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opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
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MEMOTE throws error when writing html #753

Open Wheaties91 opened 9 months ago

Wheaties91 commented 9 months ago

MEMOTE has recently been throwing errors when trying to run it. This is odd as I haven't updated MEMOTE from my end in quite a while (I'm using version 0.13.0). When I try to run MEMOTE, I get the following sets of errors (see at the end). MEMOTE was running fine a couple of months ago. I experience this same set of errors on both my computers. Further, a graduate student I am working with is using MEMOTE version 0.14.0. She only gets the error shown in the second set of images (e.g. the ones after the red line saying failed, passed, and skipped). What do we need to do to be able to use MEMOTE again?

memote_error_1 memote_error_2

Midnighter commented 9 months ago

That's a new one to me. Will need some investigation. Does this happen with all model files or only a particular one?

Wheaties91 commented 9 months ago

It appears that this it happens on particular models, but I'm not sure why it happens on certain one's. So for instance, a model I published previously, MEMOTE works fine on from command line. On the other hand, a model a graduate student I am working with who will publish her model soon does not. Using COBRApy's built in "cobra.io.validate_sbml_model" does not raise any flags, however, sbml.org's validator returns the error "no model was given, or it could not be resolved". Generally, I just verify models locally, which is why I didn't mention the error from SBML org earlier. Therefore, I'm not sure at the moment if it is a problem on the model side that COBRApy doesn't catch, or a bug in memote. Here is an old model file that give the same issues if you need a test system.

LeafModel_curated.txt