Compound names
breakthewall opened this issue · 1 comments
A guy contacted me because Retrosynthesis workflow on galaxy-synbiocad.org failed on the last step (Complete Reactions).
After reproducing locally with CLI, the message was:
Error encountered trying to assign reactant species.LibSBML returned error code -4: "A value passed as an argument to the method is not of a type that is valid for the operation or kind of object involved. For example, this return code is used when a calling program attempts to set an SBML object identifier to a string whose syntax does not conform to the SBML identifier syntax."
After investigations, it turns out that the id of one compound is missformatted (2-Oxoglutarate). Indeed, in the libSBML doc, it is clearly written that an id cannot start with a digit and must not contain -.
Fixed in 5.12.2 release.
-are removed from ids- a
_is prepended if id starts with a digit