Thanks Dannon and Bjorn for the assistance. I followed Dannon's
suggestion and that fixed my issue.
Thanks,
Iry
On 7/3/12 1:15 PM, "Dannon Baker" <dannonba...@me.com> wrote:
>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-linu
>>x-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10
>>f6e722e9a-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.eg
>>g,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-l
>>inux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_s
>>tatic-py2.6-linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff
>>194725-py2.6-linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.eg
>>g,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
>>
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r
>>6498-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.e
>>gg,
>>/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.eg
>>g,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_2005
>>0316-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.eg
>>g,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-li
>>nux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.
>>6.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/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/c
>>heck.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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