def getGINSimModel(self):
if self.model.format == LogicalModel.ZGINML:
return ginsim.load(join(settings.MEDIA_ROOT, self.model.file.path))
elif self.model.format == LogicalModel.MABOSS:
biolqm_model = self.getBioLQMModel()
ginsim_model = biolqm.to_ginsim(biolqm_model)
ginsim.service("layout").runLayout(2, ginsim_model)
return ginsim_model
elif self.model.format == LogicalModel.SBML:
biolqm_model = biolqm.load(
join(settings.MEDIA_ROOT, self.model.file.path))
for component in biolqm_model.getComponents():
if component.getName() != "":
component.setNodeID(
re.sub('[^A-Za-z0-9_]+', '', component.getName()))
ginsim_model = biolqm.to_ginsim(biolqm_model)
ginsim.service("layout").runLayout(2, ginsim_model)
return ginsim_model
else:
raise MethodNowAllowed()
def getSBMLModelFile(self):
if self.model.format == LogicalModel.ZGINML:
ginsim_model = ginsim.load(
join(settings.MEDIA_ROOT, self.model.file.path))
path = tempfile.mkdtemp()
tmp_sbml = tempfile.mkstemp(dir=path, suffix='.sbml')[1]
biolqm.save(ginsim_model, tmp_sbml, "sbml")
return tmp_sbml
elif self.model.format == LogicalModel.MABOSS:
ginsim_model = self.getBioLQMModel()
path = tempfile.mkdtemp()
tmp_sbml = tempfile.mkstemp(dir=path, suffix='.sbml')[1]
biolqm.save(ginsim_model, tmp_sbml, "sbml")
return tmp_sbml
elif self.model.format == LogicalModel.SBML:
return join(settings.MEDIA_ROOT, self.model.file.path)
else:
raise MethodNotAllowed()
def get(self, request, project_id, model_id, tag): HasModel.load(self, request, project_id, model_id) try: tagged_version = TaggedLogicalModel.objects.get(model=self.model, tag=tag) ginsim_model = ginsim.load(join(settings.MEDIA_ROOT, tagged_version.file.path)) sbml_filename = join(settings.TMP_ROOT, splitext(basename(tagged_version.file.path))[0] + ".sbml") biolqm.save(ginsim_model, sbml_filename, "sbml") return FileResponse( open(sbml_filename, 'rb'), as_attachment=True, filename=basename(sbml_filename) ) except TaggedLogicalModel.DoesNotExist: raise NotFound
def getBioLQMModel(self):
if self.model.format == LogicalModel.MABOSS:
maboss_sim = maboss.load(
join(settings.MEDIA_ROOT, self.model.bnd_file.path),
join(settings.MEDIA_ROOT, self.model.cfg_file.path))
biolqm_model = maboss.to_biolqm(maboss_sim)
return biolqm_model
elif self.model.format == LogicalModel.ZGINML:
ginsim_model = ginsim.load(
join(settings.MEDIA_ROOT, self.model.file.path))
return ginsim.to_biolqm(ginsim_model)
elif self.model.format == LogicalModel.SBML:
biolqm_model = biolqm.load(
join(settings.MEDIA_ROOT, self.model.file.path))
return biolqm_model
else:
raise MethodNotAllowed()
def getMaBoSSModel(self):
if self.model.format == LogicalModel.MABOSS:
return maboss.load(
join(settings.MEDIA_ROOT, self.model.bnd_file.path),
join(settings.MEDIA_ROOT, self.model.cfg_file.path))
elif self.model.format == LogicalModel.ZGINML:
ginsim_model = ginsim.load(self.model.file.path)
return ginsim.to_maboss(ginsim_model)
elif self.model.format == LogicalModel.SBML:
t0 = time()
biolqm_model = biolqm.load(self.model.file.path)
t1 = time()
print("Loaded sbml with biolqm : %.2gs" % (t1 - t0))
maboss_model = biolqm.to_maboss(biolqm_model)
print("Converted to MaBoSS : %.2gs" % (time() - t1))
return maboss_model
else:
raise MethodNotAllowed()
def post(self, request, project_id, model_id):
# print("Entering post function")
t0 = time()
HasModel.load(self, request, project_id, model_id)
t1 = time()
# print("Model properties loaded (%.2gs)" % (t1-t0))
if self.model.format == LogicalModel.ZGINML:
path = join(settings.MEDIA_ROOT, self.model.file.path)
