Hi Nate,
Thanks for the fix. Everything is working great now.
Jack
On 29 August 2011 09:33, Nate Coraor nate@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 ___________________________________________________________ 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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