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_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}
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:
$ 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:
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:
___________________________________________________________ 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:
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 | 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:
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participants (2)
-
Greg Von Kuster -
Oleksandr Moskalenko