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_uni!
nstalled, 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}
___________________________________________________________
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/
