When I run sh manage_db.sh upgrade I get the following error:
2 - 3...
Traceback (most recent call last):
File ./scripts/manage_db.py, line 55, in module
main( repository=repo, url=db_url )
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py,
line 150, in main
ret = command_func(**kwargs)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
line 349, in _migrate
schema.runchange(ver, change, changeset.step)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 184, in runchange
change.run(self.engine, step)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py,
line 101, in run
func()
File lib/galaxy/model/migrate/versions/0003_security_and_libraries.py, line
423, in upgrade
metadata.create_all()
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py,
line 1796, in create_all
bind.create(self, checkfirst=checkfirst, tables=tables)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py,
line 1129, in create
self._run_visitor(self.dialect.schemagenerator, entity,
connection=connection, **kwargs)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py,
line 1158, in _run_visitor
visitorcallable(self.dialect, conn, **kwargs).traverse(element)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py,
line 89, in traverse
return traverse(obj, self.__traverse_options__, self._visitor_dict)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py,
line 200, in traverse
return traverse_using(iterate(obj, opts), obj, visitors)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py,
line 194, in traverse_using
meth(target)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/compiler.py,
line 829, in visit_metadata
collection = [t for t in sql_util.sort_tables(tables) if
self._can_create(t)]
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/util.py,
line 22, in sort_tables
return topological.sort(tuples, tables)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/topological.py,
line 32, in sort
return [n.item for n in _sort(tuples, allitems, allow_cycles=False,
ignore_self_cycles=True)]
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/topological.py,
line 209, in _sort
raise CircularDependencyError(Circular dependency detected + repr(edges)
+ repr(queue))
sqlalchemy.exc.CircularDependencyError: Circular dependency detected
[(form_definition_current, form_definition), (library_item_info,
library_folder_info_association), (library_item_info,
library_item_info_element), (library_item_info, library_item_info_permissions),
(library_item_info, library_dataset_dataset_info_association),
(library_item_info, library_info_association), (library_item_info,
library_dataset_info_association), (visualization_revision, visualization),
(form_definition, external_service), (form_definition, form_values),
(form_definition, request_type), (form_definition, run), (form_definition,
form_definition_current), (history_dataset_association, job_to_input_dataset),
(history_dataset_association, job_to_output_dataset),
(history_dataset_association, implicitly_converted_dataset_association),
(history_dataset_association, history_dataset_association_tag_association),
(history_dataset_association, validation_error), (history_dataset_association,
history_dataset_association_rating_association), (history_dataset_association,
job_external_output_metadata), (history_dataset_association,
history_dataset_association_annotation_association),
(history_dataset_association,
history_dataset_association_display_at_authorization),
(history_dataset_association, metadata_file), (galaxy_user,
stored_workflow_rating_association), (galaxy_user, stored_workflow_menu_entry),
(galaxy_user, library_item_info), (galaxy_user,
visualization_user_share_association), (galaxy_user, default_user_permissions),
(galaxy_user,
