Hi Alex,

If your migration scripts through 90 executed cleanly, then your 
tool_shed_repository.uninstalled column should exist as that column is created 
in the 0090 script.  What was the log of your db migration upgrades that 
occurred when your database was migrated from version 85 to 90?

Thanks,

Greg

On Feb 7, 2012, at 3:32 PM, Oleksandr Moskalenko wrote:

> I've upgraded my developmental Galaxy instance to the latest galaxy-dist 
> release with a transplanted the drmaa.py patch from galaxy-central. All .conf 
> files have been updated. However, I can't start the instance now The error 
> listed below is generated. I tried enabling/disabling the toolshed configs, 
> but that didn't resolve the issue. The database was upgraded from version 85 
> to 90 cleanly.
> 
> Regards,
> 
> Alex
> 
> galaxy.datatypes.registry DEBUG 2012-02-07 12:32:12,345 Loaded converter: 
> pbed2ldindepconvert
> galaxy.tools.imp_exp DEBUG 2012-02-07 12:32:12,360 Loaded history export 
> tool: __EXPORT_HISTORY__
> galaxy.tools.imp_exp DEBUG 2012-02-07 12:32:12,367 Loaded history import 
> tool: __IMPORT_HISTORY__
> galaxy.datatypes.registry DEBUG 2012-02-07 12:32:12,383 Loaded external 
> metadata tool: __SET_METADATA__
> 
> <Galaxy finished loading all tools>
> 
> 
> sqlalchemy.pool.QueuePool.0x...1290 WARNING 2012-02-07 12:32:12,831 Error 
> closing cursor: current transaction is aborted, commands ignored until end of 
> transaction block
> 
> Traceback (most recent call last):
>  File "/galaxy/run/dev/lib/galaxy/web/buildapp.py", line 82, in app_factory
>    app = UniverseApplication( global_conf = global_conf, **kwargs )
>  File "/galaxy/run/dev/lib/galaxy/app.py", line 83, in __init__
>    self.installed_repository_manager.load_proprietary_datatypes()
>  File "/galaxy/run/dev/lib/galaxy/tool_shed/__init__.py", line 19, in 
> load_proprietary_datatypes
>    .order_by( self.model.ToolShedRepository.table.c.id ):
>  File 
> "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py",
>  line 1361, in __iter__
>    return self._execute_and_instances(context)
>  File 
> "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py",
>  line 1364, in _execute_and_instances
>    result = self.session.execute(querycontext.statement, params=self._params, 
> mapper=self._mapper_zero_or_none())
>  File 
> "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py",
>  line 755, in execute
>    clause, params or {})
>  File 
> "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
>  line 824, in execute
>    return Connection.executors[c](self, object, multiparams, params)
>  File 
> "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
>  line 874, in _execute_clauseelement
>    return self.__execute_context(context)
>  File 
> "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
>  line 896, in __execute_context
>    self._cursor_execute(context.cursor, context.statement, 
> context.parameters[0], context=context)
>  File 
> "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
>  line 950, in _cursor_execute
>    self._handle_dbapi_exception(e, statement, parameters, cursor, context)
>  File 
> "/galaxy/run/dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
>  line 931, in _handle_dbapi_exception
>    raise exc.DBAPIError.instance(statement, parameters, e, 
> connection_invalidated=is_disconnect)
> ProgrammingError: (ProgrammingError) column tool_shed_repository.uninstalled 
> does not exist
> LINE 1: ...pository.deleted AS tool_shed_repository_deleted, tool_shed_...
>                                                             ^
> 'SELECT tool_shed_repository.id AS tool_shed_repository_id, 
> tool_shed_repository.create_time AS tool_shed_repository_create_time, 
> tool_shed_repository.update_time AS tool_shed_repository_update_time, 
> tool_shed_repository.tool_shed AS tool_shed_repository_tool_shed, 
> tool_shed_repository.name AS tool_shed_repository_name, 
> tool_shed_repository.description AS tool_shed_repository_description, 
> tool_shed_repository.owner AS tool_shed_repository_owner, 
> tool_shed_repository.installed_changeset_revision AS 
> tool_shed_repository_installed_changeset_revision, 
> tool_shed_repository.changeset_revision AS 
> tool_shed_repository_changeset_revision, tool_shed_repository.metadata AS 
> tool_shed_repository_metadata, tool_shed_repository.includes_datatypes AS 
> tool_shed_repository_includes_datatypes, 
> tool_shed_repository.update_available AS 
> tool_shed_repository_update_available, tool_shed_repository.deleted AS 
> tool_shed_repository_deleted, tool_shed_repository.uninstalled AS 
> tool_shed_repository_un!
 installed, tool_shed_repository.dist_to_shed AS 
tool_shed_repository_dist_to_shed \nFROM tool_shed_repository \nWHERE 
tool_shed_repository.includes_datatypes = %(includes_datatypes_1)s AND 
tool_shed_repository.deleted = %(deleted_1)s ORDER BY tool_shed_repository.id' 
{'includes_datatypes_1': True, 'deleted_1': False}
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