def processMDLR(self, mdlrPath):
'''
main method. extracts species definition, creates bng-xml, creates mdl definitions
'''
nautyDict = self.xml2HNautySpeciesDefinitions(mdlrPath)
#append extended bng-xml to the bng-xml definition (the one that doesn't include seed information)
bngxmlestr = writeBXe.mergeBXBXe(namespace.input + '_total.xml', namespace.input + '_extended.xml')
with open(mdlrPath + '_total.xml', 'w') as f:
f.write(bngxmlestr)
xmlspec = readBNGXML.parseFullXML(namespace.input + '.xml')
# write out the equivalent plain mdl stuffs
mdlDict = writeMDL.constructMCell(xmlspec, namespace.input, finalName.split(os.sep)[-1], nautyDict)
writeMDL.writeMDL(mdlDict, finalName)
bnglPath = namespace.input + '.bngl'
finalName = namespace.output if namespace.output else namespace.input
# mdl to bngl
resultDict = readMDL.constructBNGFromMDLR(namespace.input, namespace.nfsim)
outputDir = os.sep.join(namespace.output.split(os.sep)[:-1])
# create bngl file
readMDL.outputBNGL(resultDict['bnglstr'], bnglPath)
# temporaryly store bng-xml information in a separate file for display purposes
with open(namespace.input + '_extended.xml', 'wb') as f:
f.write(resultDict['bngxmlestr'])
#get cannonical label -bngl label dictionary
if not namespace.nfsim:
# bngl 2 sbml 2 json
readMDL.bngl2json(namespace.input + '.bngl')
# json 2 plain mdl
mdlDict = writeMDL.constructMDL(namespace.input + '_sbml.xml.json', namespace.input, finalName)
# create an mdl with nfsim-species and nfsim-reactions
writeMDL.writeMDL(mdlDict, finalName)
else:
mdlr2mdl = MDLR2MDL(os.path.join(getScriptPath(),'mcellr.yaml'))
#get the species definitions
mdlr2mdl.processMDLR(namespace.input)
