def load(self, request, project_id, model_id):
HasProject.load(self, request, project_id)
try:
model = LogicalModel.objects.get(id=model_id)
if model.project != self.project:
raise PermissionDenied
self.model = model
except LogicalModel.DoesNotExist:
raise NotFound
def load(self, request, project_id, simulation_id):
HasProject.load(self, request, project_id)
try:
simulation = MaBoSSSimulation.objects.get(id=simulation_id)
if simulation.project != self.project:
raise PermissionDenied
self.simulation = simulation
except MaBoSSSimulation.DoesNotExist:
raise NotFound
def delete(self, request, project_id, model_id):
HasProject.load(self, request, project_id)
try:
model = LogicalModel.objects.get(id=model_id)
if model.project != self.project:
raise PermissionDenied
model.delete()
except LogicalModel.DoesNotExist:
raise NotFound
return Response(status=status.HTTP_200_OK)
def load(self, request, project_id, analysis_id):
if request.user.is_anonymous:
raise PermissionDenied
HasProject.load(self, request, project_id)
try:
analysis = MaBoSSSensitivityAnalysis.objects.get(id=analysis_id)
if analysis.project != self.project:
raise PermissionDenied
self.analysis = analysis
except MaBoSSSensitivityAnalysis.DoesNotExist:
raise NotFound
def get(self, request, project_id, model_id=None):
HasProject.load(self, request, project_id)
try:
if model_id is None:
models = LogicalModel.objects.filter(project=self.project)
serializer = LogicalModelSerializer(models, many=True)
return Response(serializer.data)
else:
model = LogicalModel.objects.get(id=model_id)
if model.project != self.project:
raise PermissionDenied
serializer = LogicalModelSerializer(model)
return Response(serializer.data)
except LogicalModel.DoesNotExist:
raise NotFound
def post(self, request, project_id):
HasProject.load(self, request, project_id)
# try:
if 'url' in request.data.keys():
print(request.data['url'])
if request.data['url'].startswith("https://www.ebi.ac.uk"):
zip_filename = tempfile.mkstemp(suffix=".zip")
os.close(zip_filename[0])
urlretrieve(request.data['url'], zip_filename[1])
with zipfile.ZipFile(zip_filename[1], 'r') as zip_file:
temp_dir = tempfile.mkdtemp()
zip_file.extract(zip_file.namelist()[0], temp_dir)
(bnd_file, cfg_file, layout_file) = sbml_to_maboss(
os.path.join(temp_dir,
zip_file.namelist()[0]),
request.data['use_sbml_names'].lower() == "true")
new_model = LogicalModel(
project=self.project,
name=request.data['name'],
bnd_file=File(open(bnd_file, 'rb'),
name=os.path.basename(bnd_file)),
cfg_file=File(open(cfg_file, 'rb'),
name=os.path.basename(cfg_file)),
layout_file=File(open(layout_file, 'rb'),
name=os.path.basename(layout_file))
if layout_file is not None else None,
format=LogicalModel.MABOSS).save()
os.remove(bnd_file)
os.remove(cfg_file)
if layout_file is not None:
os.remove(layout_file)
shutil.rmtree(temp_dir)
os.remove(zip_filename[1])
else:
sbml_file = tempfile.mkstemp(suffix=".sbml")
os.close(sbml_file[0])
urlretrieve(request.data['url'], sbml_file[1])
(bnd_file, cfg_file, layout_file) = sbml_to_maboss(
sbml_file[1],
request.data['use_sbml_names'].lower() == "true")
new_model = LogicalModel(
project=self.project,
name=request.data['name'],
bnd_file=File(open(bnd_file, 'rb'),
name=os.path.basename(bnd_file)),
cfg_file=File(open(cfg_file, 'rb'),
name=os.path.basename(cfg_file)),
layout_file=File(open(layout_file, 'rb'),
name=os.path.basename(layout_file))
if layout_file is not None else None,
format=LogicalModel.MABOSS).save()
os.remove(bnd_file)
os.remove(cfg_file)
if layout_file is not None:
os.remove(layout_file)
os.remove(sbml_file[1])
elif 'file2' in request.data.keys():
LogicalModel(project=self.project,
name=request.data['name'],
bnd_file=request.data['file'],
cfg_file=request.data['file2'],
format=LogicalModel.MABOSS).save()
elif request.data['file'].name.endswith(".zginml"):
ginsim_file = tempfile.mkstemp(suffix=".zginml")
with open(ginsim_file[0], 'wb') as f:
f.write(request.data['file'].read())
bnd_file, cfg_file = ginsim_to_maboss(ginsim_file[1])
LogicalModel(project=self.project,
name=request.data['name'],
bnd_file=File(open(bnd_file, 'rb'),
name=os.path.basename(bnd_file)),
cfg_file=File(open(cfg_file, 'rb'),
name=os.path.basename(cfg_file)),
format=LogicalModel.MABOSS).save()
elif request.data['file'].name.endswith(".bnet"):
bnet_file = tempfile.mkstemp(suffix=".bnet")
with open(bnet_file[0], 'wb') as f:
f.write(request.data['file'].read())
bnd_file, cfg_file = bnet_to_maboss(bnet_file[1])
LogicalModel(project=self.project,
name=request.data['name'],
bnd_file=File(open(bnd_file, 'rb'),
name=os.path.basename(bnd_file)),
cfg_file=File(open(cfg_file, 'rb'),
name=os.path.basename(cfg_file)),
format=LogicalModel.MABOSS).save()
else:
sbml_file = tempfile.mkstemp(suffix=".sbml")
with open(sbml_file[0], 'wb') as f:
f.write(request.data['file'].read())
bnd_file, cfg_file, layout_file = sbml_to_maboss(
sbml_file[1], request.data['use_sbml_names'].lower() == "true")
LogicalModel(project=self.project,
name=request.data['name'],
bnd_file=File(open(bnd_file, 'rb'),
name=os.path.basename(bnd_file)),
cfg_file=File(open(cfg_file, 'rb'),
name=os.path.basename(cfg_file)),
layout_file=File(open(layout_file, 'rb'),
name=os.path.basename(layout_file))
if layout_file is not None else None,
format=LogicalModel.MABOSS).save()
os.remove(bnd_file)
os.remove(cfg_file)
if layout_file is not None:
os.remove(layout_file)
os.remove(sbml_file[1])
return Response(status=status.HTTP_200_OK)
def __init__(self, *args, **kwargs):
HasProject.__init__(self, *args, **kwargs)
self.model = None
def __init__(self, *args, **kwargs):
HasProject.__init__(self, *args, **kwargs)
self.analysis = None
def __init__(self, *args, **kwargs):
HasProject.__init__(self, *args, **kwargs)
self.simulation = None