def extractMoleculeTypes(self,ticket,bnglContents, bnglContents2):
moleculeTypesList = []
for element in [bnglContents, bnglContents2]:
pointer = tempfile.mkstemp(suffix='.bngl', text=True)
with open(pointer[1], 'w') as f:
f.write(element)
print pointer[1]
consoleCommands.setBngExecutable(bngDistro)
consoleCommands.bngl2xml(pointer[1])
xmlFileName = pointer[1].split('.')[0] + '.xml'
xmlFileName = xmlFileName.split(os.sep)[-1]
moleculeTypes, _, _ = readBNGXML.parseXML(xmlFileName)
moleculeTypesList.append(moleculeTypes)
os.remove(xmlFileName)
self.addToDict(ticket, moleculeTypesList)
print 'success', ticket
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].split('/')[-1]
with open('{0}_{1}.gml'.format(name, graphtype), 'r') as f:
graphContent = f.read()
gml = networkx.read_gml('{0}_{1}.gml'.format(name, graphtype))
result = gml2cyjson(gml, graphtype=graphtype)
jsonStr = json.dumps(result, indent=1, separators=(',', ': '))
result = {'jsonStr': jsonStr, 'gmlStr': graphContent}
self.addToDict(ticket, result)
os.remove('{0}_{1}.gml'.format(name, graphtype))
print 'success', ticket
elif graphtype in ['sbgn_er']:
consoleCommands.setBngExecutable(bngDistro)
consoleCommands.generateGraph(pointer[1], 'contactmap')
name = pointer[1].split('.')[0].split('/')[-1]
# 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)
os.remove('{0}_{1}.gml'.format(name, 'contactmap'))
print 'success', ticket
elif graphtype in ['std']:
consoleCommands.setBngExecutable(bngDistro)
consoleCommands.bngl2xml(pointer[1])
xmlFileName = pointer[1].split('.')[0] + '.xml'
xmlFileName = xmlFileName.split(os.sep)[-1]
graph = stdgraph.generateSTDGML(xmlFileName)
gmlGraph = networkx.generate_gml(graph)
#os.remove('{0}.gml'.format(xmlFileName))
result = gml2cyjson(graph, graphtype=graphtype)
jsonStr = json.dumps(result, indent=1, separators=(',', ': '))
result = {'jsonStr': jsonStr, 'gmlStr': ''.join(gmlGraph)}
#self.addToDict(ticket, ''.join(gmlGraph))
self.addToDict(ticket, result)
print 'success', ticket
except:
import traceback
traceback.print_exc()
self.addToDict(ticket,-5)
print 'failure',ticket
finally:
task.deferLater(reactor, 600, freeQueue, ticket)
def compareFiles(self, ticket, bnglContents, bnglContents2, mappingFile):
finalBNGLContent = []
finalNamespace = []
try:
for mapInfo, bnglContent in zip(mappingFile['model'], [bnglContents, bnglContents2]):
pointer = tempfile.mkstemp(suffix='.bngl', text=True)
with open(pointer[1], 'w') as f:
f.write(bnglContent)
print pointer[1]
consoleCommands.setBngExecutable(bngDistro)
consoleCommands.bngl2xml(pointer[1])
xmlFileName = pointer[1].split('.')[0] + '.xml'
xmlFileName = xmlFileName.split(os.sep)[-1]
bnglNamespace = readBNGXML.parseFullXML(xmlFileName)
normalizer.normalizeNamespace(bnglNamespace, mapInfo)
finalBNGLContent.append(readBNGXML.createBNGLFromDescription(bnglNamespace))
finalNamespace.append(bnglNamespace)
# os.remove(pointer[1])
os.remove(xmlFileName)
similarity = modelComparison.evaluateSimilarity(finalNamespace[0], finalNamespace[1])
self.addToDict(ticket, [finalBNGLContent, similarity])
print 'success', ticket
except:
self.addToDict(ticket,-5)
print 'failure',ticket
finally:
task.deferLater(reactor, 600, freeQueue, ticket)
pass
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