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
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