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
