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SemBioProcess / SemGen

A tool for semantics-based annotation and composition of biosimulation models
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SBML and CellML need to be written out in UTF-8 format #273

Closed maxneal closed 6 years ago

maxneal commented 6 years ago

I've had errors show up when exporting to an SBML file, then trying to re-open in SemGen. Seems that the SBML reader encounters an invalid UTF-8 character encoding (the accented "e" in Nicolas LeNovere's last name, which is always included in SBML models from BioModels b/c of the bibliographic reference to the BioModels paper).

GrahamKim commented 6 years ago

Hmm. I'm not able to reproduce this issue. When I try exporting to SBML, the file is already encoded in UTF-8 and SemGen can read "Le Novère N". @maxneal is there a specific model or steps that causes this issue?

maxneal commented 6 years ago

I'll send you an example model where that you can use to reproduce the bug. Things might work OK in the master branch, but I'm seeing the problem in the COMBINEarchive branch that includes lots of updates to the way files are read and written so please test it on that branch.

maxneal commented 6 years ago

Fixed in commit 4b5062423fe2fecfc9156ce271eb7ac58ac45702