Hey Peter,

  That database is pretty new (not yet in stable) - but you are
tracking the master branch of galaxy on github in your tests (which is
sortof like stable). You will want to either track the dev branch (so
you can continue to catch all the errors right away :)) or track
master and use an older database.

  Someday soon I will move this logic into Galaxy's run_tests.sh so
that Galaxy always knows what version of the database it needs and we
don't have to deal with these version incompatibilities. Sorry for the
confusion.

Thanks,
-John




On Fri, Feb 27, 2015 at 9:07 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi all,
>
> I've been using the SQLite template database feature to speed up
> functional testing. Rather than starting for the initial schema and
> applying all the incremental changes (as done when installing a
> fresh Galaxy instance), this lets the test suite start with a recent
> version of the database, by setting the environment variable
> $GALAXY_TEST_DB_TEMPLATE to a URL to fetch a template
> database, e.g. from:
>
> https://github.com/jmchilton/galaxy-downloads
>
> Database schema version 120 was working, changing to 127 broke:
>
> https://github.com/peterjc/pico_galaxy/commit/412d3fe88b8011f0b690956d129fd72f5b5d4c5c
>
> TravisCI using v120, worked:
> https://travis-ci.org/peterjc/pico_galaxy/builds/52308064
>
> TravisCI using v127, broke:
> https://travis-ci.org/peterjc/pico_galaxy/builds/52398778
>
> galaxy.model.migrate.check DEBUG 2015-02-27 10:05:33,274 pysqlite>=2
> egg successfully loaded for sqlite dialect
> Traceback (most recent call last):
>   File "./scripts/functional_tests.py", line 602, in <module>
>     sys.exit( main() )
>   File "./scripts/functional_tests.py", line 409, in main
>     app = UniverseApplication( **kwargs )
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-master/lib/galaxy/app.py",
> line 49, in __init__
>     self._configure_models( check_migrate_databases=True,
> check_migrate_tools=check_migrate_tools, config_file=config_file )
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-master/lib/galaxy/config.py",
> line 779, in _configure_models
>     create_or_verify_database( db_url, config_file,
> self.config.database_engine_options, app=self )
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-master/lib/galaxy/model/migrate/check.py",
> line 61, in create_or_verify_database
>     migrate()
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-master/lib/galaxy/model/migrate/check.py",
> line 57, in migrate
>     migrate_to_current_version( engine, db_schema )
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-master/lib/galaxy/model/migrate/check.py",
> line 117, in migrate_to_current_version
>     changeset = schema.changeset( None )
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-master/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py",
> line 80, in changeset
>     changeset = self.repository.changeset(database, start_ver, version)
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-master/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/repository.py",
> line 225, in changeset
>     changes = [self.version(v).script(database, op) for v in versions]
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-master/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/repository.py",
> line 189, in version
>     return self.versions.version(*p, **k)
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-master/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/version.py",
> line 140, in version
>     return self.versions[VerNum(vernum)]
> KeyError: <VerNum(127)>
>
> This is now testing against the (beta) Galaxy on GitHub:
> https://github.com/galaxyproject/galaxy
>
> Is it possible this is out of synch with the SQLite templates John
> posts here? https://github.com/jmchilton/galaxy-downloads
>
> Peter
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