Sofia

Removed obsolete imports

Fixed multiple bugs and improved SoFIA stability

Fixed the bugs that prevented sofia.py info from working.

Fixed multiple bugs
- Gene identifier version is automatically trimmed
- Many remaining actions that produce old-style entities were updated
- Fixed many automatic conversion bugs

Entity Update II
- Entities are now described but not defined by the entities.json file. This means that any Python object can be handed around and the framework still knows how to do automatic entity extraction and conversion.
- Switches entities to nodes and actions to edges.
- Added is_a relationship to entities. Entities that have an is_a relationship with another entity can be consumed by the same actions that consume the other entity.