def get(self, request, project_id, model_id, tag=None): HasModel.load(self, request, project_id, model_id) try: if tag is None: tagged_models = TaggedLogicalModel.objects.filter(model=self.model) tags = [tagged_model.tag for tagged_model in tagged_models] return Response(tags) else: # Restoring model from tag tagged_model = TaggedLogicalModel.objects.get(model=self.model, tag=tag) # TODO : Which format fo we want ? which format do we have copyfile( join(settings.MEDIA_ROOT, tagged_model.file.path), join(settings.MEDIA_ROOT, self.model.file.path) ) return Response(status=status.HTTP_200_OK) except TaggedLogicalModel.DoesNotExist: raise NotFound
def post(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
positions = loads(request.POST["positions"])
min_x = 0
max_x = 0
min_y = 0
max_y = 0
new_positions = {}
for position in positions:
min_x = min(position['x'], min_x)
max_x = max(position['x'], max_x)
min_y = min(position['y'], min_y)
max_y = max(position['y'], max_y)
new_positions.update({
position['name']: {
'pos': [position['x'] + 30, position['y'] + 30],
'dim': [60.0, 30.0]
}
})
# print(min_x)
# print(max_x)
# print(min_y)
# print(max_y)
self.setLayout(
((60.0 + max_x - min_x, 60 + max_y - min_y), new_positions))
return Response(status=status.HTTP_200_OK)
def delete(self, request, project_id, model_id, node, field):
HasModel.load(self, request, project_id, model_id)
maboss_sim = self.getMaBoSSModel()
if field in ["rateUp", "rateDown"]:
return Response(data={'error': 'Cannot remove %s' % field})
if field == "logic":
maboss_sim.network[node].logExp = None
else:
del maboss_sim.network[node].internal_var[field]
res = simplify_messages(maboss_sim.check())
data = {'error': ''}
if any([
message == ("invalid use of alias attribute @%s in node %s" %
(field, node)) for message in res
]):
if field == "logic":
data.update({
'error':
'The logical formula is used elsewhere in the model'
})
else:
data.update(
{'error': 'The formula %s is used in the model' % field})
elif len(res) > 0:
data.update({'error': res[0]})
return Response(data=data)
def delete(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
maboss_model = self.getMaBoSSModel()
maboss_model.network.remove_node(request.POST['name'])
res = simplify_messages(maboss_model.check())
data = {'error': ''}
if len(res) > 0:
if any([
message.startswith("node")
and message.endswith("used but not defined")
for message in res
]):
for message in res:
if message.startswith("node") and message.endswith(
"used but not defined"):
data.update({'error': message})
elif any([
message == "Some logic rule had unkown variables"
for message in res
]):
data.update({
'error':
"The node %s is used in the model" % request.POST['name']
})
elif len(res) > 0:
data.update({'error': res[0]})
else:
self.saveMaBoSSModel(maboss_model)
return Response(data=data, status=status.HTTP_200_OK)
def get(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
serializer = LogicalModelNameSerializer(self.model)
return Response(serializer.data)
def get(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
ginsim_model = self.getGINSimModel()
fig = ginsim._get_image(ginsim_model)
return HttpResponse(fig, content_type="image/svg+xml")
def post(self, request, project_id, model_id, name):
HasModel.load(self, request, project_id, model_id)
maboss_sim = self.getMaBoSSModel()
maboss_sim.param[name] = request.POST['value']
self.saveMaBoSSModel(maboss_sim)
return Response(status=HTTP_200_OK)
def delete(self, request, project_id, model_id, name):
HasModel.load(self, request, project_id, model_id)
maboss_sim = self.getMaBoSSModel()
del maboss_sim.param[name]
self.saveMaBoSSModel(maboss_sim)
return Response(status=HTTP_200_OK)
def post(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
steady_state = loads(request.data['steady_state'])
ginsim_model = self.getGINSimModel()
fig = ginsim._get_image(ginsim_model, steady_state)
return HttpResponse(fig, content_type="image/svg+xml")
def get(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
maboss_model = self.getMaBoSSModel()
initial_states = maboss_model.network.get_istate()
return Response({
'initial_states': dumpIstates(initial_states),
})
def get(self, request, project_id, model_id, name):
HasModel.load(self, request, project_id, model_id)
maboss_sim = self.getMaBoSSModel()
if name in maboss_sim.param.keys():
return Response(data=maboss_sim.param[name])
else:
raise NotFound
def put(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
maboss_model = self.getMaBoSSModel()
for var, istate in parseIstates(request.POST['initialStates']).items():
maboss_model.network.set_istate(var, istate)
self.saveMaBoSSModel(maboss_model)
return Response(status=HTTP_200_OK)
def post(self, request, project_id, model_id, node):
HasModel.load(self, request, project_id, model_id)
raw_layout = self.getLayout()
if raw_layout is not None:
dims, layout = raw_layout
new_pos = loads(request.POST["position"])
layout[node].update({"pos": [new_pos["x"], new_pos["y"]]})
self.updateLayout((dims, layout))
return Response(status=status.HTTP_200_OK)
def put(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
maboss_model = self.getMaBoSSModel()
for node, is_output in json.loads(request.POST['outputs']).items():
maboss_model.network[node].is_internal = not is_output
self.saveMaBoSSModel(maboss_model)
return Response(status=HTTP_200_OK)
def get(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
cfg_filename = self.getMaBoSSCFGFile()
if cfg_filename is None:
return Response(status=status.HTTP_501_NOT_IMPLEMENTED)
return FileResponse(open(cfg_filename, 'rb'),
as_attachment=True,
filename=basename(cfg_filename))
