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....@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"
>> > in your mail client.  To manage your subscriptions to this
>> > and other Galaxy lists, please use the interface at:
>> >
>> >  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

Attachment: nbic_galaxy_2011_12_5.sql.gz
Description: GNU Zip compressed data

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