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

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--
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