DB schema upgrade problem (79 -> 85)
Dear all, Today I upgraded our NBIC server from an older release (fetched on July 5th, 2011) to the latest version in galaxy-dist. After execute "hg update" and "sh manage_db upgrade" and merge some local configurations, I successfully restarted the server. However once I access the server from a web browser, Galaxy crashed. Log file complains that some tables don't exist: == ProgrammingError: (ProgrammingError) (1146, "Table 'galaxy.user_quota_association' doesn't exist") u'SELECT user_quota_association.id AS user_quota_association_id, user_quota_association.user_id AS user_quota_association_user_id, user_quota_association.quota_id AS user_quota_association_quota_id, user_quota_association.create_time AS user_quota_association_create_time, user_quota_association.update_time AS user_quota_association_update_time \nFROM user_quota_association \nWHERE %s = user_quota_association.user_id' [1L] == A check in mysql confirms that only the following 3 tables were added during the migration from schema 79 to 85: * default_quota_association * quota * tool_shed_repository The following 9 tables are missing: cloud_*, user_quota_association, group_quota_association Has anyone experienced a similar problem? Any hint on how to solve this is highly appreciate! Thanks, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_mei Mobile: +31 6 41709231
On Dec 5, 2011, at 3:02 PM, Leon Mei wrote:
Dear all,
Today I upgraded our NBIC server from an older release (fetched on July 5th, 2011) to the latest version in galaxy-dist. After execute "hg update" and "sh manage_db upgrade" and merge some local configurations, I successfully restarted the server. However once I access the server from a web browser, Galaxy crashed.
Log file complains that some tables don't exist: == ProgrammingError: (ProgrammingError) (1146, "Table 'galaxy.user_quota_association' doesn't exist") u'SELECT user_quota_association.id AS user_quota_association_id, user_quota_association.user_id AS user_quota_association_user_id, user_quota_association.quota_id AS user_quota_association_quota_id, user_quota_association.create_time AS user_quota_association_create_time, user_quota_association.update_time AS user_quota_association_update_time \nFROM user_quota_association \nWHERE %s = user_quota_association.user_id' [1L] ==
A check in mysql confirms that only the following 3 tables were added during the migration from schema 79 to 85: * default_quota_association * quota * tool_shed_repository
The following 9 tables are missing: cloud_*, user_quota_association, group_quota_association
Hi Leon, Were there any errors output when you ran mange_db.sh upgrade? --nate
Has anyone experienced a similar problem? Any hint on how to solve this is highly appreciate!
Thanks, Leon
-- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_mei Mobile: +31 6 41709231 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Nate, Here's the output of the migration: == galaxy@galaxy2:~/prog/galaxy-2011-12-5$ sh manage_db.sh upgrade 79 -> 80... Migration script to create tables for disk quotas. done 80 -> 81... Migration script to add a 'tool_version' column to the hda/ldda tables. done 81 -> 82... Migration script to add the tool_shed_repository table. done 82 -> 83... Migration script to add 'prepare_input_files_cmd' column to the task table and to rename a column. done 83 -> 84... Migration script to add 'ldda_id' column to the implicitly_converted_dataset_association table. done 84 -> 85... Migration script to add 'info' column to the task table. done == Thanks, Leon On Mon, Dec 5, 2011 at 9:11 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Dec 5, 2011, at 3:02 PM, Leon Mei wrote:
Dear all,
Today I upgraded our NBIC server from an older release (fetched on July 5th, 2011) to the latest version in galaxy-dist. After execute "hg update" and "sh manage_db upgrade" and merge some local configurations, I successfully restarted the server. However once I access the server from a web browser, Galaxy crashed.
Log file complains that some tables don't exist: == ProgrammingError: (ProgrammingError) (1146, "Table 'galaxy.user_quota_association' doesn't exist") u'SELECT user_quota_association.id AS user_quota_association_id, user_quota_association.user_id AS user_quota_association_user_id, user_quota_association.quota_id AS user_quota_association_quota_id, user_quota_association.create_time AS user_quota_association_create_time, user_quota_association.update_time AS user_quota_association_update_time \nFROM user_quota_association \nWHERE %s = user_quota_association.user_id' [1L] ==
A check in mysql confirms that only the following 3 tables were added during the migration from schema 79 to 85: * default_quota_association * quota * tool_shed_repository
The following 9 tables are missing: cloud_*, user_quota_association, group_quota_association
Hi Leon,
Were there any errors output when you ran mange_db.sh upgrade?
--nate
Has anyone experienced a similar problem? Any hint on how to solve this
is highly appreciate!
Thanks, Leon
-- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_mei Mobile: +31 6 41709231 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_mei Mobile: +31 6 41709231
Hi Nate, Here's the schema dump from our current Galaxy. Maybe this can help you to identify something fishy. Is it safe to do a manual DB upgrade based on the scripts in ./lib/galaxy/model/migrate/versions/? Thanks, Leon On Mon, Dec 5, 2011 at 9:22 PM, Leon Mei <hailiang.mei@nbic.nl> wrote:
Hi Nate,
Here's the output of the migration:
== galaxy@galaxy2:~/prog/galaxy-2011-12-5$ sh manage_db.sh upgrade 79 -> 80...
