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(a)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. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>
http://lists.bx.psu.edu/