[galaxy-dev] 01/27 galaxy-dist startup problem (toolshed/pgsql related)
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/
Re: [galaxy-dev] 01/27 galaxy-dist startup problem (toolshed/pgsql related)
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'
Re: [galaxy-dev] 01/27 galaxy-dist startup problem (toolshed/pgsql related)
$ 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
Re: [galaxy-dev] 01/27 galaxy-dist startup problem (toolshed/pgsql related)
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
Re: [galaxy-dev] 01/27 galaxy-dist startup problem (toolshed/pgsql related)
Greg,
Startup log:
galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-07 16:13:29,613 Loading
references to tool sheds from tool_sheds_conf.xml
galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-07 16:13:29,614 Loaded
reference to tool shed: Galaxy main tool shed
galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-07 16:13:29,614 Loaded
reference to tool shed: Galaxy test tool shed
galaxy.model.migrate.check DEBUG 2012-02-07 16:13:29,852 psycopg2 egg
successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2012-02-07 16:13:29,981 At database version 90
galaxy.model.custom_types DEBUG 2012-02-07 16:13:29,986 psycopg2 egg
successfully loaded for postgres dialect
I forced a db downgrade, then ran the db upgrade again. Then, the instance
came up. It's weird, but the issue is resolved I guess.
Thanks for looking into it.
Cheers,
Alex
On Feb 7, 2012, at 4:10 PM, Greg Von Kuster wrote:
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 |
