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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