def delete(self, request, project_id, model_id, tag): HasModel.load(self, request, project_id, model_id) try: tagged_model = TaggedLogicalModel.objects.get(model=self.model, tag=tag) tagged_model.delete() except TaggedLogicalModel.DoesNotExist: raise NotFound return Response(status=status.HTTP_200_OK)
def get(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
model_file = self.getZGINMLModelFile()
if model_file is None:
return Response(status=status.HTTP_501_NOT_IMPLEMENTED)
return FileResponse(open(model_file, 'rb'),
as_attachment=True,
filename=basename(model_file))
def put(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
maboss_model = self.getMaBoSSModel()
for name, value in json.loads(request.POST['settings']).items():
maboss_model.param[name] = float(value)
self.saveMaBoSSModel(maboss_model)
return Response(status=HTTP_200_OK)
def get(self, request, project_id, model_id):
if request.user.is_anonymous:
raise PermissionDenied
HasModel.load(self, request, project_id, model_id)
simulations = MaBoSSSensitivityAnalysis.objects.filter(
model=self.model)
serializer = MaBoSSSensitivityAnalysisSerializer(simulations,
many=True)
return Response(serializer.data)
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) return FileResponse( open(join(settings.MEDIA_ROOT, tagged_version.file.path), 'rb'), as_attachment=True, filename=basename(tagged_version.file.path) ) except TaggedLogicalModel.DoesNotExist: raise NotFound
def get(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
maboss_model = self.getMaBoSSModel()
outputs = {
label: not node.is_internal
for label, node in maboss_model.network.items()
}
return Response({
'outputs':
collections.OrderedDict(sorted(outputs.items())),
})
def get(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
maboss_sim = self.getMaBoSSModel()
data = {}
for parameter, value in maboss_sim.param.items():
if parameter.startswith("$"):
data.update({parameter: value})
return Response(
data=json.dumps(collections.OrderedDict(sorted(data.items()))))
def post(self, request, project_id, model_id, node, field):
HasModel.load(self, request, project_id, model_id)
maboss_sim = self.getMaBoSSModel()
if field == "logic":
maboss_sim.network[node].logExp = request.POST['formula']
elif field == "rateUp":
maboss_sim.network[node].rt_up = request.POST['formula']
elif field == "rateDown":
maboss_sim.network[node].rt_down = request.POST['formula']
else:
maboss_sim.network[node].internal_var.update(
{field: request.POST['formula']})
res = simplify_messages(maboss_sim.check())
data = {'error': ''}
if any([
message.startswith("BND syntax error at line")
for message in res
]):
data.update({'error': 'syntax error'})
elif any([
message.startswith("node")
and message.endswith("used but not defined") for message in res
]):
for message in res:
if message.startswith("node") and message.endswith(
"used but not defined"):
data.update({'error': message})
elif any([
message.startswith(
"invalid use of alias attribute @logic in node")
for message in res
]) and field == "logExp":
data.update({'error': "Syntax error"})
elif len(res) > 0:
data.update({'error': res[0]})
return Response(data=data)
def post(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
if self.model.format == LogicalModel.MABOSS:
maboss_model = self.getMaBoSSModel()
if request.POST['name'] not in maboss_model.network.keys():
maboss_model.network.add_node(request.POST['name'])
self.saveMaBoSSModel(maboss_model)
return Response(status=status.HTTP_200_OK)
else:
return Response(status=status.HTTP_409_CONFLICT)
else:
return Response(status=status.HTTP_501_NOT_IMPLEMENTED)
def get(self, request, project_id, model_id):
HasModel.load(self, request, project_id, model_id)
maboss_model = self.getMaBoSSModel()
settings = {
key: value
for key, value in maboss_model.param.items()
if not key.startswith("$")
}
return Response({
'settings': settings,
})
def delete(self, request, project_id, model_id, node, field):
HasModel.load(self, request, project_id, model_id)
maboss_sim = self.getMaBoSSModel()
if field in ["rateUp", "rateDown"]:
return Response(
data={'error': 'Cannot remove %s' % request.POST['field']})
if field == "logic":
maboss_sim.network[node].logExp = None
else:
del maboss_sim.network[node].internal_var[field]
self.saveMaBoSSModel(maboss_sim)
return Response(status=HTTP_200_OK)
def get(self, request, project_id, model_id, node, field):
HasModel.load(self, request, project_id, model_id)
maboss_sim = self.getMaBoSSModel()
node = maboss_sim.network[node]
node_data = {}
node_data.update({'rateUp': maboss_sim.network[node].rt_up})
node_data.update({'rateDown': maboss_sim.network[node].rt_down})
if node.logExp is not None:
node_data.update({'logic': node.logExp})
node_data.update(node.internal_var)
return Response(data=json.dumps(node_data))
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 post(self, request, project_id, model_id, name):
HasModel.load(self, request, project_id, model_id)
maboss_sim = self.getMaBoSSModel()
maboss_sim.param[name] = request.POST['value']
res = simplify_messages(maboss_sim.check())
data = {'error': ''}
if any([
message.startswith("configuration syntax error")
for message in res
]):
data.update({'error': 'Syntax error'})
elif len(res) > 0:
data.update({'error': res[0]})
return Response(data=data)
def post(self, request, project_id, model_id, node, field):
HasModel.load(self, request, project_id, model_id)
maboss_sim = self.getMaBoSSModel()
if field == "rateUp":
maboss_sim.network[node].rt_up = request.POST['formula']
elif field == "rateDown":
maboss_sim.network[node].rt_down = request.POST['formula']
elif field == "logic":
maboss_sim.network[node].logExp = request.POST['formula']
else:
maboss_sim.network[node].internal_var.update(
{field: request.POST['formula']})
self.saveMaBoSSModel(maboss_sim)
return Response(status=HTTP_200_OK)