Alex, this is strange, so it'll be tricky to figure out what's causing the 
problem.  I can't think of anything that would cause this unless 2 different 
databases are somehow being used.   I assume your database configured in your 
file dev_universe_wsgi.runner.ini is the same as the database used by your 
Galaxy instance.  Can you make sure of this?  

When you start up your Galaxy instance, your paster log should include 
something like the following - this happens right after loading the Galaxy 
datatypes, and before any tools are loaded.  Can you make sure what database 
version is displayed when you start up?  Yours should be at database version 90.

galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-07 15:58:56,069 Loaded 
reference to tool shed: Bx tool shed
galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-07 15:58:56,069 Loaded 
reference to tool shed: Galaxy main tool shed
galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-07 15:58:56,069 Loaded 
reference to tool shed: Galaxy test tool shed
galaxy.model.migrate.check DEBUG 2012-02-07 15:58:56,111 psycopg2 egg 
successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2012-02-07 15:58:56,273 At database version 91



On Feb 7, 2012, at 3:55 PM, Oleksandr Moskalenko wrote:

> $ sh manage_db.sh -c ./dev_universe_wsgi.runner.ini upgrade
> 85 -> 86... 
> Migration script to add the metadata, update_available and includes_datatypes 
> columns to the tool_shed_repository table.
> done
> 86 -> 87... 
> Migration script to create the tool_id_guid_map table.
> done
> 87 -> 88...
> Migration script to add the installed_changeset_revision column to the 
> tool_shed_repository table.
> Updated the installed_changeset_revision column for  0  rows in the 
> tool_shed_repository table.  
> done
> 88 -> 89... 
> Migration script to add 'object_store_id' column to various tables
> done
> 89 -> 90... 
> Migration script to add the uninstalled and dist_to_shed columns to the 
> tool_shed_repository table.
> done
> 
> Looking around in psql seems to confirm a clean update:
> 
> galaxydev-> \d tool_shed_repository
>                                              Table 
> "public.tool_shed_repository"
>            Column            |            Type             |                  
>            Modifiers                             
> ------------------------------+-----------------------------+-------------------------------------------------------------------
> id                           | integer                     | not null default 
> nextval('tool_shed_repository_id_seq'::regclass)
> create_time                  | timestamp without time zone | 
> update_time                  | timestamp without time zone | 
> tool_shed                    | character varying(255)      | 
> name                         | character varying(255)      | 
> description                  | text                        | 
> owner                        | character varying(255)      | 
> changeset_revision           | character varying(255)      | 
> deleted                      | boolean                     | 
> metadata                     | bytea                       | 
> includes_datatypes           | boolean                     | 
> update_available             | boolean                     | 
> installed_changeset_revision | character varying(255)      | 
> uninstalled                  | boolean                     | 
> dist_to_shed                 | boolean                     | 
> Indexes:
>    "tool_shed_repository_pkey" PRIMARY KEY, btree (id)
>    "ix_tool_shed_repository_changeset_revision" btree (changeset_revision)
>    "ix_tool_shed_repository_deleted" btree (deleted)
>    "ix_tool_shed_repository_name" btree (name)
>    "ix_tool_shed_repository_owner" btree (owner)
>    "ix_tool_shed_repository_tool_shed" btree (tool_shed)
> 
> 
> The table is empty though:
> 
> galaxydev=> select * from tool_shed_repository;
> id | create_time | update_time | tool_shed | name | description | owner | 
> changeset_revision | deleted | metadata | includes_datatypes | 
> update_available | installed_changeset_revision | uninstalled | dist_to_shed 
> ----+-------------+-------------+-----------+------+-------------+-------+--------------------+---------+----------+--------------------+-
> -----------------+------------------------------+-------------+--------------
> (0 rows)
> 
> On Feb 7, 2012, at 3:42 PM, Greg Von Kuster wrote:
> 
>> 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_!
 uninstalled, 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/
>> 
> 
> 
> ___________________________________________________________
> 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/


___________________________________________________________
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/

Reply via email to