path,
dataset_2.file_size AS dataset_2_file_size,
history_dataset_association_2.id AS history_dataset_association_2_id,
history_dataset_association_2.history_id AS
history_dataset_association_2_history_id,
history_dataset_association_2.dataset_id AS
history_dataset_association_2_dataset_id,
history_dataset_association_2.create_time AS
history_dataset_association_2_create_time,
history_dataset_association_2.update_time AS
history_dataset_association_2_update_time,
history_dataset_association_2.copied_from_history_dataset_association_id
AS history_dataset_association_2_copied_from_history_dataset_association_id,
history_dataset_association_2.copied_from_library_dataset_dataset_association_id
AS history_dataset_association_2_copied_from_library_dataset_dataset_association_id,
history_dataset_association_2.hid AS
history_dataset_association_2_hid, history_dataset_association_2.name
AS history_dataset_association_2_name,
history_dataset_association_2.info AS
history_dataset_association_2_info,
history_dataset_association_2.blurb AS
history_dataset_association_2_blurb,
history_dataset_association_2.peek AS
history_dataset_association_2_peek,
history_dataset_association_2.extension AS
history_dataset_association_2_extension,
history_dataset_association_2.metadata AS
history_dataset_association_2_metadata,
history_dataset_association_2.parent_id AS
history_dataset_association_2_parent_id,
history_dataset_association_2.designation AS
history_dataset_association_2_designation,
history_dataset_association_2.deleted AS
history_dataset_association_2_deleted,
history_dataset_association_2.visible AS
history_dataset_association_2_visible, job_to_output_dataset_1.id AS
job_to_output_dataset_1_id, job_to_output_dataset_1.job_id AS
job_to_output_dataset_1_job_id, job_to_output_dataset_1.dataset_id AS
job_to_output_dataset_1_dataset_id, job_to_output_dataset_1.name AS
job_to_output_dataset_1_name
FROM job LEFT OUTER JOIN job_to_output_library_dataset AS
job_to_output_library_dataset_1 ON job.id =
job_to_output_library_dataset_1.job_id LEFT OUTER JOIN
library_dataset_dataset_association AS
library_dataset_dataset_association_1 ON
library_dataset_dataset_association_1.id =
job_to_output_library_dataset_1.ldda_id LEFT OUTER JOIN
job_to_input_dataset AS job_to_input_dataset_1 ON job.id =
job_to_input_dataset_1.job_id LEFT OUTER JOIN
history_dataset_association AS history_dataset_association_1 ON
history_dataset_association_1.id = job_to_input_dataset_1.dataset_id
LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id =
history_dataset_association_1.dataset_id LEFT OUTER JOIN
job_to_output_dataset AS job_to_output_dataset_1 ON job.id =
job_to_output_dataset_1.job_id LEFT OUTER JOIN
history_dataset_association AS history_dataset_association_2 ON
history_dataset_association_2.id = job_to_output_dataset_1.dataset_id
LEFT OUTER JOIN dataset AS dataset_2 ON dataset_2.id =
history_dataset_association_2.dataset_id
WHERE job.state = %s
2010-06-02 09:50:15,154 INFO sqlalchemy.engine.base.Engine.0x...0e50 ['new']
sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,154 ['new']
2010-06-02 09:50:15,157 INFO sqlalchemy.pool.QueuePool.0x...0c90
Connection <_mysql.connection open to 'localhost' at 1b0894d0> being
returned to pool
sqlalchemy.pool.QueuePool.0x...0c90 INFO 2010-06-02 09:50:15,157
Connection <_mysql.connection open to 'localhost' at 1b0894d0> being
returned to pool
cheers
m
--
Michael Pheasant
Software Engineer
Queensland Facility for Advanced Bioinformatics
Level 6, QBP
University of Queensland, QLD 4072
T: +61 (0)7 3346 2070
F: +61 (0)7 3346 2101
www.qfab.org
On Tue, Jun 1, 2010 at 11:24 PM, Nate Coraor <nate(a)bx.psu.edu> wrote:
Michael Pheasant wrote:
>
> Using the run.sh script, and the default 'log_level = DEBUG'
> universe_wsgi.ini file setting gives a huge amount of output.
>
> Changing the ini to either log_level = INFO, WARNING or ERROR and i
> get the same output, including the INFO messages every second.
>
> I assumed that WARNING or ERROR would not give the INFO messages; is
> there some way to not see these?
Hi Michael,
Can you provide an example of which INFO messages still appear? Â WARNING is
suppressing everything above the WARNING level for me.
--nate
>
> Cheers
> m
>
> --
> Michael Pheasant
> Software Engineer
> Queensland Facility for Advanced Bioinformatics
> Level 6, QBP
> University of Queensland, QLD 4072
> T: +61 (0)7 3346 2070
> F: +61 (0)7 3346 2101
> www.qfab.org
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
11:56 p.m.
Have you uncommented either of:
#database_engine_option_echo = true
#database_engine_option_echo_pool = true
In you universe_wsgi.ini?
On Jun 1, 2010, at 7:53 PM, Michael Pheasant wrote:
using run script with single web server/jobrunner:
universe_wsgi.ini:
log_level = WARNING
enable_job_running = True
*) During the startup sequence there is a bunch of INFO stuff;
2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
Created new connection <_mysql.connection open to 'localhost' at
1aab1730>
sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
Created new connection <_mysql.connection open to 'localhost' at
1aab1730>
2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
Connection <_mysql.connection open to 'localhost' at 1aab1730> checked
out from pool
sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
Connection <_mysql.connection open to 'localhost' at 1aab1730> checked
out from pool
2010-06-02 09:49:55,322 INFO sqlalchemy.engine.base.Engine.0x...85d0
SHOW VARIABLES LIKE 'character_set%%'
sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,322
SHOW VARIABLES LIKE 'character_set%%'
2010-06-02 09:49:55,322 INFO sqlalchemy.engine.base.Engine.0x...85d0
()
sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,322
()
2010-06-02 09:49:55,323 INFO sqlalchemy.engine.base.Engine.0x...85d0
SHOW VARIABLES LIKE 'sql_mode'
sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,323
SHOW VARIABLES LIKE 'sql_mode'
2010-06-02 09:49:55,323 INFO sqlalchemy.engine.base.Engine.0x...85d0
()
sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,323
()
2010-06-02 09:49:55,348 INFO sqlalchemy.engine.base.Engine.0x...85d0
SHOW CREATE TABLE dataset
sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,348
SHOW CREATE TABLE dataset
2010-06-02 09:49:55,348 INFO sqlalchemy.engine.base.Engine.0x...85d0
()
Then every second there is the database ping for jobs;
sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,153
SELECT job.id AS job_id, job.create_time AS job_create_time,
job.update_time AS job_update_time, job.history_id AS job_history_id,
job.library_folder_id AS job_library_folder_id, job.tool_id AS
job_tool_id, job.tool_version AS job_tool_version, job.state AS
job_state, job.info AS job_info, job.command_line AS job_command_line,
job.param_filename AS job_param_filename, job.runner_name AS
job_runner_name_1, job.stdout AS job_stdout, job.stderr AS job_stderr,
job.traceback AS job_traceback, job.session_id AS job_session_id,
job.job_runner_name AS job_job_runner_name, job.job_runner_external_id
AS job_job_runner_external_id,
library_dataset_dataset_association_1.id AS
library_dataset_dataset_association_1_id,
library_dataset_dataset_association_1.library_dataset_id AS
library_dataset_dataset_association_1_library_dataset_id,
library_dataset_dataset_association_1.dataset_id AS
library_dataset_dataset_association_1_dataset_id,
library_dataset_dataset_association_1.create_time AS
library_dataset_dataset_association_1_create_time,
library_dataset_dataset_association_1.update_time AS
library_dataset_dataset_association_1_update_time,
library_dataset_dataset_association_1
.copied_from_history_dataset_association_id
AS
library_dataset_dataset_association_1_copied_from_history_dataset_association_id
,
library_dataset_dataset_association_1
.copied_from_library_dataset_dataset_association_id
AS
library_dataset_dataset_association_1_copied_from_library_dataset_dataset_association_id
,
library_dataset_dataset_association_1.name AS
library_dataset_dataset_association_1_name,
library_dataset_dataset_association_1.info AS
library_dataset_dataset_association_1_info,
library_dataset_dataset_association_1.blurb AS
library_dataset_dataset_association_1_blurb,
library_dataset_dataset_association_1.peek AS
library_dataset_dataset_association_1_peek,
library_dataset_dataset_association_1.extension AS
library_dataset_dataset_association_1_extension,
library_dataset_dataset_association_1.metadata AS
library_dataset_dataset_association_1_metadata,
library_dataset_dataset_association_1.parent_id AS
library_dataset_dataset_association_1_parent_id,
library_dataset_dataset_association_1.designation AS
library_dataset_dataset_association_1_designation,
library_dataset_dataset_association_1.deleted AS
library_dataset_dataset_association_1_deleted,
library_dataset_dataset_association_1.visible AS
library_dataset_dataset_association_1_visible,
library_dataset_dataset_association_1.user_id AS
library_dataset_dataset_association_1_user_id,
library_dataset_dataset_association_1.message AS
library_dataset_dataset_association_1_message,
job_to_output_library_dataset_1.id AS
job_to_output_library_dataset_1_id,
job_to_output_library_dataset_1.job_id AS
job_to_output_library_dataset_1_job_id,
job_to_output_library_dataset_1.ldda_id AS
job_to_output_library_dataset_1_ldda_id,
job_to_output_library_dataset_1.name AS
job_to_output_library_dataset_1_name, dataset_1.id AS dataset_1_id,
dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time
AS dataset_1_update_time, dataset_1.state AS dataset_1_state,
dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS
dataset_1_purged, dataset_1.purgable AS dataset_1_purgable,
dataset_1.external_filename AS dataset_1_external_filename,
dataset_1._extra_files_path AS dataset_1__extra_files_path,
dataset_1.file_size AS dataset_1_file_size,
history_dataset_association_1.id AS history_dataset_association_1_id,
history_dataset_association_1.history_id AS
history_dataset_association_1_history_id,
history_dataset_association_1.dataset_id AS
history_dataset_association_1_dataset_id,
history_dataset_association_1.create_time AS
history_dataset_association_1_create_time,
history_dataset_association_1.update_time AS
history_dataset_association_1_update_time,
history_dataset_association_1
.copied_from_history_dataset_association_id
AS
history_dataset_association_1_copied_from_history_dataset_association_id
,
history_dataset_association_1
.copied_from_library_dataset_dataset_association_id
AS
history_dataset_association_1_copied_from_library_dataset_dataset_association_id
,
history_dataset_association_1.hid AS
history_dataset_association_1_hid, history_dataset_association_1.name
AS history_dataset_association_1_name,
history_dataset_association_1.info AS
history_dataset_association_1_info,
history_dataset_association_1.blurb AS
history_dataset_association_1_blurb,
history_dataset_association_1.peek AS
history_dataset_association_1_peek,
history_dataset_association_1.extension AS
history_dataset_association_1_extension,
history_dataset_association_1.metadata AS
history_dataset_association_1_metadata,
history_dataset_association_1.parent_id AS
