def exportAsCombine(self, outputpath): # parameter outputpath must be a full path of a zip file you wish to create
# Temporary failsafe - Should be revised once libphrasedml adopts returning of model name
reModel = r"""(\w*) = model ('|")(.*)('|")"""
# rePlot = r"""plot ('|")(.*)('|") (.*)"""
lines = self.phrasedmlStr.splitlines()
for i, s in enumerate(lines):
reSearchModel = re.split(reModel, s)
# reSearchPlot = re.split(rePlot, s)
if len(reSearchModel) > 1:
modelsource = str(reSearchModel[3])
modelname = os.path.basename(modelsource)
if ".xml" or ".sbml" not in modelsource:
modelname = modelname + ".xml"
s = s.replace(modelsource, modelname)
lines[i] = s
# if len(reSearchPlot) > 1:
# plottitle = str(reSearchPlot[2])
revphrasedml = "\n".join(lines)
phrasedml.setReferencedSBML(modelname, te.antimonyTosbml(self.antimonyStr))
combine.export(outputpath, self.antimonyStr, modelname, revphrasedml)
phrasedml.clearReferencedSBML()
def createpython(self): # Create and return Python script given antimony and phrasedml strings
rePath = r"(\w*).load\('(.*)'\)"
reLoad = r"(\w*) = roadrunner.RoadRunner\(\)"
reModel = r"""(\w*) = model ('|")(.*)('|")"""
phrasedmllines = self.phrasedmlStr.splitlines()
for i, s in enumerate(phrasedmllines):
reSearchModel = re.split(reModel, s)
if len(reSearchModel) > 1:
modelsource = str(reSearchModel[3])
modelname = os.path.basename(modelsource)
modelname = str(modelname).replace(".xml", "")
phrasedml.setReferencedSBML(modelsource, te.antimonyTosbml(self.antimonyStr))
sedmlstr = phrasedml.convertString(self.phrasedmlStr)
if sedmlstr == None:
raise Exception(phrasedml.getLastError())
phrasedml.clearReferencedSBML()
fd1, sedmlfilepath = tempfile.mkstemp()
os.write(fd1, sedmlstr)
pysedml = te.SedmlToRr.sedml_to_python(sedmlfilepath)
if self.modelispath == False:
lines = pysedml.splitlines()
for i, s in enumerate(lines):
reSearchPath = re.split(rePath, s)
if len(reSearchPath) > 1:
del lines[i]
for i, s in enumerate(lines):
reSearchLoad = re.split(reLoad, s)
if len(reSearchLoad) > 1:
s = s.replace("roadrunner.RoadRunner()", "te.loada(" + str(modelname) + ")")
lines[i] = s
if not "import tellurium" in pysedml:
if "import roadrunner" in pysedml:
for i, s in enumerate(lines):
if "import roadrunner" in s:
del lines[i]
lines.insert(i, "import tellurium as te")
else:
pass
pysedml = "\n".join(lines)
# List of replacements
pysedml = pysedml.replace('"compartment"', '"compartment_"')
pysedml = pysedml.replace("'compartment'", "'compartment_'")
outputstr = str(modelname) + " = '''" + self.antimonyStr + "'''\n\n" + pysedml
os.close(fd1)
os.remove(sedmlfilepath)
return outputstr
def getSbmlString(self):
return te.antimonyTosbml(self.antimonyStr)