This isn't an issue with postgresql or mysql; they don't use a temporary table for table alterations. Can you open up the sqlite database if you still have it and see what the contents of the migrate_tmp table were? They'll be a copy of a prior migrated table, I'm just curious what from -- it should have been cleaned up previously in the event of successful migrations.
My hunch is that previously various scripts threw a lot of errors for mysql and so this table wasn't automatically cleaned up after after the execution of one of those migration scripts, but the old version of sqlalchemy-migrate didn't care if it existed or not and would overwrite it, while the new version is more reticent to delete the table (which is probably more reasonable, should you need to recover data after an unsuccessful migration). In any event, to fix it, you'll want to make sure that the contents of that migrate_tmp table aren't something you want and drop it, downgrade to 114, then upgrade to 115 again. If I can recreate this I'll work on a more reasonable solution. Dannon On Thu, May 9, 2013 at 6:12 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote: > On Thu, May 9, 2013 at 11:03 AM, Peter Cock <p.j.a.c...@googlemail.com> > wrote: > > 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? > > Note that attempting to re-run the migration appeared to do nothing: > $ sh manage_db.sh upgrade > $ sh run.sh > ... > > This isn't a big issue for my development machine, but it would seem that > this migration step aborted halfway (having marked the schema as being > updated to version 115), and did not roll back the database to the previous > state labelled as version 114. If that happens just on SQLite that's > tolerable, > but if there is no transaction integrity used on MySQL or PostgreSQL the > migration framework seems very fragile. > > Regards, > > Peter >
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