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',