2021 CellML Workshop - libCellML Python scripts

afshar.py

import libcellml


p = libcellml.Parser()

with open('New_Modular_Model.cellml') as f:
    contents = f.read()
    m = p.parseModel(contents)

print(m.componentCount())

v = libcellml.Validator()

v.validateModel(m)

print(v.errorCount())

print(m.hasImports())

i = libcellml.Importer()
i.resolveImports(m, '/Users/hsor001/tut/')



v.validateModel(m)


print(v.errorCount())

with open('NaK_flux.cellml') as f:
    contents = f.read()
    m_flux = p.parseModel(contents)

v.validateModel(m_flux)

print(v.errorCount())

for index in range(v.errorCount()):
    print(v.error(index).description())

imp = libcellml.ImportSource()
imp.setUrl('Units.cellml')

for index in range(v.errorCount()):
    if v.error(index).variable() is not None:
        name = v.error(index).variable().units().name()
        if not m_flux.hasUnits(name):
            u = libcellml.Units(name)
            u.setImportSource(imp)
            u.setImportReference(name)
            print(name, m_flux.addUnits(u))

v.validateModel(m_flux)

print(v.errorCount())

cn_units_names = ['per_umol', 'per_volt4_per_second', 'per_volt3_per_second', 'per_volt2_per_second', 'per_volt_per_second']

for cn_units_name in cn_units_names:
    u = libcellml.Units(cn_units_name)
    u.setImportSource(imp)
    u.setImportReference(cn_units_name)
    print(cn_units_name, m_flux.addUnits(u))


v.validateModel(m_flux)

print(v.errorCount())


pr = libcellml.Printer()

flux_content = pr.printModel(m_flux)

print(flux_content)

with open('NaK_flux_with_units.cellml', 'w') as f:
    f.write(flux_content)