def generateGraph(self,fileName,graphType): consoleCommands.generateGraph(fileName,graphType,outputDirectory='/tmp') fileName2 = fileName.split('/')[-1] fileRoot = '.'.join(fileName2.split('.')[:-1]) inputGraph = '/tmp/{1}_{0}.gml'.format(graphType,fileRoot) with open(os.devnull,'r') as f: result = call(['gml2gv',inputGraph],stdout=f) return result
def generateGraph(self,ticket,bnglContents,graphtype): print ticket pointer = tempfile.mkstemp(suffix='.bngl',text=True) with open(pointer[1],'w' ) as f: f.write(bnglContents) #try: if graphtype in ['regulatory','contactmap']: consoleCommands.setBngExecutable(bngDistro) consoleCommands.generateGraph(pointer[1],graphtype) name = pointer[1].split('.')[0] with open('{0}_{1}.gml'.format(name,graphtype),'r') as f: graphContent = f.read() self.addToDict(ticket,graphContent) print 'success',ticket elif graphtype in ['sbgn_er']: consoleCommands.setBngExecutable(bngDistro) consoleCommands.generateGraph(pointer[1],'contactmap') name = pointer[1].split('.')[0] #with open('{0}_{1}.gml'.format(name,'contactmap'),'r') as f: # graphContent = f.read() graphContent = networkx.read_gml('{0}_{1}.gml'.format(name,'contactmap')) sbgn = libsbgn.createSBNG_ER_gml(graphContent) self.addToDict(ticket,sbgn) print 'success',ticket