Hi Nate,
Thanks for the fix. Everything is working great now.
Jack
On 29 August 2011 09:33, Nate Coraor n...@bx.psu.edu wrote:
Jack Zhu wrote:
Hi all,
I have problems with updating my local instance of Galaxy.
Specifically I can not migrate the database schema from 80 to 81:
Hi Jack,
Thanks for reporting this issue. It has been fixed in changeset
5951:62d51750d7df.
--nate
--
$$ sh manage_db.sh upgrade
80 - 81...
Migration script to add a 'tool_version' column to the hda/ldda tables.
Traceback (most recent call last):
File ./scripts/manage_db.py, line 63, in module
main( repository=repo, url=db_url )
File
/home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py,
line 150, in main
ret = command_func(**kwargs)
File
/home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File
/home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
line 349, in _migrate
schema.runchange(ver, change, changeset.step)
File
/home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 184, in runchange
change.run(self.engine, step)
File
/home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py,
line 101, in run
func()
File
lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py,
line 17, in upgrade
metadata.reflect()
File
/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py,
line 1733, in reflect
Table(name, self, **reflect_opts)
File
/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py,
line 108, in __call__
return type.__call__(self, name, metadata, *args, **kwargs)
File
/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py,
line 236, in __init__
_bind_or_error(metadata).reflecttable(self,
include_columns=include_columns)
File
/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py,
line 1265, in reflecttable
self.dialect.reflecttable(conn, table, include_columns)
File
/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py,
line 1673, in reflecttable
only=include_columns)
File
/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py,
line 2139, in reflect
self._add_column(table, line, charset, only)
File
/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py,
line 2227, in _add_column
type_instance = col_type(*type_args, **type_kw)
File
/home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py,
line 569, in __init__
super(MSBigInteger, self).__init__(display_width, **kw)
TypeError: super(type, obj): obj must be an instance or subtype of type
--
Your help will be greatly appreciated.
Jack
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