history_dataset_association_1_parent_id,
history_dataset_association_1.designation AS
history_dataset_association_1_designation,
history_dataset_association_1.deleted AS
history_dataset_association_1_deleted,
history_dataset_association_1.visible AS
history_dataset_association_1_visible, job_to_input_dataset_1.id AS
job_to_input_dataset_1_id, job_to_input_dataset_1.job_id AS
job_to_input_dataset_1_job_id, job_to_input_dataset_1.dataset_id AS
job_to_input_dataset_1_dataset_id, job_to_input_dataset_1.name AS
job_to_input_dataset_1_name, dataset_2.id AS dataset_2_id,
dataset_2.create_time AS dataset_2_create_time, dataset_2.update_time
AS dataset_2_update_time, dataset_2.state AS dataset_2_state,
dataset_2.deleted AS dataset_2_deleted, dataset_2.purged AS
dataset_2_purged, dataset_2.purgable AS dataset_2_purgable,
dataset_2.external_filename AS dataset_2_external_filename,
dataset_2._extra_files_path AS dataset_2__extra_files_path,
dataset_2.file_size AS dataset_2_file_size,
history_dataset_association_2.id AS history_dataset_association_2_id,
history_dataset_association_2.history_id AS
history_dataset_association_2_history_id,
history_dataset_association_2.dataset_id AS
history_dataset_association_2_dataset_id,
history_dataset_association_2.create_time AS
history_dataset_association_2_create_time,
history_dataset_association_2.update_time AS
history_dataset_association_2_update_time,
history_dataset_association_2
.copied_from_history_dataset_association_id
AS
history_dataset_association_2_copied_from_history_dataset_association_id
,
history_dataset_association_2
.copied_from_library_dataset_dataset_association_id
AS
history_dataset_association_2_copied_from_library_dataset_dataset_association_id
,
history_dataset_association_2.hid AS
history_dataset_association_2_hid, history_dataset_association_2.name
AS history_dataset_association_2_name,
history_dataset_association_2.info AS
history_dataset_association_2_info,
history_dataset_association_2.blurb AS
history_dataset_association_2_blurb,
history_dataset_association_2.peek AS
history_dataset_association_2_peek,
history_dataset_association_2.extension AS
history_dataset_association_2_extension,
history_dataset_association_2.metadata AS
history_dataset_association_2_metadata,
history_dataset_association_2.parent_id AS
history_dataset_association_2_parent_id,
history_dataset_association_2.designation AS
history_dataset_association_2_designation,
history_dataset_association_2.deleted AS
history_dataset_association_2_deleted,
history_dataset_association_2.visible AS
history_dataset_association_2_visible, job_to_output_dataset_1.id AS
job_to_output_dataset_1_id, job_to_output_dataset_1.job_id AS
job_to_output_dataset_1_job_id, job_to_output_dataset_1.dataset_id AS
job_to_output_dataset_1_dataset_id, job_to_output_dataset_1.name AS
job_to_output_dataset_1_name
FROM job LEFT OUTER JOIN job_to_output_library_dataset AS
job_to_output_library_dataset_1 ON job.id =
job_to_output_library_dataset_1.job_id LEFT OUTER JOIN
library_dataset_dataset_association AS
library_dataset_dataset_association_1 ON
library_dataset_dataset_association_1.id =
job_to_output_library_dataset_1.ldda_id LEFT OUTER JOIN
job_to_input_dataset AS job_to_input_dataset_1 ON job.id =
job_to_input_dataset_1.job_id LEFT OUTER JOIN
history_dataset_association AS history_dataset_association_1 ON
history_dataset_association_1.id = job_to_input_dataset_1.dataset_id
LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id =
history_dataset_association_1.dataset_id LEFT OUTER JOIN
job_to_output_dataset AS job_to_output_dataset_1 ON job.id =
job_to_output_dataset_1.job_id LEFT OUTER JOIN
history_dataset_association AS history_dataset_association_2 ON
history_dataset_association_2.id = job_to_output_dataset_1.dataset_id
LEFT OUTER JOIN dataset AS dataset_2 ON dataset_2.id =
history_dataset_association_2.dataset_id
WHERE job.state = %s
2010-06-02 09:50:15,154 INFO sqlalchemy.engine.base.Engine.0x...0e50
['new']
sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,154
['new']
2010-06-02 09:50:15,157 INFO sqlalchemy.pool.QueuePool.0x...0c90
Connection <_mysql.connection open to 'localhost' at 1b0894d0> being
returned to pool
sqlalchemy.pool.QueuePool.0x...0c90 INFO 2010-06-02 09:50:15,157
Connection <_mysql.connection open to 'localhost' at 1b0894d0> being
returned to pool
cheers
m
--
Michael Pheasant
Software Engineer
Queensland Facility for Advanced Bioinformatics
Level 6, QBP
University of Queensland, QLD 4072
T: +61 (0)7 3346 2070
F: +61 (0)7 3346 2101
www.qfab.org
On Tue, Jun 1, 2010 at 11:24 PM, Nate Coraor <nate(a)bx.psu.edu> wrote:
> Michael Pheasant wrote:
>>
>> Using the run.sh script, and the default 'log_level = DEBUG'
>> universe_wsgi.ini file setting gives a huge amount of output.
>>
>> Changing the ini to either log_level = INFO, WARNING or ERROR and i
>> get the same output, including the INFO messages every second.
>>
>> I assumed that WARNING or ERROR would not give the INFO messages; is
>> there some way to not see these?
>
> Hi Michael,
>
> Can you provide an example of which INFO messages still appear?
> WARNING is
> suppressing everything above the WARNING level for me.
>
> --nate
>
>>
>> Cheers
>> m
>>
>> --
>> Michael Pheasant
>> Software Engineer
>> Queensland Facility for Advanced Bioinformatics
>> Level 6, QBP
>> University of Queensland, QLD 4072
>> T: +61 (0)7 3346 2070
>> F: +61 (0)7 3346 2101
>> www.qfab.org
>> _______________________________________________
>> galaxy-dev mailing list
>> galaxy-dev(a)lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
>
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
1:15 a.m.
Thanks, that fixed it, they were uncommented!
CHeers
m
--
Michael Pheasant
Software Engineer
Queensland Facility for Advanced Bioinformatics
Level 6, QBP
University of Queensland, QLD 4072
T: +61 (0)7 3346 2070
F: +61 (0)7 3346 2101
www.qfab.org
On Wed, Jun 2, 2010 at 9:56 AM, James Taylor <james(a)bx.psu.edu> wrote:
Have you uncommented either of:
#database_engine_option_echo = true
#database_engine_option_echo_pool = true
In you universe_wsgi.ini?
On Jun 1, 2010, at 7:53 PM, Michael Pheasant wrote:
> using run script with single web server/jobrunner:
> universe_wsgi.ini:
> Â log_level = WARNING
> Â enable_job_running = True
>
> *) During the startup sequence there is a bunch of INFO stuff;
>
> 2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
> Created new connection <_mysql.connection open to 'localhost' at
> 1aab1730>
> sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
> Created new connection <_mysql.connection open to 'localhost' at
> 1aab1730>
> 2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
> Connection <_mysql.connection open to 'localhost' at 1aab1730> checked
> out from pool
> sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
> Connection <_mysql.connection open to 'localhost' at 1aab1730> checked
> out from pool
> 2010-06-02 09:49:55,322 INFO sqlalchemy.engine.base.Engine.0x...85d0
> SHOW VARIABLES LIKE 'character_set%%'
> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,322
> SHOW VARIABLES LIKE 'character_set%%'
> 2010-06-02 09:49:55,322 INFO sqlalchemy.engine.base.Engine.0x...85d0 ()
> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,322 ()
> 2010-06-02 09:49:55,323 INFO sqlalchemy.engine.base.Engine.0x...85d0
> SHOW VARIABLES LIKE 'sql_mode'
> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,323
> SHOW VARIABLES LIKE 'sql_mode'
> 2010-06-02 09:49:55,323 INFO sqlalchemy.engine.base.Engine.0x...85d0 ()
> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,323 ()
> 2010-06-02 09:49:55,348 INFO sqlalchemy.engine.base.Engine.0x...85d0
> SHOW CREATE TABLE dataset
> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,348
> SHOW CREATE TABLE dataset
> 2010-06-02 09:49:55,348 INFO sqlalchemy.engine.base.Engine.0x...85d0 ()
>
>
> Then every second there is the database ping for jobs;
>
> sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,153
> SELECT job.id AS job_id, job.create_time AS job_create_time,
> job.update_time AS job_update_time, job.history_id AS job_history_id,
> job.library_folder_id AS job_library_folder_id, job.tool_id AS
> job_tool_id, job.tool_version AS job_tool_version, job.state AS
> job_state, job.info AS job_info, job.command_line AS job_command_line,
> job.param_filename AS job_param_filename, job.runner_name AS
> job_runner_name_1, job.stdout AS job_stdout, job.stderr AS job_stderr,
> job.traceback AS job_traceback, job.session_id AS job_session_id,
> job.job_runner_name AS job_job_runner_name, job.job_runner_external_id
> AS job_job_runner_external_id,
> library_dataset_dataset_association_1.id AS
> library_dataset_dataset_association_1_id,
> library_dataset_dataset_association_1.library_dataset_id AS
> library_dataset_dataset_association_1_library_dataset_id,
> library_dataset_dataset_association_1.dataset_id AS
> library_dataset_dataset_association_1_dataset_id,
> library_dataset_dataset_association_1.create_time AS
> library_dataset_dataset_association_1_create_time,
> library_dataset_dataset_association_1.update_time AS
> library_dataset_dataset_association_1_update_time,
>
> library_dataset_dataset_association_1.copied_from_history_dataset_association_id
> AS
> library_dataset_dataset_association_1_copied_from_history_dataset_association_id,
>
>
library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id
> AS
>
library_dataset_dataset_association_1_copied_from_library_dataset_dataset_association_id,
> library_dataset_dataset_association_1.name AS
> library_dataset_dataset_association_1_name,
> library_dataset_dataset_association_1.info AS
> library_dataset_dataset_association_1_info,
> library_dataset_dataset_association_1.blurb AS
> library_dataset_dataset_association_1_blurb,
> library_dataset_dataset_association_1.peek AS
> library_dataset_dataset_association_1_peek,
> library_dataset_dataset_association_1.extension AS
> library_dataset_dataset_association_1_extension,
> library_dataset_dataset_association_1.metadata AS
> library_dataset_dataset_association_1_metadata,
> library_dataset_dataset_association_1.parent_id AS
> library_dataset_dataset_association_1_parent_id,
> library_dataset_dataset_association_1.designation AS
> library_dataset_dataset_association_1_designation,
> library_dataset_dataset_association_1.deleted AS
> library_dataset_dataset_association_1_deleted,
> library_dataset_dataset_association_1.visible AS
> library_dataset_dataset_association_1_visible,
> library_dataset_dataset_association_1.user_id AS
> library_dataset_dataset_association_1_user_id,
> library_dataset_dataset_association_1.message AS
> library_dataset_dataset_association_1_message,
> job_to_output_library_dataset_1.id AS
> job_to_output_library_dataset_1_id,
> job_to_output_library_dataset_1.job_id AS
> job_to_output_library_dataset_1_job_id,
> job_to_output_library_dataset_1.ldda_id AS
> job_to_output_library_dataset_1_ldda_id,
> job_to_output_library_dataset_1.name AS
> job_to_output_library_dataset_1_name, dataset_1.id AS dataset_1_id,
> dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time
> AS dataset_1_update_time, dataset_1.state AS dataset_1_state,
> dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS
> dataset_1_purged, dataset_1.purgable AS dataset_1_purgable,
> dataset_1.external_filename AS dataset_1_external_filename,
> dataset_1._extra_files_path AS dataset_1__extra_files_path,
> dataset_1.file_size AS dataset_1_file_size,
> history_dataset_association_1.id AS history_dataset_association_1_id,
> history_dataset_association_1.history_id AS
> history_dataset_association_1_history_id,
> history_dataset_association_1.dataset_id AS
> history_dataset_association_1_dataset_id,
> history_dataset_association_1.create_time AS
> history_dataset_association_1_create_time,
> history_dataset_association_1.update_time AS
> history_dataset_association_1_update_time,
> history_dataset_association_1.copied_from_history_dataset_association_id
> AS
> history_dataset_association_1_copied_from_history_dataset_association_id,
>
> history_dataset_association_1.copied_from_library_dataset_dataset_association_id
> AS
> history_dataset_association_1_copied_from_library_dataset_dataset_association_id,
> history_dataset_association_1.hid AS
> history_dataset_association_1_hid, history_dataset_association_1.name
> AS history_dataset_association_1_name,
> history_dataset_association_1.info AS
> history_dataset_association_1_info,
> history_dataset_association_1.blurb AS
> history_dataset_association_1_blurb,
> history_dataset_association_1.peek AS
> history_dataset_association_1_peek,
> history_dataset_association_1.extension AS
> history_dataset_association_1_extension,
> history_dataset_association_1.metadata AS
> history_dataset_association_1_metadata,
> history_dataset_association_1.parent_id AS
> history_dataset_association_1_parent_id,
> history_dataset_association_1.designation AS
> history_dataset_association_1_designation,
> history_dataset_association_1.deleted AS
> history_dataset_association_1_deleted,
> history_dataset_association_1.visible AS
> history_dataset_association_1_visible, job_to_input_dataset_1.id AS
> job_to_input_dataset_1_id, job_to_input_dataset_1.job_id AS
> job_to_input_dataset_1_job_id, job_to_input_dataset_1.dataset_id AS
> job_to_input_dataset_1_dataset_id, job_to_input_dataset_1.name AS
> job_to_input_dataset_1_name, dataset_2.id AS dataset_2_id,
> dataset_2.create_time AS dataset_2_create_time, dataset_2.update_time
> AS dataset_2_update_time, dataset_2.state AS dataset_2_state,
> dataset_2.deleted AS dataset_2_deleted, dataset_2.purged AS
> dataset_2_purged, dataset_2.purgable AS dataset_2_purgable,
> dataset_2.external_filename AS dataset_2_external_filename,
> dataset_2._extra_files_path AS dataset_2__extra_files_path,
> dataset_2.file_size AS dataset_2_file_size,
> history_dataset_association_2.id AS history_dataset_association_2_id,
> history_dataset_association_2.history_id AS
> history_dataset_association_2_history_id,
> history_dataset_association_2.dataset_id AS
> history_dataset_association_2_dataset_id,
> history_dataset_association_2.create_time AS
> history_dataset_association_2_create_time,
> history_dataset_association_2.update_time AS
> history_dataset_association_2_update_time,
> history_dataset_association_2.copied_from_history_dataset_association_id
> AS
> history_dataset_association_2_copied_from_history_dataset_association_id,
>
> history_dataset_association_2.copied_from_library_dataset_dataset_association_id
> AS
> history_dataset_association_2_copied_from_library_dataset_dataset_association_id,
> history_dataset_association_2.hid AS
> history_dataset_association_2_hid, history_dataset_association_2.name
> AS history_dataset_association_2_name,
> history_dataset_association_2.info AS
> history_dataset_association_2_info,
> history_dataset_association_2.blurb AS
> history_dataset_association_2_blurb,
> history_dataset_association_2.peek AS
> history_dataset_association_2_peek,
> history_dataset_association_2.extension AS
> history_dataset_association_2_extension,
> history_dataset_association_2.metadata AS
> history_dataset_association_2_metadata,
> history_dataset_association_2.parent_id AS
> history_dataset_association_2_parent_id,
> history_dataset_association_2.designation AS
> history_dataset_association_2_designation,
> history_dataset_association_2.deleted AS
> history_dataset_association_2_deleted,
> history_dataset_association_2.visible AS
> history_dataset_association_2_visible, job_to_output_dataset_1.id AS
> job_to_output_dataset_1_id, job_to_output_dataset_1.job_id AS
> job_to_output_dataset_1_job_id, job_to_output_dataset_1.dataset_id AS
> job_to_output_dataset_1_dataset_id, job_to_output_dataset_1.name AS
> job_to_output_dataset_1_name
> FROM job LEFT OUTER JOIN job_to_output_library_dataset AS
> job_to_output_library_dataset_1 ON job.id =
> job_to_output_library_dataset_1.job_id LEFT OUTER JOIN
> library_dataset_dataset_association AS
> library_dataset_dataset_association_1 ON
> library_dataset_dataset_association_1.id =
> job_to_output_library_dataset_1.ldda_id LEFT OUTER JOIN
> job_to_input_dataset AS job_to_input_dataset_1 ON job.id =
> job_to_input_dataset_1.job_id LEFT OUTER JOIN
> history_dataset_association AS history_dataset_association_1 ON
> history_dataset_association_1.id = job_to_input_dataset_1.dataset_id
> LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id =
> history_dataset_association_1.dataset_id LEFT OUTER JOIN
> job_to_output_dataset AS job_to_output_dataset_1 ON job.id =
> job_to_output_dataset_1.job_id LEFT OUTER JOIN
> history_dataset_association AS history_dataset_association_2 ON
> history_dataset_association_2.id = job_to_output_dataset_1.dataset_id
> LEFT OUTER JOIN dataset AS dataset_2 ON dataset_2.id =
> history_dataset_association_2.dataset_id
> WHERE job.state = %s
> 2010-06-02 09:50:15,154 INFO sqlalchemy.engine.base.Engine.0x...0e50
> ['new']
> sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,154
> ['new']
> 2010-06-02 09:50:15,157 INFO sqlalchemy.pool.QueuePool.0x...0c90
> Connection <_mysql.connection open to 'localhost' at 1b0894d0> being
> returned to pool
> sqlalchemy.pool.QueuePool.0x...0c90 INFO 2010-06-02 09:50:15,157
> Connection <_mysql.connection open to 'localhost' at 1b0894d0> being
> returned to pool
>
>
> cheers
> m
>
> --
> Michael Pheasant
> Software Engineer
> Queensland Facility for Advanced Bioinformatics
> Level 6, QBP
> University of Queensland, QLD 4072
> T: +61 (0)7 3346 2070
> F: +61 (0)7 3346 2101
> www.qfab.org
>
>
>
> On Tue, Jun 1, 2010 at 11:24 PM, Nate Coraor <nate(a)bx.psu.edu> wrote:
>>
>> Michael Pheasant wrote:
>>>
>>> Using the run.sh script, and the default 'log_level = DEBUG'
>>> universe_wsgi.ini file setting gives a huge amount of output.
>>>
>>> Changing the ini to either log_level = INFO, WARNING or ERROR and i
>>> get the same output, including the INFO messages every second.
>>>
>>> I assumed that WARNING or ERROR would not give the INFO messages; is
>>> there some way to not see these?
>>
>> Hi Michael,
>>
>> Can you provide an example of which INFO messages still appear? Â WARNING
>> is
>> suppressing everything above the WARNING level for me.
>>
>> --nate
>>
>>>
>>> Cheers
>>> m
>>>
>>> --
>>> Michael Pheasant
>>> Software Engineer
>>> Queensland Facility for Advanced Bioinformatics
>>> Level 6, QBP
>>> University of Queensland, QLD 4072
>>> T: +61 (0)7 3346 2070
>>> F: +61 (0)7 3346 2101
>>> www.qfab.org
>>> _______________________________________________
>>> galaxy-dev mailing list
>>> galaxy-dev(a)lists.bx.psu.edu
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>>
>
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
11:06 a.m.
Is there also a way to supress these:
192.168.3.61 - - [07/Sep/2010:13:05:48 +0200] "POST
/root/history_item_updates HTTP/1.1" 200 - "http://galaxy/history"
"Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.8) Gecko/20100723
Ubuntu/10.04 (lucid) Firefox/3.6.8"
Logging Messages?
Thx Michael
Am 06/02/2010 03:15 AM, schrieb Michael Pheasant:
Thanks, that fixed it, they were uncommented!
CHeers
m
--
Michael Pheasant
Software Engineer
Queensland Facility for Advanced Bioinformatics
Level 6, QBP
University of Queensland, QLD 4072
T: +61 (0)7 3346 2070
F: +61 (0)7 3346 2101
www.qfab.org
On Wed, Jun 2, 2010 at 9:56 AM, James Taylor<james(a)bx.psu.edu> wrote:
> Have you uncommented either of:
>
> #database_engine_option_echo = true
> #database_engine_option_echo_pool = true
>
> In you universe_wsgi.ini?
>
> On Jun 1, 2010, at 7:53 PM, Michael Pheasant wrote:
>
>> using run script with single web server/jobrunner:
>> universe_wsgi.ini:
>> log_level = WARNING
>> enable_job_running = True
>>
>> *) During the startup sequence there is a bunch of INFO stuff;
>>
>> 2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
>> Created new connection<_mysql.connection open to 'localhost' at
>> 1aab1730>
>> sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
>> Created new connection<_mysql.connection open to 'localhost' at
>> 1aab1730>
>> 2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
>> Connection<_mysql.connection open to 'localhost' at 1aab1730>
checked
>> out from pool
>> sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
>> Connection<_mysql.connection open to 'localhost' at 1aab1730>
checked
>> out from pool
>> 2010-06-02 09:49:55,322 INFO sqlalchemy.engine.base.Engine.0x...85d0
>> SHOW VARIABLES LIKE 'character_set%%'
>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,322
>> SHOW VARIABLES LIKE 'character_set%%'
>> 2010-06-02 09:49:55,322 INFO sqlalchemy.engine.base.Engine.0x...85d0 ()
>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,322 ()
>> 2010-06-02 09:49:55,323 INFO sqlalchemy.engine.base.Engine.0x...85d0
>> SHOW VARIABLES LIKE 'sql_mode'
>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,323
>> SHOW VARIABLES LIKE 'sql_mode'
>> 2010-06-02 09:49:55,323 INFO sqlalchemy.engine.base.Engine.0x...85d0 ()
>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,323 ()
>> 2010-06-02 09:49:55,348 INFO sqlalchemy.engine.base.Engine.0x...85d0
>> SHOW CREATE TABLE dataset
>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,348
>> SHOW CREATE TABLE dataset
>> 2010-06-02 09:49:55,348 INFO sqlalchemy.engine.base.Engine.0x...85d0 ()
>>
>>
>> Then every second there is the database ping for jobs;
>>
>> sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,153
>> SELECT job.id AS job_id, job.create_time AS job_create_time,
>> job.update_time AS job_update_time, job.history_id AS job_history_id,
>> job.library_folder_id AS job_library_folder_id, job.tool_id AS
>> job_tool_id, job.tool_version AS job_tool_version, job.state AS
>> job_state, job.info AS job_info, job.command_line AS job_command_line,
>> job.param_filename AS job_param_filename, job.runner_name AS
>> job_runner_name_1, job.stdout AS job_stdout, job.stderr AS job_stderr,
>> job.traceback AS job_traceback, job.session_id AS job_session_id,
>> job.job_runner_name AS job_job_runner_name, job.job_runner_external_id
>> AS job_job_runner_external_id,
>> library_dataset_dataset_association_1.id AS
>> library_dataset_dataset_association_1_id,
>> library_dataset_dataset_association_1.library_dataset_id AS
>> library_dataset_dataset_association_1_library_dataset_id,
