Hello Victor,
The following statement in your log is concerning because it looks like
something in your environment got corrupted in some way.
Exception: Your database has version '90' but this code expects version '79'.
Clean database schema migration upgrades go from smaller to larger numbers
(e.g., 89 -> 90, 90 -> 91, etc). Your migrate_versions.version database table
column has a value of 90, but your ~/lib/galaxy/model/migrate/versions
sub-directory has scripts only up to 0079... (or so it seems). Not sure how
best to fix the problem...
Greg Von Kuster
On Feb 21, 2012, at 2:21 PM, Victor Ruotti wrote:
> Hi,
> I'm trying to use the upgrade script given that the current schema is now
> version 90.
> I get the following error.
> Can anyone point me out, maybe there is something to do before upgrading?
>
> thanks in advance.
> Victor
>
>
>
> ----------------trying to start galaxy I get
> Traceback (most recent call last):
> File "/opt/galaxy/galaxy-dist-original/lib/galaxy/web/buildapp.py", line 82,
> in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
> File "/opt/galaxy/galaxy-dist-original/lib/galaxy/app.py", line 32, in
> __init__
> create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
> '__file__', None ), self.config.database_engine_options )
> File "/opt/galaxy/galaxy-dist-original/lib/galaxy/model/migrate/check.py",
> line 105, in create_or_verify_database
> % ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
> Exception: Your database has version '90' but this code expects version '79'.
> Please backup your database and then migrate the schema by running 'sh
> manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
> Removing PID file runner0.pid
>
> --------------trying to upgrade
>
> sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade
> Traceback (most recent call last):
> File "./scripts/manage_db.py", line 63, in <module>
> main( repository=repo, url=db_url )
> File
> "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py",
> line 150, in main
> ret = command_func(**kwargs)
> File
> "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
> line 221, in upgrade
> return _migrate(url, repository, version, upgrade=True, err=err, **opts)
> File
> "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
> line 327, in _migrate
> changeset = schema.changeset(version)
> File
> "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
> line 173, in changeset
> changeset = self.repository.changeset(database, start_ver, version)
> File
> "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py",
> line 170, in changeset
> changes = [self.version(v).script(database, op) for v in versions]
> File
> "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py",
> line 145, in version
> return self.versions.version(*p, **k)
> File
> "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/version.py",
> line 125, in version
> return self.versions[VerNum(vernum)]
> KeyError: <VerNum(90)>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
