It looks like what happened is that you've updated the instance that was
originally connected to this database from galaxy-central at some point
recently. The current tip of galaxy-central is at database version 103.
The first two options that come to mind are:
1) Hook a fresh galaxy-central clone up to this database and `manage_db.sh
downgrade 97` which should set your database back to the version appropriate
for galaxy-dist.
2) Swap to galaxy-central instead of -dist
Taking a brief look at the migrations, #1 looks fairly safe, but as always --
back up the database first.
-Dannon
On Jul 3, 2012, at 1:03 PM, Iry Witham wrote:
> I am still experiencing issues getting my galaxy server to start since the
> upgrade. The logs are all getting this type of error:
>
> galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> cat runner0.log
> python path is:
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
>
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-linux-x86_64-ucs4.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg,
>
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
>
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchem!
y-0.5.6_dev_r6498-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDe!
ploy-1.3.3-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy!
-dist/eg
gs/PasteScript-1.7.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip,
/usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2,
/usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old,
/usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages/Numeric,
/usr/lib64/python2.6/site-packages/gtk-2.0,
/usr/local/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages
> galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg
> successfully loaded for postgres dialect
> Traceback (most recent call last):
> File
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py",
> line 82, in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
> File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py",
> line 35, in __init__
> create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
> '__file__', None ), self.config.database_engine_options, app=self )
> File
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/check.py",
> line 103, in create_or_verify_database
> % ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
> Exception: Your database has version '101' but this code expects version
> '97'. 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
>
> I have not dropped my database and built it fresh. However, I have attempted
> the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade' for
> both the runner and web app ini files with the following error:
>
> galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> sh manage_db.sh
> -c ./universe_wsgi.webapp.ini upgrade
> Traceback (most recent call last):
> File "./scripts/manage_db.py", line 63, in <module>
> main( repository=repo, url=db_url )
> File
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py",
> line 150, in main
> ret = command_func(**kwargs)
> File
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/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
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
> line 327, in _migrate
> changeset = schema.changeset(version)
> File
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/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
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/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
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py",
> line 145, in version
> return self.versions.version(*p, **k)
> File
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/version.py",
> line 125, in version
> return self.versions[VerNum(vernum)]
> KeyError: <VerNum(101)>
>
> Any suggestions?
>
> Thanks,
> Iry
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