>> library_dataset_dataset_association_1.dataset_id AS
>> library_dataset_dataset_association_1_dataset_id,
>> library_dataset_dataset_association_1.create_time AS
>> library_dataset_dataset_association_1_create_time,
>> library_dataset_dataset_association_1.update_time AS
>> library_dataset_dataset_association_1_update_time,
>>
>> library_dataset_dataset_association_1.copied_from_history_dataset_association_id
>> AS
>>
library_dataset_dataset_association_1_copied_from_history_dataset_association_id,
>>
>>
library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id
>> AS
>>
library_dataset_dataset_association_1_copied_from_library_dataset_dataset_association_id,
>> library_dataset_dataset_association_1.name AS
>> library_dataset_dataset_association_1_name,
>> library_dataset_dataset_association_1.info AS
>> library_dataset_dataset_association_1_info,
>> library_dataset_dataset_association_1.blurb AS
>> library_dataset_dataset_association_1_blurb,
>> library_dataset_dataset_association_1.peek AS
>> library_dataset_dataset_association_1_peek,
>> library_dataset_dataset_association_1.extension AS
>> library_dataset_dataset_association_1_extension,
>> library_dataset_dataset_association_1.metadata AS
>> library_dataset_dataset_association_1_metadata,
>> library_dataset_dataset_association_1.parent_id AS
>> library_dataset_dataset_association_1_parent_id,
>> library_dataset_dataset_association_1.designation AS
>> library_dataset_dataset_association_1_designation,
>> library_dataset_dataset_association_1.deleted AS
>> library_dataset_dataset_association_1_deleted,
>> library_dataset_dataset_association_1.visible AS
>> library_dataset_dataset_association_1_visible,
>> library_dataset_dataset_association_1.user_id AS
>> library_dataset_dataset_association_1_user_id,
>> library_dataset_dataset_association_1.message AS
>> library_dataset_dataset_association_1_message,
>> job_to_output_library_dataset_1.id AS
>> job_to_output_library_dataset_1_id,
>> job_to_output_library_dataset_1.job_id AS
>> job_to_output_library_dataset_1_job_id,
>> job_to_output_library_dataset_1.ldda_id AS
>> job_to_output_library_dataset_1_ldda_id,
>> job_to_output_library_dataset_1.name AS
>> job_to_output_library_dataset_1_name, dataset_1.id AS dataset_1_id,
>> dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time
>> AS dataset_1_update_time, dataset_1.state AS dataset_1_state,
>> dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS
>> dataset_1_purged, dataset_1.purgable AS dataset_1_purgable,
>> dataset_1.external_filename AS dataset_1_external_filename,
>> dataset_1._extra_files_path AS dataset_1__extra_files_path,
>> dataset_1.file_size AS dataset_1_file_size,
>> history_dataset_association_1.id AS history_dataset_association_1_id,
>> history_dataset_association_1.history_id AS
>> history_dataset_association_1_history_id,
>> history_dataset_association_1.dataset_id AS
>> history_dataset_association_1_dataset_id,
>> history_dataset_association_1.create_time AS
>> history_dataset_association_1_create_time,
>> history_dataset_association_1.update_time AS
>> history_dataset_association_1_update_time,
>> history_dataset_association_1.copied_from_history_dataset_association_id
>> AS
>> history_dataset_association_1_copied_from_history_dataset_association_id,
>>
>> history_dataset_association_1.copied_from_library_dataset_dataset_association_id
>> AS
>>
history_dataset_association_1_copied_from_library_dataset_dataset_association_id,
>> history_dataset_association_1.hid AS
>> history_dataset_association_1_hid, history_dataset_association_1.name
>> AS history_dataset_association_1_name,
>> history_dataset_association_1.info AS
>> history_dataset_association_1_info,
>> history_dataset_association_1.blurb AS
>> history_dataset_association_1_blurb,
>> history_dataset_association_1.peek AS
>> history_dataset_association_1_peek,
>> history_dataset_association_1.extension AS
>> history_dataset_association_1_extension,
>> history_dataset_association_1.metadata AS
>> history_dataset_association_1_metadata,
>> history_dataset_association_1.parent_id AS
>> history_dataset_association_1_parent_id,
>> history_dataset_association_1.designation AS
>> history_dataset_association_1_designation,
>> history_dataset_association_1.deleted AS
>> history_dataset_association_1_deleted,
>> history_dataset_association_1.visible AS
>> history_dataset_association_1_visible, job_to_input_dataset_1.id AS
>> job_to_input_dataset_1_id, job_to_input_dataset_1.job_id AS
>> job_to_input_dataset_1_job_id, job_to_input_dataset_1.dataset_id AS
>> job_to_input_dataset_1_dataset_id, job_to_input_dataset_1.name AS
>> job_to_input_dataset_1_name, dataset_2.id AS dataset_2_id,
>> dataset_2.create_time AS dataset_2_create_time, dataset_2.update_time
>> AS dataset_2_update_time, dataset_2.state AS dataset_2_state,
>> dataset_2.deleted AS dataset_2_deleted, dataset_2.purged AS
>> dataset_2_purged, dataset_2.purgable AS dataset_2_purgable,
>> dataset_2.external_filename AS dataset_2_external_filename,
>> dataset_2._extra_files_path AS dataset_2__extra_files_path,
>> dataset_2.file_size AS dataset_2_file_size,
>> history_dataset_association_2.id AS history_dataset_association_2_id,
>> history_dataset_association_2.history_id AS
>> history_dataset_association_2_history_id,
>> history_dataset_association_2.dataset_id AS
>> history_dataset_association_2_dataset_id,
>> history_dataset_association_2.create_time AS
>> history_dataset_association_2_create_time,
>> history_dataset_association_2.update_time AS
>> history_dataset_association_2_update_time,
>> history_dataset_association_2.copied_from_history_dataset_association_id
>> AS
>> history_dataset_association_2_copied_from_history_dataset_association_id,
>>
>> history_dataset_association_2.copied_from_library_dataset_dataset_association_id
>> AS
>>
history_dataset_association_2_copied_from_library_dataset_dataset_association_id,
>> history_dataset_association_2.hid AS
>> history_dataset_association_2_hid, history_dataset_association_2.name
>> AS history_dataset_association_2_name,
>> history_dataset_association_2.info AS
>> history_dataset_association_2_info,
>> history_dataset_association_2.blurb AS
>> history_dataset_association_2_blurb,
>> history_dataset_association_2.peek AS
>> history_dataset_association_2_peek,
>> history_dataset_association_2.extension AS
>> history_dataset_association_2_extension,
>> history_dataset_association_2.metadata AS
>> history_dataset_association_2_metadata,
>> history_dataset_association_2.parent_id AS
>> history_dataset_association_2_parent_id,
>> history_dataset_association_2.designation AS
>> history_dataset_association_2_designation,
>> history_dataset_association_2.deleted AS
>> history_dataset_association_2_deleted,
>> history_dataset_association_2.visible AS
>> history_dataset_association_2_visible, job_to_output_dataset_1.id AS
>> job_to_output_dataset_1_id, job_to_output_dataset_1.job_id AS
>> job_to_output_dataset_1_job_id, job_to_output_dataset_1.dataset_id AS
>> job_to_output_dataset_1_dataset_id, job_to_output_dataset_1.name AS
>> job_to_output_dataset_1_name
>> FROM job LEFT OUTER JOIN job_to_output_library_dataset AS
>> job_to_output_library_dataset_1 ON job.id =
>> job_to_output_library_dataset_1.job_id LEFT OUTER JOIN
>> library_dataset_dataset_association AS
>> library_dataset_dataset_association_1 ON
>> library_dataset_dataset_association_1.id =
>> job_to_output_library_dataset_1.ldda_id LEFT OUTER JOIN
>> job_to_input_dataset AS job_to_input_dataset_1 ON job.id =
>> job_to_input_dataset_1.job_id LEFT OUTER JOIN
>> history_dataset_association AS history_dataset_association_1 ON
>> history_dataset_association_1.id = job_to_input_dataset_1.dataset_id
>> LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id =
>> history_dataset_association_1.dataset_id LEFT OUTER JOIN
>> job_to_output_dataset AS job_to_output_dataset_1 ON job.id =
>> job_to_output_dataset_1.job_id LEFT OUTER JOIN
>> history_dataset_association AS history_dataset_association_2 ON
>> history_dataset_association_2.id = job_to_output_dataset_1.dataset_id
>> LEFT OUTER JOIN dataset AS dataset_2 ON dataset_2.id =
>> history_dataset_association_2.dataset_id
>> WHERE job.state = %s
>> 2010-06-02 09:50:15,154 INFO sqlalchemy.engine.base.Engine.0x...0e50
>> ['new']
>> sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,154
>> ['new']
>> 2010-06-02 09:50:15,157 INFO sqlalchemy.pool.QueuePool.0x...0c90
>> Connection<_mysql.connection open to 'localhost' at 1b0894d0>
being
>> returned to pool
>> sqlalchemy.pool.QueuePool.0x...0c90 INFO 2010-06-02 09:50:15,157
>> Connection<_mysql.connection open to 'localhost' at 1b0894d0>
being
>> returned to pool
>>
>>
>> cheers
>> m
>>
>> --
>> Michael Pheasant
>> Software Engineer
>> Queensland Facility for Advanced Bioinformatics
>> Level 6, QBP
>> University of Queensland, QLD 4072
>> T: +61 (0)7 3346 2070
>> F: +61 (0)7 3346 2101
>> www.qfab.org
>>
>>
>>
>> On Tue, Jun 1, 2010 at 11:24 PM, Nate Coraor<nate(a)bx.psu.edu> wrote:
>>> Michael Pheasant wrote:
>>>> Using the run.sh script, and the default 'log_level = DEBUG'
>>>> universe_wsgi.ini file setting gives a huge amount of output.
>>>>
>>>> Changing the ini to either log_level = INFO, WARNING or ERROR and i
>>>> get the same output, including the INFO messages every second.
>>>>
>>>> I assumed that WARNING or ERROR would not give the INFO messages; is
>>>> there some way to not see these?
>>> Hi Michael,
>>>
>>> Can you provide an example of which INFO messages still appear? WARNING
>>> is
>>> suppressing everything above the WARNING level for me.
>>>
>>> --nate
>>>
>>>> Cheers
>>>> m
>>>>
>>>> --
>>>> Michael Pheasant
>>>> Software Engineer
>>>> Queensland Facility for Advanced Bioinformatics
>>>> Level 6, QBP
>>>> University of Queensland, QLD 4072
>>>> T: +61 (0)7 3346 2070
>>>> F: +61 (0)7 3346 2101
>>>> www.qfab.org
>>>> _______________________________________________
>>>> galaxy-dev mailing list
>>>> galaxy-dev(a)lists.bx.psu.edu
>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>
>> _______________________________________________
>> galaxy-dev mailing list
>> galaxy-dev(a)lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
6:02 p.m.
Michael Siebauer wrote:
Is there also a way to supress these:
192.168.3.61 - - [07/Sep/2010:13:05:48 +0200] "POST
/root/history_item_updates HTTP/1.1" 200 - "http://galaxy/history"
"Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.8) Gecko/20100723
Ubuntu/10.04 (lucid) Firefox/3.6.8"
Logging Messages?
Just the hits to history_item_updates, or all Apache-style web logging?
--nate
Thx Michael
Am 06/02/2010 03:15 AM, schrieb Michael Pheasant:
> Thanks, that fixed it, they were uncommented!
> CHeers
> m
>
> --
> Michael Pheasant
> Software Engineer
> Queensland Facility for Advanced Bioinformatics
> Level 6, QBP
> University of Queensland, QLD 4072
> T: +61 (0)7 3346 2070
> F: +61 (0)7 3346 2101
> www.qfab.org
>
>
>
> On Wed, Jun 2, 2010 at 9:56 AM, James Taylor<james(a)bx.psu.edu> wrote:
>> Have you uncommented either of:
>>
>> #database_engine_option_echo = true
>> #database_engine_option_echo_pool = true
>>
>> In you universe_wsgi.ini?