ginsim_model = ginsim.load(path)
maboss_model = ginsim.to_maboss(ginsim_model)
tmp_bnd_path = join(settings.TMP_ROOT, splitext(basename(self.model.file.path))[0] + ".bnd")
bnd_file = open(tmp_bnd_path, 'w')
maboss_model.print_bnd(out=bnd_file)
bnd_file.close()
tmp_cfg_path = join(settings.TMP_ROOT, splitext(basename(self.model.file.path))[0] + ".cfg")
cfg_file = open(tmp_cfg_path, 'w')
maboss_model.print_cfg(out=cfg_file)
cfg_file.close()
maboss_simulation = MaBoSSSimulation(
project=self.project,
model=self.model,
name=request.POST['name'],
bnd_file=File(open(tmp_bnd_path, 'rb'), name=basename(tmp_bnd_path)),
cfg_file=File(open(tmp_cfg_path, 'rb'), name=basename(tmp_cfg_path)),
status=MaBoSSSimulation.BUSY
)
maboss_simulation.save()
remove(tmp_bnd_path)
remove(tmp_cfg_path)
elif self.model.format == LogicalModel.MABOSS:
bnd_path = join(settings.MEDIA_ROOT, self.model.bnd_file.path)
cfg_path = join(settings.MEDIA_ROOT, self.model.cfg_file.path)
maboss_simulation = MaBoSSSimulation(
project=self.project,
model=self.model,
name=request.POST['name'],
bnd_file=File(open(bnd_path, 'rb'), name=basename(bnd_path)),
cfg_file=File(open(cfg_path, 'rb'), name=basename(cfg_path)),
status=MaBoSSSimulation.BUSY
)
maboss_simulation.save()
maboss_model = maboss.load(bnd_path, cfg_path)
elif self.model.format == LogicalModel.SBML:
maboss_model = self.getMaBoSSModel()
tmp_bnd_path = join(settings.TMP_ROOT, splitext(basename(self.model.file.path))[0] + ".bnd")
bnd_file = open(tmp_bnd_path, 'w')
maboss_model.print_bnd(out=bnd_file)
bnd_file.close()
tmp_cfg_path = join(settings.TMP_ROOT, splitext(basename(self.model.file.path))[0] + ".cfg")
cfg_file = open(tmp_cfg_path, 'w')
maboss_model.print_cfg(out=cfg_file)
cfg_file.close()
maboss_simulation = MaBoSSSimulation(
project=self.project,
model=self.model,
name=request.POST['name'],
bnd_file=File(open(tmp_bnd_path, 'rb'), name=basename(tmp_bnd_path)),
cfg_file=File(open(tmp_cfg_path, 'rb'), name=basename(tmp_cfg_path)),
status=MaBoSSSimulation.BUSY
)
maboss_simulation.save()
remove(tmp_bnd_path)
remove(tmp_cfg_path)
else:
return HttpResponse(status=500)
# t2 = time()
# print("Model loaded (%.2gs)" % (t2-t1))
cfg_settings = loads(request.POST['settings'])
maboss_model.param.update(cfg_settings)
maboss_model.param['thread_count'] = 6
maboss_model.param['time_tick'] = float(maboss_model.param['max_time'])/100
mutations = loads(request.POST['mutations'])
for var, mutation in mutations.items():
maboss_model.mutate(var, mutation)
maboss_model.network.set_output(
[key for key, value in loads(request.POST['outputVariables']).items() if value]
)
for var, istate in parseIstates(request.POST['initialStates']).items():
maboss_model.network.set_istate(var, istate)
maboss_simulation.update_model(maboss_model)
server_host = request.POST.get('serverHost')
server_port = request.POST.get('serverPort')
thread = Thread(target=run_simulation, args=(maboss_model, maboss_simulation.id, server_host, server_port))
# t3 = time()
# print("Thread built (%.2gs)" % (t3-t2))
thread.start()
return Response({'simulation_id': maboss_simulation.id}, status=status.HTTP_200_OK)
# Author: CoLoMoTo # Affiliation: CoLoMoTo # Aim: Export a GINsim model into NuSMV-compatible format. # Date: 20/07/2017 # Example of a CL # python3 ginsim_export_as_NuSMV.py model.zginml ./model.smv import sys import ginsim import biolqm from shutil import copyfile # Load a model model = ginsim.load(sys.argv[1]) # Convert model to NuSMV s = ginsim.to_nusmv(model) # Export converted model copyfile(s.input_smv, sys.argv[2])
