If you're just starting out with this install, I'd try to figure out what's going wrong just to avoid any issues.  This happens reproducibly every time, if you drop/recreate?  Are you able to add any extra debugging output to migration script 103 (I'm assuming it failed on exit of 103, or in 104) to get an error message?


On Thu, Nov 21, 2013 at 6:53 AM, Jager, Victor de <V.deJager@nioo.knaw.nl> wrote:
Hi all,

I'm installing a new galaxy instance and run into an issue after switching to postgres. During the migration setps I get the following error


galaxy.model.migrate.check INFO 2013-11-21 15:37:23,238
galaxy.model.migrate.check INFO 2013-11-21 15:37:23,238 Migrating 103 -> 104...
galaxy.model.migrate.check INFO 2013-11-21 15:37:23,257
galaxy.model.migrate.check INFO 2013-11-21 15:37:23,257 Migrating 104 -> 105...
galaxy.model.migrate.check INFO 2013-11-21 15:37:25,413
galaxy.model.migrate.check INFO 2013-11-21 15:37:25,414 Migration script to add the cleanup_event* tables.
galaxy.model.migrate.check INFO 2013-11-21 15:37:25,414
galaxy.model.migrate.check INFO 2013-11-21 15:37:25,414
galaxy.model.migrate.check INFO 2013-11-21 15:37:25,414 Migrating 105 -> 106...
galaxy.model.migrate.check INFO 2013-11-21 15:37:25,414
Traceback (most recent call last):
  File "/mnt/data/home/NIOO/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/mnt/data/home/NIOO/galaxy/galaxy-dist/lib/galaxy/app.py", line 54, in __init__
    create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self )
  File "/mnt/data/home/NIOO/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 66, in create_or_verify_database
    migrate_to_current_version( engine, db_schema )
  File "/mnt/data/home/NIOO/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 124, in migrate_to_current_version
    schema.runchange( ver, change, changeset.step )
  File "/mnt/data/home/NIOO/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py", line 89, in runchange
    (self.version, startver))
InvalidVersionError: 103 is not 105

./manage_db.sh upgrade
seems to finish the migration.

How do I ensure the database is in a healthy state?

Ubuntu 12.04.3 LTS
PostgreSQL 9.1
Connection via socket
Installation as local galaxy user
Installation started in virtual environment

Victor



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