>>
>> On Jun 1, 2010, at 7:53 PM, Michael Pheasant wrote:
>>
>>> using run script with single web server/jobrunner:
>>> universe_wsgi.ini:
>>> log_level = WARNING
>>> enable_job_running = True
>>>
>>> *) During the startup sequence there is a bunch of INFO stuff;
>>>
>>> 2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
>>> Created new connection<_mysql.connection open to 'localhost' at
>>> 1aab1730>
>>> sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
>>> Created new connection<_mysql.connection open to 'localhost' at
>>> 1aab1730>
>>> 2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
>>> Connection<_mysql.connection open to 'localhost' at 1aab1730>
checked
>>> out from pool
>>> sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
>>> Connection<_mysql.connection open to 'localhost' at 1aab1730>
checked
>>> out from pool
>>> 2010-06-02 09:49:55,322 INFO sqlalchemy.engine.base.Engine.0x...85d0
>>> SHOW VARIABLES LIKE 'character_set%%'
>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,322
>>> SHOW VARIABLES LIKE 'character_set%%'
>>> 2010-06-02 09:49:55,322 INFO sqlalchemy.engine.base.Engine.0x...85d0 ()
>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,322 ()
>>> 2010-06-02 09:49:55,323 INFO sqlalchemy.engine.base.Engine.0x...85d0
>>> SHOW VARIABLES LIKE 'sql_mode'
>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,323
>>> SHOW VARIABLES LIKE 'sql_mode'
>>> 2010-06-02 09:49:55,323 INFO sqlalchemy.engine.base.Engine.0x...85d0 ()
>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,323 ()
>>> 2010-06-02 09:49:55,348 INFO sqlalchemy.engine.base.Engine.0x...85d0
>>> SHOW CREATE TABLE dataset
>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,348
>>> SHOW CREATE TABLE dataset
>>> 2010-06-02 09:49:55,348 INFO sqlalchemy.engine.base.Engine.0x...85d0 ()
>>>
>>>
>>> Then every second there is the database ping for jobs;
>>>
>>> sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,153
>>> SELECT job.id AS job_id, job.create_time AS job_create_time,
>>> job.update_time AS job_update_time, job.history_id AS job_history_id,
>>> job.library_folder_id AS job_library_folder_id, job.tool_id AS
>>> job_tool_id, job.tool_version AS job_tool_version, job.state AS
>>> job_state, job.info AS job_info, job.command_line AS job_command_line,
>>> job.param_filename AS job_param_filename, job.runner_name AS
>>> job_runner_name_1, job.stdout AS job_stdout, job.stderr AS job_stderr,
>>> job.traceback AS job_traceback, job.session_id AS job_session_id,
>>> job.job_runner_name AS job_job_runner_name, job.job_runner_external_id
>>> AS job_job_runner_external_id,
>>> library_dataset_dataset_association_1.id AS
>>> library_dataset_dataset_association_1_id,
>>> library_dataset_dataset_association_1.library_dataset_id AS
>>> library_dataset_dataset_association_1_library_dataset_id,
>>> library_dataset_dataset_association_1.dataset_id AS
>>> library_dataset_dataset_association_1_dataset_id,
>>> library_dataset_dataset_association_1.create_time AS
>>> library_dataset_dataset_association_1_create_time,
>>> library_dataset_dataset_association_1.update_time AS
>>> library_dataset_dataset_association_1_update_time,
>>>
>>>
library_dataset_dataset_association_1.copied_from_history_dataset_association_id
>>>
>>> AS
>>>
library_dataset_dataset_association_1_copied_from_history_dataset_association_id,
>>>
>>>
>>>
library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id
>>>
>>> AS
>>>
library_dataset_dataset_association_1_copied_from_library_dataset_dataset_association_id,
>>>
>>> library_dataset_dataset_association_1.name AS
>>> library_dataset_dataset_association_1_name,
>>> library_dataset_dataset_association_1.info AS
>>> library_dataset_dataset_association_1_info,
>>> library_dataset_dataset_association_1.blurb AS
>>> library_dataset_dataset_association_1_blurb,
>>> library_dataset_dataset_association_1.peek AS
>>> library_dataset_dataset_association_1_peek,
>>> library_dataset_dataset_association_1.extension AS
>>> library_dataset_dataset_association_1_extension,
>>> library_dataset_dataset_association_1.metadata AS
>>> library_dataset_dataset_association_1_metadata,
>>> library_dataset_dataset_association_1.parent_id AS
>>> library_dataset_dataset_association_1_parent_id,
>>> library_dataset_dataset_association_1.designation AS
>>> library_dataset_dataset_association_1_designation,
>>> library_dataset_dataset_association_1.deleted AS
>>> library_dataset_dataset_association_1_deleted,
>>> library_dataset_dataset_association_1.visible AS
>>> library_dataset_dataset_association_1_visible,
>>> library_dataset_dataset_association_1.user_id AS
>>> library_dataset_dataset_association_1_user_id,
>>> library_dataset_dataset_association_1.message AS
>>> library_dataset_dataset_association_1_message,
>>> job_to_output_library_dataset_1.id AS
>>> job_to_output_library_dataset_1_id,
>>> job_to_output_library_dataset_1.job_id AS
>>> job_to_output_library_dataset_1_job_id,
>>> job_to_output_library_dataset_1.ldda_id AS
>>> job_to_output_library_dataset_1_ldda_id,
>>> job_to_output_library_dataset_1.name AS
>>> job_to_output_library_dataset_1_name, dataset_1.id AS dataset_1_id,
>>> dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time
>>> AS dataset_1_update_time, dataset_1.state AS dataset_1_state,
>>> dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS
>>> dataset_1_purged, dataset_1.purgable AS dataset_1_purgable,
>>> dataset_1.external_filename AS dataset_1_external_filename,
>>> dataset_1._extra_files_path AS dataset_1__extra_files_path,
>>> dataset_1.file_size AS dataset_1_file_size,
>>> history_dataset_association_1.id AS history_dataset_association_1_id,
>>> history_dataset_association_1.history_id AS
>>> history_dataset_association_1_history_id,
>>> history_dataset_association_1.dataset_id AS
>>> history_dataset_association_1_dataset_id,
>>> history_dataset_association_1.create_time AS
>>> history_dataset_association_1_create_time,
>>> history_dataset_association_1.update_time AS
>>> history_dataset_association_1_update_time,
>>> history_dataset_association_1.copied_from_history_dataset_association_id
>>>
>>> AS
>>> history_dataset_association_1_copied_from_history_dataset_association_id,
>>>
>>>
>>>
history_dataset_association_1.copied_from_library_dataset_dataset_association_id
>>>
>>> AS
>>>
history_dataset_association_1_copied_from_library_dataset_dataset_association_id,
>>>
>>> history_dataset_association_1.hid AS
>>> history_dataset_association_1_hid, history_dataset_association_1.name
>>> AS history_dataset_association_1_name,
>>> history_dataset_association_1.info AS
>>> history_dataset_association_1_info,
>>> history_dataset_association_1.blurb AS
>>> history_dataset_association_1_blurb,
>>> history_dataset_association_1.peek AS
>>> history_dataset_association_1_peek,
>>> history_dataset_association_1.extension AS
>>> history_dataset_association_1_extension,
>>> history_dataset_association_1.metadata AS
>>> history_dataset_association_1_metadata,
>>> history_dataset_association_1.parent_id AS
>>> history_dataset_association_1_parent_id,
>>> history_dataset_association_1.designation AS
>>> history_dataset_association_1_designation,
>>> history_dataset_association_1.deleted AS
>>> history_dataset_association_1_deleted,
>>> history_dataset_association_1.visible AS
>>> history_dataset_association_1_visible, job_to_input_dataset_1.id AS
>>> job_to_input_dataset_1_id, job_to_input_dataset_1.job_id AS
>>> job_to_input_dataset_1_job_id, job_to_input_dataset_1.dataset_id AS
>>> job_to_input_dataset_1_dataset_id, job_to_input_dataset_1.name AS
>>> job_to_input_dataset_1_name, dataset_2.id AS dataset_2_id,
>>> dataset_2.create_time AS dataset_2_create_time, dataset_2.update_time
>>> AS dataset_2_update_time, dataset_2.state AS dataset_2_state,
>>> dataset_2.deleted AS dataset_2_deleted, dataset_2.purged AS
>>> dataset_2_purged, dataset_2.purgable AS dataset_2_purgable,
>>> dataset_2.external_filename AS dataset_2_external_filename,
>>> dataset_2._extra_files_path AS dataset_2__extra_files_path,
>>> dataset_2.file_size AS dataset_2_file_size,
>>> history_dataset_association_2.id AS history_dataset_association_2_id,
>>> history_dataset_association_2.history_id AS
>>> history_dataset_association_2_history_id,
>>> history_dataset_association_2.dataset_id AS
>>> history_dataset_association_2_dataset_id,
>>> history_dataset_association_2.create_time AS
>>> history_dataset_association_2_create_time,
>>> history_dataset_association_2.update_time AS
>>> history_dataset_association_2_update_time,
>>> history_dataset_association_2.copied_from_history_dataset_association_id
>>>
>>> AS
>>> history_dataset_association_2_copied_from_history_dataset_association_id,
>>>
>>>
>>>
history_dataset_association_2.copied_from_library_dataset_dataset_association_id
>>>
>>> AS
>>>
history_dataset_association_2_copied_from_library_dataset_dataset_association_id,
>>>
>>> history_dataset_association_2.hid AS
>>> history_dataset_association_2_hid, history_dataset_association_2.name
>>> AS history_dataset_association_2_name,
>>> history_dataset_association_2.info AS
>>> history_dataset_association_2_info,
>>> history_dataset_association_2.blurb AS
>>> history_dataset_association_2_blurb,
>>> history_dataset_association_2.peek AS
>>> history_dataset_association_2_peek,
>>> history_dataset_association_2.extension AS
>>> history_dataset_association_2_extension,
>>> history_dataset_association_2.metadata AS
>>> history_dataset_association_2_metadata,
>>> history_dataset_association_2.parent_id AS
>>> history_dataset_association_2_parent_id,
>>> history_dataset_association_2.designation AS
>>> history_dataset_association_2_designation,
>>> history_dataset_association_2.deleted AS
>>> history_dataset_association_2_deleted,
>>> history_dataset_association_2.visible AS
>>> history_dataset_association_2_visible, job_to_output_dataset_1.id AS
>>> job_to_output_dataset_1_id, job_to_output_dataset_1.job_id AS
>>> job_to_output_dataset_1_job_id, job_to_output_dataset_1.dataset_id AS
>>> job_to_output_dataset_1_dataset_id, job_to_output_dataset_1.name AS
>>> job_to_output_dataset_1_name
>>> FROM job LEFT OUTER JOIN job_to_output_library_dataset AS
>>> job_to_output_library_dataset_1 ON job.id =
>>> job_to_output_library_dataset_1.job_id LEFT OUTER JOIN
>>> library_dataset_dataset_association AS
>>> library_dataset_dataset_association_1 ON
>>> library_dataset_dataset_association_1.id =
>>> job_to_output_library_dataset_1.ldda_id LEFT OUTER JOIN
>>> job_to_input_dataset AS job_to_input_dataset_1 ON job.id =
>>> job_to_input_dataset_1.job_id LEFT OUTER JOIN
>>> history_dataset_association AS history_dataset_association_1 ON
>>> history_dataset_association_1.id = job_to_input_dataset_1.dataset_id
>>> LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id =
>>> history_dataset_association_1.dataset_id LEFT OUTER JOIN
>>> job_to_output_dataset AS job_to_output_dataset_1 ON job.id =
>>> job_to_output_dataset_1.job_id LEFT OUTER JOIN
>>> history_dataset_association AS history_dataset_association_2 ON
>>> history_dataset_association_2.id = job_to_output_dataset_1.dataset_id
>>> LEFT OUTER JOIN dataset AS dataset_2 ON dataset_2.id =
>>> history_dataset_association_2.dataset_id
>>> WHERE job.state = %s
>>> 2010-06-02 09:50:15,154 INFO sqlalchemy.engine.base.Engine.0x...0e50
>>> ['new']
>>> sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,154
>>> ['new']
>>> 2010-06-02 09:50:15,157 INFO sqlalchemy.pool.QueuePool.0x...0c90
>>> Connection<_mysql.connection open to 'localhost' at 1b0894d0>
being
>>> returned to pool
>>> sqlalchemy.pool.QueuePool.0x...0c90 INFO 2010-06-02 09:50:15,157
>>> Connection<_mysql.connection open to 'localhost' at 1b0894d0>
being
>>> returned to pool
>>>
>>>
>>> cheers
>>> m
>>>
>>> --
>>> Michael Pheasant
>>> Software Engineer
>>> Queensland Facility for Advanced Bioinformatics
>>> Level 6, QBP
>>> University of Queensland, QLD 4072
>>> T: +61 (0)7 3346 2070
>>> F: +61 (0)7 3346 2101
>>> www.qfab.org
>>>
>>>
>>>
>>> On Tue, Jun 1, 2010 at 11:24 PM, Nate Coraor<nate(a)bx.psu.edu> wrote:
>>>> Michael Pheasant wrote:
>>>>> Using the run.sh script, and the default 'log_level = DEBUG'
>>>>> universe_wsgi.ini file setting gives a huge amount of output.
>>>>>
>>>>> Changing the ini to either log_level = INFO, WARNING or ERROR and i
>>>>> get the same output, including the INFO messages every second.
>>>>>
>>>>> I assumed that WARNING or ERROR would not give the INFO messages; is
>>>>> there some way to not see these?
>>>> Hi Michael,
>>>>
>>>> Can you provide an example of which INFO messages still appear?
>>>> WARNING
>>>> is
>>>> suppressing everything above the WARNING level for me.
