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ModelSEED / Model-SEED-core

The Model SEED is a tool for building, curating, and analyzing gonome-scale metabolic models. Visit the Model SEED homepage for installation instructions and full feature documentation.
http://bionet.mcs.anl.gov/index.php/Model_SEED_Homepage
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Overwrite option in mdl-importmodel not truly working for biochemistry #86

Open samseaver opened 12 years ago

samseaver commented 12 years ago

If you use the overwrite option then the ClearModelProvenance option in FIGMODELmodel::GenerateModelProvenance is set to '1', as it should. When re-creating the biochemistry files, the code calls from the ppo() (you again?) object. However, it seems that the lines from the original biochemistry files are already loaded into the ppo() object before they are deleted.

This means that the original biochemistry is still preserved, and actually appended to the newly created files. This is especially pertinent when I want to start a model from scratch, without using any previously-used biochemistry from a different model. However, the biochemistry from the previous model re-appears.

samseaver commented 12 years ago

Update on this issue: It seems that the original intention of the overwrite value works fine, it actually overwrites the biochemistry of the model but only the model. I see now that what might be needed is a "refresh/original" option, where all other models except for those originally in database, are removed. I can't see that such an option would be used very often, but it would be useful for testing purposes. I'm closing this issue for now, as I don't think it is of any priority.

samseaver commented 12 years ago

I'm re-opening this issue, because for the new database I want to be sure that overwrite does exactly what is intended, for all reactions, compounds, model details, and biomass.