Re: [galaxy-dev] manage_db.sh upgrade error

2011-11-08 Thread Iry Witham 
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"  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 
>> 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_datase

Re: [galaxy-dev] manage_db.sh upgrade error

2011-11-07 Thread Nate Coraor 
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 
> 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_associatio

[galaxy-dev] manage_db.sh upgrade error

2011-09-30 Thread Iry Witham 
When I run sh manage_db.sh upgrade I get the following error:

2 -> 3...
Traceback (most recent call last):
  File "./scripts/manage_db.py", line 55, in 
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, v