>>>>
>>>> --nate
>>>>
>>>>> Cheers
>>>>> m
>>>>>
>>>>> --
>>>>> Michael Pheasant
>>>>> Software Engineer
>>>>> Queensland Facility for Advanced Bioinformatics
>>>>> Level 6, QBP
>>>>> University of Queensland, QLD 4072
>>>>> T: +61 (0)7 3346 2070
>>>>> F: +61 (0)7 3346 2101
>>>>> www.qfab.org
>>>>> _______________________________________________
>>>>> galaxy-dev mailing list
>>>>> galaxy-dev(a)lists.bx.psu.edu
>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>>
>>> _______________________________________________
>>> galaxy-dev mailing list
>>> galaxy-dev(a)lists.bx.psu.edu
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>
>>
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
7:52 p.m.
Am 07.09.2010 20:02, schrieb Nate Coraor:
Michael Siebauer wrote:
> Is there also a way to supress these:
>
> 192.168.3.61 - - [07/Sep/2010:13:05:48 +0200] "POST
> /root/history_item_updates HTTP/1.1" 200 - "http://galaxy/history"
> "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.8) Gecko/20100723
> Ubuntu/10.04 (lucid) Firefox/3.6.8"
>
> Logging Messages?
Just the hits to history_item_updates, or all Apache-style web logging?
--nate
I think all can be removed.
-michael
>
> Thx Michael
>
> Am 06/02/2010 03:15 AM, schrieb Michael Pheasant:
>> Thanks, that fixed it, they were uncommented!
>> CHeers
>> m
>>
>> --
>> Michael Pheasant
>> Software Engineer
>> Queensland Facility for Advanced Bioinformatics
>> Level 6, QBP
>> University of Queensland, QLD 4072
>> T: +61 (0)7 3346 2070
>> F: +61 (0)7 3346 2101
>> www.qfab.org
>>
>>
>>
>> On Wed, Jun 2, 2010 at 9:56 AM, James Taylor<james(a)bx.psu.edu> wrote:
>>> Have you uncommented either of:
>>>
>>> #database_engine_option_echo = true
>>> #database_engine_option_echo_pool = true
>>>
>>> In you universe_wsgi.ini?
>>>
>>> On Jun 1, 2010, at 7:53 PM, Michael Pheasant wrote:
>>>
>>>> using run script with single web server/jobrunner:
>>>> universe_wsgi.ini:
>>>> log_level = WARNING
>>>> enable_job_running = True
>>>>
>>>> *) During the startup sequence there is a bunch of INFO stuff;
>>>>
>>>> 2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
>>>> Created new connection<_mysql.connection open to 'localhost'
at
>>>> 1aab1730>
>>>> sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
>>>> Created new connection<_mysql.connection open to 'localhost'
at
>>>> 1aab1730>
>>>> 2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
>>>> Connection<_mysql.connection open to 'localhost' at
1aab1730>
>>>> checked
>>>> out from pool
>>>> sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
>>>> Connection<_mysql.connection open to 'localhost' at
1aab1730>
>>>> checked
>>>> out from pool
>>>> 2010-06-02 09:49:55,322 INFO sqlalchemy.engine.base.Engine.0x...85d0
>>>> SHOW VARIABLES LIKE 'character_set%%'
>>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,322
>>>> SHOW VARIABLES LIKE 'character_set%%'
>>>> 2010-06-02 09:49:55,322 INFO
>>>> sqlalchemy.engine.base.Engine.0x...85d0 ()
>>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02
>>>> 09:49:55,322 ()
>>>> 2010-06-02 09:49:55,323 INFO sqlalchemy.engine.base.Engine.0x...85d0
>>>> SHOW VARIABLES LIKE 'sql_mode'
>>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,323
>>>> SHOW VARIABLES LIKE 'sql_mode'
>>>> 2010-06-02 09:49:55,323 INFO
>>>> sqlalchemy.engine.base.Engine.0x...85d0 ()
>>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02
>>>> 09:49:55,323 ()
>>>> 2010-06-02 09:49:55,348 INFO sqlalchemy.engine.base.Engine.0x...85d0
>>>> SHOW CREATE TABLE dataset
>>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,348
>>>> SHOW CREATE TABLE dataset
>>>> 2010-06-02 09:49:55,348 INFO
>>>> sqlalchemy.engine.base.Engine.0x...85d0 ()
>>>>
>>>>
>>>> Then every second there is the database ping for jobs;
>>>>
>>>> sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,153
>>>> SELECT job.id AS job_id, job.create_time AS job_create_time,
>>>> job.update_time AS job_update_time, job.history_id AS job_history_id,
>>>> job.library_folder_id AS job_library_folder_id, job.tool_id AS
>>>> job_tool_id, job.tool_version AS job_tool_version, job.state AS
>>>> job_state, job.info AS job_info, job.command_line AS
>>>> job_command_line,
>>>> job.param_filename AS job_param_filename, job.runner_name AS
>>>> job_runner_name_1, job.stdout AS job_stdout, job.stderr AS
>>>> job_stderr,
>>>> job.traceback AS job_traceback, job.session_id AS job_session_id,
>>>> job.job_runner_name AS job_job_runner_name,
>>>> job.job_runner_external_id
>>>> AS job_job_runner_external_id,
>>>> library_dataset_dataset_association_1.id AS
>>>> library_dataset_dataset_association_1_id,
>>>> library_dataset_dataset_association_1.library_dataset_id AS
>>>> library_dataset_dataset_association_1_library_dataset_id,
>>>> library_dataset_dataset_association_1.dataset_id AS
>>>> library_dataset_dataset_association_1_dataset_id,
>>>> library_dataset_dataset_association_1.create_time AS
>>>> library_dataset_dataset_association_1_create_time,
>>>> library_dataset_dataset_association_1.update_time AS
>>>> library_dataset_dataset_association_1_update_time,
>>>>
>>>>
library_dataset_dataset_association_1.copied_from_history_dataset_association_id
>>>>
>>>> AS
>>>>
library_dataset_dataset_association_1_copied_from_history_dataset_association_id,
>>>>
>>>>
>>>>
library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id
>>>>
>>>> AS
>>>>
library_dataset_dataset_association_1_copied_from_library_dataset_dataset_association_id,
>>>>
>>>> library_dataset_dataset_association_1.name AS
>>>> library_dataset_dataset_association_1_name,
>>>> library_dataset_dataset_association_1.info AS
>>>> library_dataset_dataset_association_1_info,
>>>> library_dataset_dataset_association_1.blurb AS
>>>> library_dataset_dataset_association_1_blurb,
>>>> library_dataset_dataset_association_1.peek AS
>>>> library_dataset_dataset_association_1_peek,
>>>> library_dataset_dataset_association_1.extension AS
>>>> library_dataset_dataset_association_1_extension,
>>>> library_dataset_dataset_association_1.metadata AS
>>>> library_dataset_dataset_association_1_metadata,
>>>> library_dataset_dataset_association_1.parent_id AS
>>>> library_dataset_dataset_association_1_parent_id,
>>>> library_dataset_dataset_association_1.designation AS
>>>> library_dataset_dataset_association_1_designation,
>>>> library_dataset_dataset_association_1.deleted AS
>>>> library_dataset_dataset_association_1_deleted,
>>>> library_dataset_dataset_association_1.visible AS
>>>> library_dataset_dataset_association_1_visible,
>>>> library_dataset_dataset_association_1.user_id AS
>>>> library_dataset_dataset_association_1_user_id,
>>>> library_dataset_dataset_association_1.message AS
>>>> library_dataset_dataset_association_1_message,
>>>> job_to_output_library_dataset_1.id AS
>>>> job_to_output_library_dataset_1_id,
>>>> job_to_output_library_dataset_1.job_id AS
>>>> job_to_output_library_dataset_1_job_id,
>>>> job_to_output_library_dataset_1.ldda_id AS
>>>> job_to_output_library_dataset_1_ldda_id,
>>>> job_to_output_library_dataset_1.name AS
>>>> job_to_output_library_dataset_1_name, dataset_1.id AS dataset_1_id,
>>>> dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time
>>>> AS dataset_1_update_time, dataset_1.state AS dataset_1_state,
>>>> dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS
>>>> dataset_1_purged, dataset_1.purgable AS dataset_1_purgable,
>>>> dataset_1.external_filename AS dataset_1_external_filename,
>>>> dataset_1._extra_files_path AS dataset_1__extra_files_path,
>>>> dataset_1.file_size AS dataset_1_file_size,
>>>> history_dataset_association_1.id AS history_dataset_association_1_id,
>>>> history_dataset_association_1.history_id AS
>>>> history_dataset_association_1_history_id,
>>>> history_dataset_association_1.dataset_id AS
>>>> history_dataset_association_1_dataset_id,
>>>> history_dataset_association_1.create_time AS
>>>> history_dataset_association_1_create_time,
>>>> history_dataset_association_1.update_time AS
>>>> history_dataset_association_1_update_time,
>>>> history_dataset_association_1.copied_from_history_dataset_association_id
>>>>
>>>> AS
>>>>
history_dataset_association_1_copied_from_history_dataset_association_id,
>>>>
>>>>
>>>>
history_dataset_association_1.copied_from_library_dataset_dataset_association_id
>>>>
>>>> AS
>>>>
history_dataset_association_1_copied_from_library_dataset_dataset_association_id,
>>>>
>>>> history_dataset_association_1.hid AS
>>>> history_dataset_association_1_hid, history_dataset_association_1.name
>>>> AS history_dataset_association_1_name,
>>>> history_dataset_association_1.info AS
>>>> history_dataset_association_1_info,
>>>> history_dataset_association_1.blurb AS
>>>> history_dataset_association_1_blurb,
>>>> history_dataset_association_1.peek AS
>>>> history_dataset_association_1_peek,
>>>> history_dataset_association_1.extension AS
>>>> history_dataset_association_1_extension,
>>>> history_dataset_association_1.metadata AS
>>>> history_dataset_association_1_metadata,
>>>> history_dataset_association_1.parent_id AS
>>>> history_dataset_association_1_parent_id,
>>>> history_dataset_association_1.designation AS
>>>> history_dataset_association_1_designation,
>>>> history_dataset_association_1.deleted AS
>>>> history_dataset_association_1_deleted,
>>>> history_dataset_association_1.visible AS
>>>> history_dataset_association_1_visible, job_to_input_dataset_1.id AS
>>>> job_to_input_dataset_1_id, job_to_input_dataset_1.job_id AS
>>>> job_to_input_dataset_1_job_id, job_to_input_dataset_1.dataset_id AS
>>>> job_to_input_dataset_1_dataset_id, job_to_input_dataset_1.name AS
>>>> job_to_input_dataset_1_name, dataset_2.id AS dataset_2_id,
>>>> dataset_2.create_time AS dataset_2_create_time, dataset_2.update_time
>>>> AS dataset_2_update_time, dataset_2.state AS dataset_2_state,
>>>> dataset_2.deleted AS dataset_2_deleted, dataset_2.purged AS
>>>> dataset_2_purged, dataset_2.purgable AS dataset_2_purgable,
>>>> dataset_2.external_filename AS dataset_2_external_filename,
>>>> dataset_2._extra_files_path AS dataset_2__extra_files_path,
>>>> dataset_2.file_size AS dataset_2_file_size,
>>>> history_dataset_association_2.id AS history_dataset_association_2_id,
>>>> history_dataset_association_2.history_id AS
>>>> history_dataset_association_2_history_id,
>>>> history_dataset_association_2.dataset_id AS
>>>> history_dataset_association_2_dataset_id,
>>>> history_dataset_association_2.create_time AS
>>>> history_dataset_association_2_create_time,
