It looks like the Galaxy server was downgraded relative the database. Do
you know how this may have happened?
It also looks like this instance is probably quite a bit out of date, in
any event, so I'd be hesitant to give advice recommending a major upgrade
given the current state of things. I'd say you should really get in touch
with the Galaxy Admin prior to trying much.
Is using a cloud instance for the training an option?
On Thu, Oct 29, 2015 at 11:44 AM Ali Al-Shahib <ali.al-sha...@phe.gov.uk>
wrote:
> Hi all
>
> I am due to give galaxy training tomorrow and the Galaxy server has gone
> down. Our galaxy admin is travelling and not responding and I appreciate a
> quick response to this issue.
>
> When I run galaxy_restart.sh I get the following error in web0.pid:
>
> migrate.versioning.repository DEBUG 2015-10-28 23:07:47,285 Config:
> {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]',
> 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}}
>
> lib/galaxy/model/migrate
>
> galaxy.model.migrate.check DEBUG 2015-10-28 23:07:47,296 psycopg2 egg
> successfully loaded for postgresql dialect
>
> Traceback (most recent call last):
>
> File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
> line 35, in app_factory
>
> app = UniverseApplication( global_conf = global_conf, **kwargs )
>
> File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in __init__
>
> create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
> ).get( '__file__', None ), self.config.database_engine_options, app=self )
>
> File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line
> 104, in create_or_verify_database
>
> % ( db_schema.version, migrate_repository.versions.latest, config_arg
> ) )
>
> Exception: Your database has version '124' but this code expects version
> '115'. Please backup your database and then migrate the schema by running
> 'sh manage_db.sh upgrade'.
>
>
> ------
>
>
>
> I did then try to do sh manage_db.sh downgrade 115 but I got this error:
>
>
> Traceback (most recent call last):
>
> File "./scripts/manage_db.py", line 62, in <module>
>
> main( repository=repo, url=db_url )
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py",
> line 207, in main
>
> ret = command_func(**kwargs)
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py",
> line 202, in downgrade
>
> return _migrate(url, repository, version, upgrade=False, err=err,
> **opts)
>
> File "<string>", line 2, in _migrate
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py",
> line 159, in with_engine
>
> return f(*a, **kw)
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py",
> line 345, in _migrate
>
> changeset = schema.changeset(version)
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py",
> line 80, in changeset
>
> changeset = self.repository.changeset(database, start_ver, version)
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py",
> line 225, in changeset
>
> changes = [self.version(v).script(database, op) for v in versions]
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py",
> line 189, in version
>
> return self.versions.version(*p, **k)
>
> File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py",
> line 140, in version
>
> return self.versions[VerNum(vernum)]
>
> KeyError: <VerNum(124)>
>
>
> Any help asap will be greatly appreciated.
>
>
> Ali
>
> **************************************************************************
> The information contained in the EMail and any attachments is confidential
> and intended solely and for the attention and use of the named
> addressee(s). It may not be disclosed to any other person without the
> express authority of Public Health England, or the intended recipient, or
> both. If you are not the intended recipient, you must not disclose, copy,
> distribute or retain this message or any part of it. This footnote also
> confirms that this EMail has been swept for computer viruses by
> Symantec.Cloud, but please re-sweep any attachments before opening or
> saving. http://www.gov.uk/PHE
> **************************************************************************
> ___________________________________________________________
> 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:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
