Hell all, Michael discovered a bug in the lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py migration script. To get the fix, you can pull from our development repo at https://bitbucket.org/galaxy/galaxy-central/wiki/Home. As another option, I've attached a corrected script to this message. Ypou'll need to place it in ~/lib/galaxy/model/migrate/versions, replacing the script with the bug in it. Let us know if you have any problems with this.
Thanks! Greg Von Kuster
0065_add_name_to_form_fields_and_values.pyc
Description: Binary data
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.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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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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