Good Afternoon,
Firstly am a massive fan of galaxy, really like the things that it can do, but I am a bit stuck updating our instance here and its starting to hold us back.
I was hoping someone could offer me some assistance with a database migration (I am pulling my hair out). I am using postgresql and galaxy is updated to …
galaxy@jic55119:~/software/galaxy-ceneral$ hg tip
changeset: 5751:e132a1398caa
tag: tip
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Mon Jun 27 17:25:32 2011 -0400
summary: Additional security for loading visualizations.
And I receive the following error which is blocking me,
galaxy@jic55119:~/software/galaxy-ceneral$ sh manage_db.sh upgrade
64 -> 65...
Migration script to add 'name' attribute to the JSON dict which describes
a form definition field and the form values in the database. In the 'form_values'
table, the 'content' column is now a JSON dict instead of a list.
Traceback (most recent call last):
File "./scripts/manage_db.py", line 63, in <module>
main( repository=repo, url=db_url )
File "/home/galaxy/software/galaxy-ceneral/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/shell.py", line 150, in main
ret = command_func(**kwargs)
File "/home/galaxy/software/galaxy-ceneral/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/galaxy/software/galaxy-ceneral/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/galaxy/software/galaxy-ceneral/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py", line 184, in runchange
change.run(self.engine, step)
File "/home/galaxy/software/galaxy-ceneral/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/0065_add_name_to_form_fields_and_values.py", line 57, in upgrade
db_session.execute( cmd )
File "/home/galaxy/software/galaxy-ceneral/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/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py", line 755, in execute
clause, params or {})
File "/home/galaxy/software/galaxy-ceneral/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/galaxy/software/galaxy-ceneral/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/galaxy/software/galaxy-ceneral/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/galaxy/software/galaxy-ceneral/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/galaxy/software/galaxy-ceneral/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) column "f" of relation "form_definition" does not exist
LINE 1: UPDATE form_definition AS f SET f.fields='[{"layout": "", "n...
^
'UPDATE form_definition AS f SET f.fields=\'[{"layout": "", "name": "field_0", "default": "yer nom", "required": "required", "label": "Sample Name", "visible": true, "helptext": "??", "type": "TextField"}, {"layout": "", "name": "field_1", "default": "", "required": "required", "label": "run_this?", "visible": true, "helptext": "??", "type": "CheckboxField"}]\' WHERE f.id=2' {}
Thank you for all your assistance.
Michael Burrell.