Comments (3)
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.
Related Issues (20)
- Feature request: source of annotation for reactions
- mdl-autocomplete crashes HOT 6
- ./fba-checkgrowth and MetaboliteProduction.txt HOT 1
- Saved FVA results are invalid after model is changed HOT 1
- Error Running mdl-autocomplete HOT 6
- Autocomplete not filling gaps with new biomass HOT 1
- object rights not working, perhaps because of case mismatch
- Why is mdl-loadmodel having http request timeouts?
- Error Accessing Model Information HOT 7
- Behavior of the mdl-createmodel command HOT 3
- Segmentation fault with new biomass HOT 1
- ModelSEED commands aren't working HOT 3
- New fba function fails
- generating model IDs
- Use of FIGMODEL Table in MSSupport
- No argument list returned HOT 3
- Autocompletion Failing
- Install Error about MFATOOLKIT in Mac OS 10.7 HOT 1
- ms login error( 502 Bad Gateway)
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from model-seed-core.