Migration script to create tables for disk quotas.
done 80 -> 81...
Migration script to add a 'tool_version' column to the hda/ldda tables.
done 81 -> 82...
Migration script to add the tool_shed_repository table.
done 82 -> 83...
Migration script to add 'prepare_input_files_cmd' column to the task table and to rename a column.
done 83 -> 84...
Migration script to add 'ldda_id' column to the implicitly_converted_dataset_association table.
done 84 -> 85...
Migration script to add 'info' column to the task table.
done ==
Thanks, Leon
On Mon, Dec 5, 2011 at 9:11 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Dec 5, 2011, at 3:02 PM, Leon Mei wrote:
Dear all,
Today I upgraded our NBIC server from an older release (fetched on July 5th, 2011) to the latest version in galaxy-dist. After execute "hg update" and "sh manage_db upgrade" and merge some local configurations, I successfully restarted the server. However once I access the server from a web browser, Galaxy crashed.
Log file complains that some tables don't exist: == ProgrammingError: (ProgrammingError) (1146, "Table 'galaxy.user_quota_association' doesn't exist") u'SELECT user_quota_association.id AS user_quota_association_id, user_quota_association.user_id AS user_quota_association_user_id, user_quota_association.quota_id AS user_quota_association_quota_id, user_quota_association.create_time AS user_quota_association_create_time, user_quota_association.update_time AS user_quota_association_update_time \nFROM user_quota_association \nWHERE %s = user_quota_association.user_id' [1L] ==
A check in mysql confirms that only the following 3 tables were added during the migration from schema 79 to 85: * default_quota_association * quota * tool_shed_repository
The following 9 tables are missing: cloud_*, user_quota_association, group_quota_association
Hi Leon,
Were there any errors output when you ran mange_db.sh upgrade?
--nate
Has anyone experienced a similar problem? Any hint on how to solve this
is highly appreciate!
Thanks, Leon
-- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_mei Mobile: +31 6 41709231 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_mei Mobile: +31 6 41709231
-- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_mei Mobile: +31 6 41709231
On Dec 6, 2011, at 7:31 AM, Leon Mei wrote:
Hi Nate,
Here's the schema dump from our current Galaxy. Maybe this can help you to identify something fishy.
Is it safe to do a manual DB upgrade based on the scripts in ./lib/galaxy/model/migrate/versions/?
Anything is safe as long as you back up your database first. You could also make a copy of it and manually upgrade that. If ALL of the changes >= 80 are missing, you can update your migrate_version table back to 79 and retry with manage_db.sh. If not, you may be able to manage_db.sh downgrade 79 and then retry. I'd suggest opening the migration scripts >= 80 and changing log.debug to log.error, most likely creation errors are being silently dropped by the default logging configuration. --nate
Thanks, Leon
On Mon, Dec 5, 2011 at 9:22 PM, Leon Mei <hailiang.mei@nbic.nl> wrote: Hi Nate,
Here's the output of the migration:
== galaxy@galaxy2:~/prog/galaxy-2011-12-5$ sh manage_db.sh upgrade 79 -> 80...
Migration script to create tables for disk quotas.
done 80 -> 81...
Migration script to add a 'tool_version' column to the hda/ldda tables.
done 81 -> 82...
Migration script to add the tool_shed_repository table.
done 82 -> 83...
Migration script to add 'prepare_input_files_cmd' column to the task table and to rename a column.
done 83 -> 84...
Migration script to add 'ldda_id' column to the implicitly_converted_dataset_association table.
done 84 -> 85...
Migration script to add 'info' column to the task table.
done ==
Thanks, Leon
On Mon, Dec 5, 2011 at 9:11 PM, Nate Coraor <nate@bx.psu.edu> wrote: On Dec 5, 2011, at 3:02 PM, Leon Mei wrote:
Dear all,
Today I upgraded our NBIC server from an older release (fetched on July 5th, 2011) to the latest version in galaxy-dist. After execute "hg update" and "sh manage_db upgrade" and merge some local configurations, I successfully restarted the server. However once I access the server from a web browser, Galaxy crashed.
Log file complains that some tables don't exist: == ProgrammingError: (ProgrammingError) (1146, "Table 'galaxy.user_quota_association' doesn't exist") u'SELECT user_quota_association.id AS user_quota_association_id, user_quota_association.user_id AS user_quota_association_user_id, user_quota_association.quota_id AS user_quota_association_quota_id, user_quota_association.create_time AS user_quota_association_create_time, user_quota_association.update_time AS user_quota_association_update_time \nFROM user_quota_association \nWHERE %s = user_quota_association.user_id' [1L] ==
A check in mysql confirms that only the following 3 tables were added during the migration from schema 79 to 85: * default_quota_association * quota * tool_shed_repository
The following 9 tables are missing: cloud_*, user_quota_association, group_quota_association
Hi Leon,
Were there any errors output when you ran mange_db.sh upgrade?
--nate
Has anyone experienced a similar problem? Any hint on how to solve this is highly appreciate!
Thanks, Leon
-- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_mei Mobile: +31 6 41709231 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_mei Mobile: +31 6 41709231
-- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_mei Mobile: +31 6 41709231 <nbic_galaxy_2011_12_5.sql.gz>
participants (2)
-
Leon Mei -
Nate Coraor