def atomize(self, ticket, xmlFile, atomize, userConf = None):
reaction = 'config/reactionDefinitions.json'
try:
logStream = StringIO.StringIO()
if userConf:
jsonpointer = tempfile.mkstemp(suffix='.json', text=True)
with open(jsonpointer[1], 'w') as f:
f.write(userConf)
jsonpointer = jsonpointer[1]
else:
jsonpointer = None
result = libsbml2bngl.readFromString(xmlFile,
reaction, False, jsonpointer, atomize, logStream)
if result and atomize:
pointer = tempfile.mkstemp(suffix='.bngl', text=True)
with open(pointer[1], 'w') as f:
f.write(result.finalString)
print pointer[1]
bnglresult = libsbml2bngl.postAnalyzeString(pointer[1], bngDistro, result.database)
else:
bnglresult = result.finalString
self.addToDict(ticket, [bnglresult, logStream.getvalue(), {'finalspecies':result.database.species, 'rawreactions':result.database.rawreactions}])
print 'success', ticket
except:
self.addToDict(ticket, -5)
print 'failure', ticket
finally:
task.deferLater(reactor, 600, freeQueue, ticket)
def atomize(self,ticket,xmlFile,atomize):
reaction = 'config/reactionDefinitions.json'
print ticket
try:
result = libsbml2bngl.readFromString(xmlFile,
reaction,False,None,atomize)
self.addToDict(ticket,result)
print 'sucess',result
except:
self.addToDict(ticket,-5)
print 'failure'
def generateAnnotation(self,ticket,xmlFile):
print ticket
reaction = 'config/reactionDefinitions.json'
pointer = tempfile.mkstemp(suffix='.xml',text=True)
with open(pointer[1],'w' ) as f:
f.write(xmlFile)
'''
call(['python','annotationExtender.py',
'-i',pointer[1],
'-o',pointer[1]+'.xml'])
with open(pointer[1]+'.xml','r') as f:
result = f.read()
'''
bnglFile = libsbml2bngl.readFromString(xmlFile,
reaction,False,None,True)
result = annotationExtender.expandAnnotation(pointer[1],bnglFile)
self.addToDict(ticket,result)
print 'success',