>>>> history_dataset_association_2.update_time AS
>>>> history_dataset_association_2_update_time,
>>>> history_dataset_association_2.copied_from_history_dataset_association_id
>>>>
>>>> AS
>>>>
history_dataset_association_2_copied_from_history_dataset_association_id,
>>>>
>>>>
>>>>
history_dataset_association_2.copied_from_library_dataset_dataset_association_id
>>>>
>>>> AS
>>>>
history_dataset_association_2_copied_from_library_dataset_dataset_association_id,
>>>>
>>>> history_dataset_association_2.hid AS
>>>> history_dataset_association_2_hid, history_dataset_association_2.name
>>>> AS history_dataset_association_2_name,
>>>> history_dataset_association_2.info AS
>>>> history_dataset_association_2_info,
>>>> history_dataset_association_2.blurb AS
>>>> history_dataset_association_2_blurb,
>>>> history_dataset_association_2.peek AS
>>>> history_dataset_association_2_peek,
>>>> history_dataset_association_2.extension AS
>>>> history_dataset_association_2_extension,
>>>> history_dataset_association_2.metadata AS
>>>> history_dataset_association_2_metadata,
>>>> history_dataset_association_2.parent_id AS
>>>> history_dataset_association_2_parent_id,
>>>> history_dataset_association_2.designation AS
>>>> history_dataset_association_2_designation,
>>>> history_dataset_association_2.deleted AS
>>>> history_dataset_association_2_deleted,
>>>> history_dataset_association_2.visible AS
>>>> history_dataset_association_2_visible, job_to_output_dataset_1.id AS
>>>> job_to_output_dataset_1_id, job_to_output_dataset_1.job_id AS
>>>> job_to_output_dataset_1_job_id, job_to_output_dataset_1.dataset_id AS
>>>> job_to_output_dataset_1_dataset_id, job_to_output_dataset_1.name AS
>>>> job_to_output_dataset_1_name
>>>> FROM job LEFT OUTER JOIN job_to_output_library_dataset AS
>>>> job_to_output_library_dataset_1 ON job.id =
>>>> job_to_output_library_dataset_1.job_id LEFT OUTER JOIN
>>>> library_dataset_dataset_association AS
>>>> library_dataset_dataset_association_1 ON
>>>> library_dataset_dataset_association_1.id =
>>>> job_to_output_library_dataset_1.ldda_id LEFT OUTER JOIN
>>>> job_to_input_dataset AS job_to_input_dataset_1 ON job.id =
>>>> job_to_input_dataset_1.job_id LEFT OUTER JOIN
>>>> history_dataset_association AS history_dataset_association_1 ON
>>>> history_dataset_association_1.id = job_to_input_dataset_1.dataset_id
>>>> LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id =
>>>> history_dataset_association_1.dataset_id LEFT OUTER JOIN
>>>> job_to_output_dataset AS job_to_output_dataset_1 ON job.id =
>>>> job_to_output_dataset_1.job_id LEFT OUTER JOIN
>>>> history_dataset_association AS history_dataset_association_2 ON
>>>> history_dataset_association_2.id = job_to_output_dataset_1.dataset_id
>>>> LEFT OUTER JOIN dataset AS dataset_2 ON dataset_2.id =
>>>> history_dataset_association_2.dataset_id
>>>> WHERE job.state = %s
>>>> 2010-06-02 09:50:15,154 INFO sqlalchemy.engine.base.Engine.0x...0e50
>>>> ['new']
>>>> sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,154
>>>> ['new']
>>>> 2010-06-02 09:50:15,157 INFO sqlalchemy.pool.QueuePool.0x...0c90
>>>> Connection<_mysql.connection open to 'localhost' at
1b0894d0> being
>>>> returned to pool
>>>> sqlalchemy.pool.QueuePool.0x...0c90 INFO 2010-06-02 09:50:15,157
>>>> Connection<_mysql.connection open to 'localhost' at
1b0894d0> being
>>>> returned to pool
>>>>
>>>>
>>>> cheers
>>>> m
>>>>
>>>> --
>>>> Michael Pheasant
>>>> Software Engineer
>>>> Queensland Facility for Advanced Bioinformatics
>>>> Level 6, QBP
>>>> University of Queensland, QLD 4072
>>>> T: +61 (0)7 3346 2070
>>>> F: +61 (0)7 3346 2101
>>>> www.qfab.org
>>>>
>>>>
>>>>
>>>> On Tue, Jun 1, 2010 at 11:24 PM, Nate Coraor<nate(a)bx.psu.edu>
wrote:
>>>>> Michael Pheasant wrote:
>>>>>> Using the run.sh script, and the default 'log_level =
DEBUG'
>>>>>> universe_wsgi.ini file setting gives a huge amount of output.
>>>>>>
>>>>>> Changing the ini to either log_level = INFO, WARNING or ERROR and
i
>>>>>> get the same output, including the INFO messages every second.
>>>>>>
>>>>>> I assumed that WARNING or ERROR would not give the INFO
>>>>>> messages; is
>>>>>> there some way to not see these?
>>>>> Hi Michael,
>>>>>
>>>>> Can you provide an example of which INFO messages still appear?
>>>>> WARNING
>>>>> is
>>>>> suppressing everything above the WARNING level for me.
>>>>>
>>>>> --nate
>>>>>
>>>>>> Cheers
>>>>>> m
>>>>>>
>>>>>> --
>>>>>> Michael Pheasant
>>>>>> Software Engineer
>>>>>> Queensland Facility for Advanced Bioinformatics
>>>>>> Level 6, QBP
>>>>>> University of Queensland, QLD 4072
>>>>>> T: +61 (0)7 3346 2070
>>>>>> F: +61 (0)7 3346 2101
>>>>>> www.qfab.org
>>>>>> _______________________________________________
>>>>>> galaxy-dev mailing list
>>>>>> galaxy-dev(a)lists.bx.psu.edu
>>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>>>
>>>> _______________________________________________
>>>> galaxy-dev mailing list
>>>> galaxy-dev(a)lists.bx.psu.edu
>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>>
>>>
>> _______________________________________________
>> galaxy-dev mailing list
>> galaxy-dev(a)lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
8:39 p.m.
Michael Siebauer wrote:
Am 07.09.2010 20:02, schrieb Nate Coraor:
> Michael Siebauer wrote:
>> Is there also a way to supress these:
>>
>> 192.168.3.61 - - [07/Sep/2010:13:05:48 +0200] "POST
>> /root/history_item_updates HTTP/1.1" 200 -
"http://galaxy/history"
>> "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.8) Gecko/20100723
>> Ubuntu/10.04 (lucid) Firefox/3.6.8"
>>
>> Logging Messages?
> Just the hits to history_item_updates, or all Apache-style web logging?
>
> --nate
I think all can be removed.
Set the following under [app:main] in universe_wsgi.ini:
use_translogger = False
--nate
-michael
>> Thx Michael
>>
>> Am 06/02/2010 03:15 AM, schrieb Michael Pheasant:
>>> Thanks, that fixed it, they were uncommented!
>>> CHeers
>>> m
>>>
>>> --
>>> Michael Pheasant
>>> Software Engineer
>>> Queensland Facility for Advanced Bioinformatics
>>> Level 6, QBP
>>> University of Queensland, QLD 4072
>>> T: +61 (0)7 3346 2070
>>> F: +61 (0)7 3346 2101
>>> www.qfab.org
>>>
>>>
>>>
>>> On Wed, Jun 2, 2010 at 9:56 AM, James Taylor<james(a)bx.psu.edu> wrote:
>>>> Have you uncommented either of:
>>>>
>>>> #database_engine_option_echo = true
>>>> #database_engine_option_echo_pool = true
>>>>
>>>> In you universe_wsgi.ini?
>>>>
>>>> On Jun 1, 2010, at 7:53 PM, Michael Pheasant wrote:
>>>>
>>>>> using run script with single web server/jobrunner:
>>>>> universe_wsgi.ini:
>>>>> log_level = WARNING
>>>>> enable_job_running = True
>>>>>
>>>>> *) During the startup sequence there is a bunch of INFO stuff;
>>>>>
>>>>> 2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
>>>>> Created new connection<_mysql.connection open to
'localhost' at
>>>>> 1aab1730>
>>>>> sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
>>>>> Created new connection<_mysql.connection open to
'localhost' at
>>>>> 1aab1730>
>>>>> 2010-06-02 09:49:55,321 INFO sqlalchemy.pool.QueuePool.0x...8410
>>>>> Connection<_mysql.connection open to 'localhost' at
1aab1730>
>>>>> checked
>>>>> out from pool
>>>>> sqlalchemy.pool.QueuePool.0x...8410 INFO 2010-06-02 09:49:55,321
>>>>> Connection<_mysql.connection open to 'localhost' at
1aab1730>
>>>>> checked
>>>>> out from pool
>>>>> 2010-06-02 09:49:55,322 INFO sqlalchemy.engine.base.Engine.0x...85d0
>>>>> SHOW VARIABLES LIKE 'character_set%%'
>>>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,322
>>>>> SHOW VARIABLES LIKE 'character_set%%'
>>>>> 2010-06-02 09:49:55,322 INFO
>>>>> sqlalchemy.engine.base.Engine.0x...85d0 ()
>>>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02
>>>>> 09:49:55,322 ()
>>>>> 2010-06-02 09:49:55,323 INFO sqlalchemy.engine.base.Engine.0x...85d0
>>>>> SHOW VARIABLES LIKE 'sql_mode'
>>>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,323
>>>>> SHOW VARIABLES LIKE 'sql_mode'
>>>>> 2010-06-02 09:49:55,323 INFO
>>>>> sqlalchemy.engine.base.Engine.0x...85d0 ()
>>>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02
>>>>> 09:49:55,323 ()
>>>>> 2010-06-02 09:49:55,348 INFO sqlalchemy.engine.base.Engine.0x...85d0
>>>>> SHOW CREATE TABLE dataset
>>>>> sqlalchemy.engine.base.Engine.0x...85d0 INFO 2010-06-02 09:49:55,348
>>>>> SHOW CREATE TABLE dataset
>>>>> 2010-06-02 09:49:55,348 INFO
>>>>> sqlalchemy.engine.base.Engine.0x...85d0 ()
>>>>>
>>>>>
>>>>> Then every second there is the database ping for jobs;
>>>>>
>>>>> sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,153
>>>>> SELECT job.id AS job_id, job.create_time AS job_create_time,
>>>>> job.update_time AS job_update_time, job.history_id AS
job_history_id,
>>>>> job.library_folder_id AS job_library_folder_id, job.tool_id AS
>>>>> job_tool_id, job.tool_version AS job_tool_version, job.state AS
>>>>> job_state, job.info AS job_info, job.command_line AS
>>>>> job_command_line,
>>>>> job.param_filename AS job_param_filename, job.runner_name AS
>>>>> job_runner_name_1, job.stdout AS job_stdout, job.stderr AS
>>>>> job_stderr,
>>>>> job.traceback AS job_traceback, job.session_id AS job_session_id,
>>>>> job.job_runner_name AS job_job_runner_name,
>>>>> job.job_runner_external_id
>>>>> AS job_job_runner_external_id,
>>>>> library_dataset_dataset_association_1.id AS
>>>>> library_dataset_dataset_association_1_id,
>>>>> library_dataset_dataset_association_1.library_dataset_id AS
>>>>> library_dataset_dataset_association_1_library_dataset_id,
>>>>> library_dataset_dataset_association_1.dataset_id AS
>>>>> library_dataset_dataset_association_1_dataset_id,
>>>>> library_dataset_dataset_association_1.create_time AS
>>>>> library_dataset_dataset_association_1_create_time,
>>>>> library_dataset_dataset_association_1.update_time AS
>>>>> library_dataset_dataset_association_1_update_time,
>>>>>
>>>>>
library_dataset_dataset_association_1.copied_from_history_dataset_association_id
>>>>>
>>>>> AS
>>>>>
library_dataset_dataset_association_1_copied_from_history_dataset_association_id,
>>>>>
>>>>>
>>>>>
library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id
>>>>>
>>>>> AS
>>>>>
library_dataset_dataset_association_1_copied_from_library_dataset_dataset_association_id,
>>>>>
>>>>> library_dataset_dataset_association_1.name AS
>>>>> library_dataset_dataset_association_1_name,
>>>>> library_dataset_dataset_association_1.info AS
>>>>> library_dataset_dataset_association_1_info,
>>>>> library_dataset_dataset_association_1.blurb AS
>>>>> library_dataset_dataset_association_1_blurb,
