Thanks! I did hg pull -u. For the database, I downgraded to 108 and then upgraded again but got this error when upgrading. Is it due to the Ubuntu bug? Or something else? Should I be sticking with a particular Hg version instead of the latest?
$ sh manage_db.sh upgrade
115 -> 116...
Tables for a next generation sequencing lims tied to requests.
/home/galaxy/bin/chapman-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/dialects/sqlite/base.py:723: SAWarning: Did not recognize type 'BIGINT' of column 'bytes'
Traceback (most recent call last):
File "./scripts/manage_db.py", line 65, in <module>
main( repository=repo, url=db_url )
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py", line 207, in main
ret = command_func(**kwargs)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 186, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File "<string>", line 2, in _migrate
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py", line 159, in with_engine
return f(*a, **kw)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 366, in _migrate
schema.runchange(ver, change, changeset.step)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py", line 91, in runchange
change.run(self.engine, step)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/script/py.py", line 145, in run
script_func(engine)
File "lib/galaxy/model/migrate/versions/0116_seq_lims.py", line 52, in upgrade
for table in _get_tables(metadata):
File "lib/galaxy/model/migrate/versions/0116_seq_lims.py", line 34, in _get_tables
primary_key = True),
File "build/bdist.linux-x86_64/egg/sqlalchemy/schema.py", line 305, in __new__
sqlalchemy.exc.InvalidRequestError: Table 'sample_request_map' is already defined for this MetaData instance. Specify 'extend_existing=True' to redefine options and columns on an existing Table object.