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), (galax!
y_user, page), (galaxy_user, history_rating_association), (gal!
axy_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_annotati!
on_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, requ!
est_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_histor!
y_archive), (job, job_parameter), (job, job_external_output_me!
tadata),
(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)][]
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