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....@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 <n...@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"
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> >
> >  http://lists.bx.psu.edu/
> 
> 
> 
> 
> -- 
> 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>


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