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' {}
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