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
Description: GNU Zip compressed data
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