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" <n...@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)][]
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