[galaxy-dev] migrate the database schema from 80 to 81

[Nate Coraor]

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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