>>>>> library_dataset_dataset_association_1.peek AS
>>>>> library_dataset_dataset_association_1_peek,
>>>>> library_dataset_dataset_association_1.extension AS
>>>>> library_dataset_dataset_association_1_extension,
>>>>> library_dataset_dataset_association_1.metadata AS
>>>>> library_dataset_dataset_association_1_metadata,
>>>>> library_dataset_dataset_association_1.parent_id AS
>>>>> library_dataset_dataset_association_1_parent_id,
>>>>> library_dataset_dataset_association_1.designation AS
>>>>> library_dataset_dataset_association_1_designation,
>>>>> library_dataset_dataset_association_1.deleted AS
>>>>> library_dataset_dataset_association_1_deleted,
>>>>> library_dataset_dataset_association_1.visible AS
>>>>> library_dataset_dataset_association_1_visible,
>>>>> library_dataset_dataset_association_1.user_id AS
>>>>> library_dataset_dataset_association_1_user_id,
>>>>> library_dataset_dataset_association_1.message AS
>>>>> library_dataset_dataset_association_1_message,
>>>>> job_to_output_library_dataset_1.id AS
>>>>> job_to_output_library_dataset_1_id,
>>>>> job_to_output_library_dataset_1.job_id AS
>>>>> job_to_output_library_dataset_1_job_id,
>>>>> job_to_output_library_dataset_1.ldda_id AS
>>>>> job_to_output_library_dataset_1_ldda_id,
>>>>> job_to_output_library_dataset_1.name AS
>>>>> job_to_output_library_dataset_1_name, dataset_1.id AS dataset_1_id,
>>>>> dataset_1.create_time AS dataset_1_create_time,
dataset_1.update_time
>>>>> AS dataset_1_update_time, dataset_1.state AS dataset_1_state,
>>>>> dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS
>>>>> dataset_1_purged, dataset_1.purgable AS dataset_1_purgable,
>>>>> dataset_1.external_filename AS dataset_1_external_filename,
>>>>> dataset_1._extra_files_path AS dataset_1__extra_files_path,
>>>>> dataset_1.file_size AS dataset_1_file_size,
>>>>> history_dataset_association_1.id AS
history_dataset_association_1_id,
>>>>> history_dataset_association_1.history_id AS
>>>>> history_dataset_association_1_history_id,
>>>>> history_dataset_association_1.dataset_id AS
>>>>> history_dataset_association_1_dataset_id,
>>>>> history_dataset_association_1.create_time AS
>>>>> history_dataset_association_1_create_time,
>>>>> history_dataset_association_1.update_time AS
>>>>> history_dataset_association_1_update_time,
>>>>>
history_dataset_association_1.copied_from_history_dataset_association_id
>>>>>
>>>>> AS
>>>>>
history_dataset_association_1_copied_from_history_dataset_association_id,
>>>>>
>>>>>
>>>>>
history_dataset_association_1.copied_from_library_dataset_dataset_association_id
>>>>>
>>>>> AS
>>>>>
history_dataset_association_1_copied_from_library_dataset_dataset_association_id,
>>>>>
>>>>> history_dataset_association_1.hid AS
>>>>> history_dataset_association_1_hid,
history_dataset_association_1.name
>>>>> AS history_dataset_association_1_name,
>>>>> history_dataset_association_1.info AS
>>>>> history_dataset_association_1_info,
>>>>> history_dataset_association_1.blurb AS
>>>>> history_dataset_association_1_blurb,
>>>>> history_dataset_association_1.peek AS
>>>>> history_dataset_association_1_peek,
>>>>> history_dataset_association_1.extension AS
>>>>> history_dataset_association_1_extension,
>>>>> history_dataset_association_1.metadata AS
>>>>> history_dataset_association_1_metadata,
>>>>> history_dataset_association_1.parent_id AS
>>>>> history_dataset_association_1_parent_id,
>>>>> history_dataset_association_1.designation AS
>>>>> history_dataset_association_1_designation,
>>>>> history_dataset_association_1.deleted AS
>>>>> history_dataset_association_1_deleted,
>>>>> history_dataset_association_1.visible AS
>>>>> history_dataset_association_1_visible, job_to_input_dataset_1.id AS
>>>>> job_to_input_dataset_1_id, job_to_input_dataset_1.job_id AS
>>>>> job_to_input_dataset_1_job_id, job_to_input_dataset_1.dataset_id AS
>>>>> job_to_input_dataset_1_dataset_id, job_to_input_dataset_1.name AS
>>>>> job_to_input_dataset_1_name, dataset_2.id AS dataset_2_id,
>>>>> dataset_2.create_time AS dataset_2_create_time,
dataset_2.update_time
>>>>> AS dataset_2_update_time, dataset_2.state AS dataset_2_state,
>>>>> dataset_2.deleted AS dataset_2_deleted, dataset_2.purged AS
>>>>> dataset_2_purged, dataset_2.purgable AS dataset_2_purgable,
>>>>> dataset_2.external_filename AS dataset_2_external_filename,
>>>>> dataset_2._extra_files_path AS dataset_2__extra_files_path,
>>>>> dataset_2.file_size AS dataset_2_file_size,
>>>>> history_dataset_association_2.id AS
history_dataset_association_2_id,
>>>>> history_dataset_association_2.history_id AS
>>>>> history_dataset_association_2_history_id,
>>>>> history_dataset_association_2.dataset_id AS
>>>>> history_dataset_association_2_dataset_id,
>>>>> history_dataset_association_2.create_time AS
>>>>> history_dataset_association_2_create_time,
>>>>> history_dataset_association_2.update_time AS
>>>>> history_dataset_association_2_update_time,
>>>>>
history_dataset_association_2.copied_from_history_dataset_association_id
>>>>>
>>>>> AS
>>>>>
history_dataset_association_2_copied_from_history_dataset_association_id,
>>>>>
>>>>>
>>>>>
history_dataset_association_2.copied_from_library_dataset_dataset_association_id
>>>>>
>>>>> AS
>>>>>
history_dataset_association_2_copied_from_library_dataset_dataset_association_id,
>>>>>
>>>>> history_dataset_association_2.hid AS
>>>>> history_dataset_association_2_hid,
history_dataset_association_2.name
>>>>> AS history_dataset_association_2_name,
>>>>> history_dataset_association_2.info AS
>>>>> history_dataset_association_2_info,
>>>>> history_dataset_association_2.blurb AS
>>>>> history_dataset_association_2_blurb,
>>>>> history_dataset_association_2.peek AS
>>>>> history_dataset_association_2_peek,
>>>>> history_dataset_association_2.extension AS
>>>>> history_dataset_association_2_extension,
>>>>> history_dataset_association_2.metadata AS
>>>>> history_dataset_association_2_metadata,
>>>>> history_dataset_association_2.parent_id AS
>>>>> history_dataset_association_2_parent_id,
>>>>> history_dataset_association_2.designation AS
>>>>> history_dataset_association_2_designation,
>>>>> history_dataset_association_2.deleted AS
>>>>> history_dataset_association_2_deleted,
>>>>> history_dataset_association_2.visible AS
>>>>> history_dataset_association_2_visible, job_to_output_dataset_1.id AS
>>>>> job_to_output_dataset_1_id, job_to_output_dataset_1.job_id AS
>>>>> job_to_output_dataset_1_job_id, job_to_output_dataset_1.dataset_id
AS
>>>>> job_to_output_dataset_1_dataset_id, job_to_output_dataset_1.name AS
>>>>> job_to_output_dataset_1_name
>>>>> FROM job LEFT OUTER JOIN job_to_output_library_dataset AS
>>>>> job_to_output_library_dataset_1 ON job.id =
>>>>> job_to_output_library_dataset_1.job_id LEFT OUTER JOIN
>>>>> library_dataset_dataset_association AS
>>>>> library_dataset_dataset_association_1 ON
>>>>> library_dataset_dataset_association_1.id =
>>>>> job_to_output_library_dataset_1.ldda_id LEFT OUTER JOIN
>>>>> job_to_input_dataset AS job_to_input_dataset_1 ON job.id =
>>>>> job_to_input_dataset_1.job_id LEFT OUTER JOIN
>>>>> history_dataset_association AS history_dataset_association_1 ON
>>>>> history_dataset_association_1.id = job_to_input_dataset_1.dataset_id
>>>>> LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id =
>>>>> history_dataset_association_1.dataset_id LEFT OUTER JOIN
>>>>> job_to_output_dataset AS job_to_output_dataset_1 ON job.id =
>>>>> job_to_output_dataset_1.job_id LEFT OUTER JOIN
>>>>> history_dataset_association AS history_dataset_association_2 ON
>>>>> history_dataset_association_2.id =
job_to_output_dataset_1.dataset_id
>>>>> LEFT OUTER JOIN dataset AS dataset_2 ON dataset_2.id =
>>>>> history_dataset_association_2.dataset_id
>>>>> WHERE job.state = %s
>>>>> 2010-06-02 09:50:15,154 INFO sqlalchemy.engine.base.Engine.0x...0e50
>>>>> ['new']
>>>>> sqlalchemy.engine.base.Engine.0x...0e50 INFO 2010-06-02 09:50:15,154
>>>>> ['new']
>>>>> 2010-06-02 09:50:15,157 INFO sqlalchemy.pool.QueuePool.0x...0c90
>>>>> Connection<_mysql.connection open to 'localhost' at
1b0894d0> being
>>>>> returned to pool
>>>>> sqlalchemy.pool.QueuePool.0x...0c90 INFO 2010-06-02 09:50:15,157
>>>>> Connection<_mysql.connection open to 'localhost' at
1b0894d0> being
>>>>> returned to pool
>>>>>
>>>>>
>>>>> cheers
>>>>> m
>>>>>
>>>>> --
>>>>> Michael Pheasant
>>>>> Software Engineer
>>>>> Queensland Facility for Advanced Bioinformatics
>>>>> Level 6, QBP
>>>>> University of Queensland, QLD 4072
>>>>> T: +61 (0)7 3346 2070
>>>>> F: +61 (0)7 3346 2101
>>>>> www.qfab.org
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Jun 1, 2010 at 11:24 PM, Nate Coraor<nate(a)bx.psu.edu>
wrote:
>>>>>> Michael Pheasant wrote:
>>>>>>> Using the run.sh script, and the default 'log_level =
DEBUG'
>>>>>>> universe_wsgi.ini file setting gives a huge amount of
output.
>>>>>>>
>>>>>>> Changing the ini to either log_level = INFO, WARNING or ERROR
and i
>>>>>>> get the same output, including the INFO messages every
second.
>>>>>>>
>>>>>>> I assumed that WARNING or ERROR would not give the INFO
>>>>>>> messages; is
>>>>>>> there some way to not see these?
>>>>>> Hi Michael,
>>>>>>
>>>>>> Can you provide an example of which INFO messages still appear?
>>>>>> WARNING
>>>>>> is
>>>>>> suppressing everything above the WARNING level for me.
>>>>>>
>>>>>> --nate
>>>>>>
>>>>>>> Cheers
>>>>>>> m
>>>>>>>
>>>>>>> --
>>>>>>> Michael Pheasant
>>>>>>> Software Engineer
>>>>>>> Queensland Facility for Advanced Bioinformatics
>>>>>>> Level 6, QBP
>>>>>>> University of Queensland, QLD 4072
>>>>>>> T: +61 (0)7 3346 2070
>>>>>>> F: +61 (0)7 3346 2101
>>>>>>> www.qfab.org
>>>>>>> _______________________________________________
>>>>>>> galaxy-dev mailing list
>>>>>>> galaxy-dev(a)lists.bx.psu.edu
>>>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>>> _______________________________________________
>>>>> galaxy-dev mailing list
>>>>> galaxy-dev(a)lists.bx.psu.edu
>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>>>
>>> _______________________________________________
>>> galaxy-dev mailing list
>>> galaxy-dev(a)lists.bx.psu.edu
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>> _______________________________________________
>> galaxy-dev mailing list
>> galaxy-dev(a)lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
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8 comments
4 participants
participants (4)
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James Taylor -
Michael Pheasant -
Michael Siebauer -
Nate Coraor