Refactoring upload to support collection of meta-data

[mwhitesi]

Currently, only way to upload is via the subtyping module. This upload function only supports sequence based upload.

• Possibly we want to add meta-data fields to upload
• A refactored upload workflow so individual modules do not need to handle upload and running of other analysis. This feature is currently tightly integrated into the subtyping module. Some separation/abstraction would benefit future development
• Maybe consider a division of functions in the spfy site (genome annotate, group compare, genome context)

[mwhitesi]

Other things to consider:

• How to properly handling complicated analyses dependency chains, especially in light of rq does not propagate earlier failures down the chain.
• Do we run all the analysis for each uploaded genome (single large analysis pipeline), or do we run analysis on demand (tracking for each genome what is complete and what is not)