yaml2sbml-dev / yaml2sbml

Tool to convert an ODE model specified in the YAML format to SBML.
https://yaml2sbml.readthedocs.io/en/latest/
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validation error for formulas starting with minus #99

Closed jvanhoefer closed 3 years ago

jvanhoefer commented 3 years ago

As @yannikschaelte pointed out to me: If a right hand side/formula starts with a minus, the translator/validator throws ScannerError: sequence entries are not allowed here (Since yaml-blocks start with a -, and the validator complains...). I don't know, wether there is a direct fix (but doubt this a bit, since this is how yaml are parsed??).

Possible ways around would be setting the formula either in quotes ("...") or in brackets... Therefore I propose

jvanhoefer commented 3 years ago

Other points in a similar direction

yannikschaelte commented 3 years ago

One could reference the sbml specification, but there may also be constraints from libsbml or mathml, so eventually only the successful export to sbml may give full validity.