On Wed, May 8, 2013 at 10:19 PM, Dannon Baker <dannon.ba...@gmail.com> wrote:
>
> Hey Robert,
>
> I assume this is sqlite? And, when you say you ran this without any
> existing database -- was this was a completely new clone of galaxy, or did
> you update a prior installation and delete database/universe.sqlite manually
> before running?
>
> -Dannon
Hi guys,
I've just hit this bug too, using SQLite on a working development machine
which was running with schema 114 until I grabbed the latest galaxy-central
just now, revision 80ab774559f8405a46082286c6cf35db420db002
$ sh manage_db.sh upgrade
114 -> 115...
Altering password column failed
Traceback (most recent call last):
File "lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py",
line 15, in upgrade
user.c.password.alter(type=String(255))
File
"/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py",
line 491, in alter
return alter_column(self, *p, **k)
File
"/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py",
line 136, in alter_column
engine._run_visitor(visitorcallable, delta)
File
"/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 2302, in _run_visitor
conn._run_visitor(visitorcallable, element, **kwargs)
File
"/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1972, in _run_visitor
**kwargs).traverse_single(element)
File
"/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py",
line 53, in traverse_single
ret = super(AlterTableVisitor, self).traverse_single(elem)
File
"/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/visitors.py",
line 106, in traverse_single
return meth(obj, **kw)
File
"/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py",
line 53, in visit_column
self.recreate_table(table,column,delta)
File
"/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py",
line 36, in recreate_table
self.execute()
File
"/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py",
line 42, in execute
return self.connection.execute(self.buffer.getvalue())
File
"/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1449, in execute
params)
File
"/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1628, in _execute_text
statement, parameters
File
"/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1698, in _execute_context
context)
File
"/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1691, in _execute_context
context)
File
"/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
line 331, in do_execute
cursor.execute(statement, parameters)
OperationalError: (OperationalError) there is already another table or
index with this name: migration_tmp 'ALTER TABLE galaxy_user RENAME TO
migration_tmp' ()
done
Presumably one of the previous migration scripts has left an old
migration_tmp table in place?
Peter
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