mdl-loadbiomass has stopped working about model-seed-core HOT 3 CLOSED

I figured out that this was an interesting case of the code not removing old biomass reactions, and when I went back to a previous one, it rejected it because it was already in the REACTION_MODEL table, along with 5 other biomass reactions.

However, when I deleted the biomass reactions for my model in the database directly, I still got this error message:

ModelDriver encountered an unrecoverable error:

Can't call method "database" on an undefined value at /home/seaver/ModelSEEDCore/lib/ModelSEED/FIGMODEL/FIGMODELdata.pm line 48.

Model-SEED-core revision: cd06ebe

The biomass reaction was still inserted correctly into the database though.

from model-seed-core.

OK, here's more data:

The whole thing falls apart in FIGMODELmodel when doing this:

            $self->ppo()->biomassReaction($newBiomass)

So, it's unable to update its own PPO object. The result is that there's no synchrony between the biomass reaction in the REACTION_MODEL table and the biomass reaction in the MODEL table, and thereafter, I get weird errors.

from model-seed-core.

This bug was introduced in commits:
2571b58
When this line was added to FIGMODEL->new():
ModelSEED::globals::SETFIGMODEL($self);
You absolutely positively cannot do this in FIGMODEL->new(). I understand this was introduced to solve a bug, but it must be solved a different way. If you do this in FIGMODEL->new(), the global FIGMODEL is reset everytime you create a new FIGMODEL, and very very bad things happen.

from model-seed-core.