accuracy

[jslu9]

• genes count are not correct due to copies.
  • find a way to logging.warn() these in the code
• for all "old IDs", use the new OldIDModelSynonym table to store old ids
  • columns: synonym_id and model_id
  • cases where we record old ids:
    1. when COBRA gene matches a database Gene.name or Gene synonym
    2. If Theseus changes the reaction or metabolite ID
• write a test script that loads published model and dump model into COBRApy and compares counts for reactions, metabolites, genes