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.
On Tue, Jul 2, 2013 at 10:59 AM, Dannon Baker dannon.baker@gmail.comwrote:
On Mon, Jul 1, 2013 at 8:34 PM, Brad Chapman chapmanb@50mail.com wrote:
This was a typo in the downgrade function for one of the patches. I pushed a fix so if you update from bitbucket things should work smoothly again (once we get to problem 2 below).
For anyone with galaxy-dist commit privileges, here's the one liner:
https://bitbucket.org/chapmanb/galaxy-central/commits/463852762a6eeadcf17731...
Thanks Brad, added to stable branch in https://bitbucket.org/galaxy/galaxy-central/commits/0a06df7da177a204c7f3800e...