Hi,
Trying to upgrade DB schema ('sh manage_db.sh upgrade') from 67 to 68 fails
with the following message:
===
sqlalchemy.exc.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' {}
===
Full back-trace attached at the end of this email.
My postgres version is 8.1.18 on CentOS 5.4.
I suspect the error is that "ALTER SEQUENCE RENAME" is new to Postgres 9:
http://www.postgresql.org/docs/9.0/static/sql-altersequence.html
Where as in Postgres 8.1, there"s no "ALTER SEQUENCE RENAME":
http://www.postgresql.org/docs/8.1/interactive/sql-altersequence.html
The bottom notes on the 8.1 help page say:
" Some variants of ALTER TABLE can be used with sequences as well; for example,
to rename a sequence use ALTER TABLE RENAME. ".
Any recommendations on how to proceed will be appreciated, otherwise I'll just
change:
lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
Thanks,
-gordon
----------------------
sh manage_db.sh upgrade
67 -> 68...
This migration script renames the sequencer table to 'external_service' table
and
creates a association table, 'request_type_external_service_association' and
populates it. The 'sequencer_id' foreign_key from the 'request_type' table is
removed.
The 'sequencer_type_id' column is renamed to 'external_service_type_id' in the
renamed
table 'external_service'. Finally, adds a foreign key to the external_service
table in the
sample_dataset table and populates it.
Traceback (most recent call last):
File "./scripts/manage_db.py", line 55, in <module>
main( repository=repo, url=db_url )
File
"/home/gordon/projects/galaxy_devel/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/shell.py",
line 150, in main
ret = command_func(**kwargs)
File
"/home/gordon/projects/galaxy_devel/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/api.py",
line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File
"/home/gordon/projects/galaxy_devel/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/api.py",
line 349, in _migrate
schema.runchange(ver, change, changeset.step)
File
"/home/gordon/projects/galaxy_devel/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py",
line 184, in runchange
change.run(self.engine, step)
File
"/home/gordon/projects/galaxy_devel/eggs/sqlalchemy_migrate-0.5.4-py2.5.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/gordon/projects/galaxy_devel/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/scoping.py",
line 127, in do
return getattr(self.registry(), name)(*args, **kwargs)
File
"/home/gordon/projects/galaxy_devel/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py",
line 755, in execute
clause, params or {})
File
"/home/gordon/projects/galaxy_devel/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py",
line 824, in execute
return Connection.executors[c](self, object, multiparams, params)
File
"/home/gordon/projects/galaxy_devel/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py",
line 874, in _execute_clauseelement
return self.__execute_context(context)
File
"/home/gordon/projects/galaxy_devel/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py",
line 896, in __execute_context
self._cursor_execute(context.cursor, context.statement,
context.parameters[0], context=context)
File
"/home/gordon/projects/galaxy_devel/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py",
line 950, in _cursor_execute
self._handle_dbapi_exception(e, statement, parameters, cursor, context)
File
"/home/gordon/projects/galaxy_devel/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py",
line 931, in _handle_dbapi_exception
raise exc.DBAPIError.instance(statement, parameters, e,
connection_invalidated=is_disconnect)
sqlalchemy.exc.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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