Hi Nate,
I was able to resolve it. I had an issue with my Postgres configuration.
Thanks, Iry
On 11/7/11 3:48 PM, "Nate Coraor" nate@bx.psu.edu wrote:
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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