I ran into the error shown at the end of this email today. It looks like someone is trying to rename a sequence generator but using the wrong syntax for postogres (at least for my 8.1.2 version). Anyways, I worked around the problem by switching lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py to use "ATLER TABLE" instead of "ALTER SEQUENCE" and I migrated successfully.
I'm a little confused why I was asked to migrate, as I wiped out my galaxy installation including my postgres database and ran it with a new (2.6.6) version of python. Also, I can't seem to kill the galaxy process with the usual control-c (used to be able to do this) but I have to explicitly kill it from another shell. I also can't get the stop-daemon thing to work from run.sh, I get "No PID file exists in paster.pid".
Any thoughts on this?
-John
galaxy.model.migrate.check INFO 2011-02-03 17:15:19,544 The 'sequencer_type_id' column is renamed to 'external_service_type_id' in the renamed galaxy.model.migrate.check INFO 2011-02-03 17:15:19,544 table 'external_service'. Finally, adds a foreign key to the external_service table in the galaxy.model.migrate.check INFO 2011-02-03 17:15:19,544 sample_dataset table and populates it. galaxy.model.migrate.check INFO 2011-02-03 17:15:19,545 galaxy.model.migrate.check INFO 2011-02-03 17:15:19,545 Traceback (most recent call last): File "/home/galaxy/galaxy_dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy_dist/lib/galaxy/app.py", line 32, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/home/galaxy/galaxy_dist/lib/galaxy/model/migrate/check.py", line 67, in create_or_verify_database migrate_to_current_version( engine, db_schema ) File "/home/galaxy/galaxy_dist/lib/galaxy/model/migrate/check.py", line 122, in migrate_to_current_version schema.runchange( ver, change, changeset.step ) File "/home/galaxy/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange change.run(self.engine, step) File "/home/galaxy/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 101, in run func() File "lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py", line 106, in upgrade db_session.execute( cmd ) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) ProgrammingError: (ProgrammingError) syntax error at or near "RENAME" LINE 1: ALTER SEQUENCE sequencer_id_seq RENAME TO external_service_i... ^ 'ALTER SEQUENCE sequencer_id_seq RENAME TO external_service_id_seq' {}