Hi Michael,

I'm not exactly sure why this migration script is not working for you( and unfortunately, er maybe fortunately,  I didn't write it ), so we may be forced to try a few things.  How are you bumping into this error?  Are you trying to upgrade a clean Galaxy instance (where you have not yet seen this error), or are you trying multiple times to upgrade the same instance, and you're continually seeing this issue?

Can you paste the result of the following sql query against your db?

select * from migrate_version;

I'm not sure the following will help, but look at line # 56 in ~/lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py - it should look like this:
cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i" %( fields_json, form_definition_id )

Change the line to look like this, and try the migration.
cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE id=%i" %( fields_json, form_definition_id )

Greg Von Kuster

On Jun 28, 2011, at 6:58 AM, michael burrell (TSL) wrote:

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@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
 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.

Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:


Greg Von Kuster
Galaxy Development Team