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.goe...@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.


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