On Sep 30, 2011, at 9:32 AM, Iry Witham wrote: > When I run sh manage_db.sh upgrade I get the following error: Hi Iry, Sorry for missing this - were you ever able to resolve it? Thanks, --nate > > 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, >visualization_rating_association), (galaxy_user, >dataset_tag_association), (galaxy_user, page_user_share_association), >(galaxy_user, library_dataset_info_association), (galaxy_user, >user_action), (galaxy_user, history), (galaxy_user, >library_info_association), (galaxy_user, >history_dataset_association_tag_association), (galaxy_user, >workflow_step_tag_association), (galaxy_user, >history_dataset_association_rating_association), (galaxy_user, page), >(galaxy_user, history_rating_association), (galaxy_user, >stored_workflow), (galaxy_user, history_annotation_association), >(galaxy_user, user_role_association), (galaxy_user, api_keys), >(galaxy_user, request), (galaxy_user, history_user_share_association), >(galaxy_user, user_address), (galaxy_user, >library_dataset_dataset_association), (galaxy_user, >history_tag_association), (galaxy_user, page_rating_association), >(galaxy_user, library_dataset_dataset_info_association), (galaxy_user, >library_folder_info_association), (galaxy_user, >visualization_tag_association), (galaxy_user, >stored_workflow_user_share_connection), (galaxy_user, galaxy_session), >(galaxy_user, visualization), (galaxy_user, >history_dataset_association_display_at_authorization), (galaxy_user, >job), (galaxy_user, galaxy_user_openid), (galaxy_user, event), >(galaxy_user, stored_workflow_tag_association), (galaxy_user, >stored_workflow_annotation_association), (galaxy_user, user_preference), >(galaxy_user, workflow_step_annotation_association), (galaxy_user, >page_annotation_association), (galaxy_user, >history_dataset_association_annotation_association), (galaxy_user, >page_tag_association), (galaxy_user, user_group_association), >(galaxy_user, visualization_annotation_association), (sample, >sample_dataset), (sample, sample_run_association), (sample, >sample_event), (workflow_invocation, workflow_invocation_step), >(history, job), (history, history_annotation_association), (history, >job_export_history_archive), (history, history_tag_association), >(history, history_dataset_association), (history, >job_import_history_archive), (history, default_history_permissions), >(history, history_user_share_association), (history, >history_rating_association), (history, event), (history, >galaxy_session_to_history), (history, galaxy_session), (history, >sample), (run, sample_run_association), (run, >request_type_run_association), (request_type, sample_state), >(request_type, request_type_permissions), (request_type, >request_type_run_association), (request_type, >request_type_external_service_association), (request_type, request), >(page, page_tag_association), (page, page_user_share_association), >(page, page_revision), (page, page_rating_association), (page, >page_annotation_association), (stored_workflow, workflow), >(stored_workflow, stored_workflow_rating_association), (stored_workflow, >stored_workflow_menu_entry), (stored_workflow, >stored_workflow_tag_association), (stored_workflow, >stored_workflow_annotation_association), (stored_workflow, >stored_workflow_user_share_connection), >(library_dataset_dataset_association, >library_dataset_dataset_info_association), >(library_dataset_dataset_association, job_to_output_library_dataset), >(library_dataset_dataset_association, job_external_output_metadata), >(library_dataset_dataset_association, >library_dataset_dataset_info_template_association), >(library_dataset_dataset_association, >library_dataset_dataset_association_permissions), >(library_dataset_dataset_association, >implicitly_converted_dataset_association), (request, sample), (request, >request_event), (post_job_action, post_job_action_association), >(workflow, workflow_step), (workflow, workflow_invocation), >(galaxy_session, job), (galaxy_session, galaxy_user_openid), >(galaxy_session, user_action), (galaxy_session, >galaxy_session_to_history), (galaxy_session, event), (visualization, >visualization_user_share_association), (visualization, >visualization_tag_association), (visualization, >visualization_rating_association), (visualization, >visualization_revision), (visualization, >visualization_annotation_association), (workflow_step, >workflow_invocation_step), (workflow_step, workflow_step_connection), >(workflow_step, workflow_step_annotation_association), (workflow_step, >workflow_step_tag_association), (workflow_step, workflow_output), >(workflow_step, post_job_action), (sample_state, sample_event), (job, >post_job_action_association), (job, job_to_output_library_dataset), >(job, job_to_output_dataset), (job, job_export_history_archive), (job, >job_to_input_dataset), (job, job_import_history_archive), (job, >job_parameter), (job, job_external_output_metadata), (job, >workflow_invocation_step), (job, task), (form_values, external_service), >(form_values, run), (form_values, galaxy_user), (form_values, request), >(form_values, sample), (external_service, sample_dataset), >(external_service, request_type_external_service_association), >(page_revision, page)][] > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. 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