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 > ___________________________________________________________ > 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/ ___________________________________________________________ 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/
