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 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 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 greg@bx.psu.edu