def cellmlFileToAntimony(CellMLFileName):
"""Load a cellml file and return the
equivalent antimony string:
ant = cellMLToAntimony('mymodel.cellml')
"""
if antimony.loadCellMLFile(CellMLFileName) == -1:
raise Exception("Error calling loadCellMLFile")
antimony.loadCellMLFile(CellMLFileName)
return antimony.getAntimonyString(None)
def cellmlStrToSBML(CellMLStr):
"""Convert a cellml string into the
equivalent SBML string:
sbmlStr = cellMLStrToSBML('mymodel.cellml')
"""
if antimony.loadCellMLFile(CellMLStr) < 0:
raise Exception("Error calling cellMLStrToSBML" + antimony.getLastError())
return antimony.getSBMLString(None)
def cellmlStrToAntimony(CellMLStr):
"""Convert a cellml string into the
equivalent antimony string:
ant = cellMLStrToAntimony('mymodel.cellml')
"""
if antimony.loadCellMLFile(CellMLStr) < 0:
raise Exception("Error calling cellMLStrToAntimony" + antimony.getLastError())
return antimony.getAntimonyString(None)
def cellmlFileToSBML(CellMLFileName):
"""Load a cellml file and return the
equivalent SBML string:
sbmlStr = cellMLToSBML('mymodel.cellml')
"""
if antimony.loadCellMLFile(CellMLFileName) < 0:
raise Exception("Error calling loadCellMLFile" + antimony.getLastError())
return antimony.getSBMLString(None)
def cellmlToSBML(cellml):
""" Convert CellML to SBML string.
:param cellml: CellML string or file
:type cellml: str | file
:return: SBML
:rtype: str
"""
if os.path.isfile(cellml):
code = antimony.loadCellMLFile(cellml)
else:
code = antimony.loadCellMLString(cellml)
_checkAntimonyReturnCode(code)
return antimony.getSBMLString(None)
def cellmlToSBML(cellml):
""" Convert CellML to SBML string.
:param cellml: CellML string or file
:type cellml: str | file
:return: SBML
:rtype: str
"""
if os.path.isfile(cellml):
code = antimony.loadCellMLFile(cellml)
else:
code = antimony.loadCellMLString(cellml)
_checkAntimonyReturnCode(code)
return antimony.getSBMLString(None)
def cellmlFileToAntimony(self, sbml_path):
""" Converts a CellML file to Antimony source.
:param sbml_path: The path to the CellML file
:returns: A 2-tuple (module_name, antimony_source)
"""
import antimony as sb
# try to load the Antimony code`
code = sb.loadCellMLFile(sbml_path)
# if errors, bail
if self.checkAntimonyReturnCode(code):
errors = sb.getLastError()
raise RuntimeError('Errors encountered when trying to load model:\n{}'.format(errors))
module = sb.getMainModuleName()
sb_source = sb.getAntimonyString(module)
return (module, sb_source)
def cellmlFileToAntimony(self, sbml_path):
""" Converts a CellML file to Antimony source.
:param sbml_path: The path to the CellML file
:returns: A 2-tuple (module_name, antimony_source)
"""
import antimony as sb
# try to load the Antimony code`
code = sb.loadCellMLFile(sbml_path)
# if errors, bail
if self.checkAntimonyReturnCode(code):
errors = sb.getLastError()
raise RuntimeError('Errors encountered when trying to load model:\n{}'.format(errors))
module = sb.getMainModuleName()
sb_source = sb.getAntimonyString(module)
return (module, sb_source)
