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' {}