def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingProject.__init__(self) self.listOfSimulations = None self.fileUploadForm = DocumentForm()
def get(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
if len(args) > 0:
if Experiment.objects.filter(id=int(args[0])).exists():
experiment = Experiment.objects.get(id=int(args[0]))
if experiment.project.access == 'PU' or experiment.project.user == request.user:
filename = exportExperiment(experiment)
response = HttpResponse(open(filename, 'rb'),
content_type='text/xml')
response[
'Content-Disposition'] = 'attachment; filename=' + basename(
filename)
remove(filename)
return response
else:
raise PermissionDenied
else:
raise Http404("Data doesn't exists")
redirect('experimental_data')
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingProject.__init__(self)
self.listOfSimulations = None
self.fileUploadForm = DocumentForm()
def post(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
self.loadExperiments(request)
if "action" in request.POST:
if HasWorkingProject.isChooseProject(self, request):
self.loadExperiments(request)
elif request.POST['action'] == "create":
self.newExperiment(request)
elif request.POST['action'] == "delete":
self.deleteExperiment(request)
elif request.POST['action'] == "edit":
self.editExperiment(request)
elif request.POST['action'] == "save":
self.saveExperiment(request)
elif request.POST['action'] == "duplicate":
self.duplicateExperiment(request)
return TemplateView.get(self, request, *args, **kwargs)
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingProject.__init__(self) self.optimizationId = None self.parameters = None self.inputParameters = None self.outputParameters = None self.modelName = None self.submodelNames = None self.modifiedSubmodelNames = None self.optimizationStatus = None self.showGraph = None self.optimPath = None self.experiments = None self.experimentsData = None self.scoreTime = [] self.scoreValues = [] self.scoreRawValues = [] self.scoreMinEv = [] self.scoreMaxEv = [] self.optimizationModel = None
def get(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
self.load(request, *args, **kwargs)
return TemplateView.get(self, request, *args, **kwargs)
def load(self, request, *args, **kwargs): HasWorkingProject.load(self, request, *args, **kwargs) self.loadExperiment(request, *args) self.loadCondition(request, *args) self.loadObservations() self.loadTreatments()
def load(self, request, *args, **kwargs): HasWorkingProject.load(self, request, *args, **kwargs) self.loadExperiment(request, *args) self.loadCondition(request, *args) self.loadObservations() self.loadTreatments()
def get(self, request, *args, **kwargs):
if len(args) > 0:
HasWorkingProject.load(self, request, *args, **kwargs)
self.setProject(request, args[0])
return redirect('models')
self.load(request, *args, **kwargs)
return TemplateView.get(self, request, *args, **kwargs)
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingProject.__init__(self) HasUserLoggedIn.__init__(self) HasErrorMessages.__init__(self) self.listOfModels = None self.fileUploadForm = DocumentForm()
def get(self, request, *args, **kwargs):
if len(args) > 0:
HasWorkingProject.load(self, request, *args, **kwargs)
self.setProject(request, args[0])
return redirect('models')
self.load(request, *args, **kwargs)
return TemplateView.get(self, request, *args, **kwargs)
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingProject.__init__(self)
self.listOfExperiments = None
self.experimentId = None
self.experimentName = None
self.experimentNotes = None
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingProject.__init__(self)
HasUserLoggedIn.__init__(self)
HasErrorMessages.__init__(self)
self.listOfModels = None
self.fileUploadForm = DocumentForm()
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingProject.__init__(self) self.listOfFolders = None self.createFolderShow = None self.createFolderError = None self.sendFolderShow = None self.sendFolderError = None
def load(self, request, recompute=True, *args, **kwargs):
# print("> Model loading")
HasWorkingProject.load(self, request, *args, **kwargs)
HasVariablesInSession.load(self, request, *args, **kwargs)
self.__request = request
self.__loadModels(request)
self.__loadModel(request, *args)
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingProject.__init__(self)
self.listOfFolders = None
self.createFolderShow = None
self.createFolderError = None
self.sendFolderShow = None
self.sendFolderError = None
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingProject.__init__(self) self.listOfExperiments = None self.experimentId = None self.experimentName = None self.experimentNotes = None self.fileUploadForm = DocumentForm()
def load(self, request, recompute=True, *args, **kwargs):
# print("> Model loading")
HasWorkingProject.load(self, request, *args, **kwargs)
HasVariablesInSession.load(self, request, *args, **kwargs)
self.__request = request
self.__loadModels(request)
self.__loadModel(request, *args)
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingProject.__init__(self)
self.experiment = None
self.listOfConditions = None
self.conditionId = None
self.conditionName = None
self.conditionNotes = None
def post(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
if (Condition.objects.filter(id=int(request.POST['id'])).exists()):
condition = Condition.objects.get(id=int(request.POST['id']))
self.data.update({
'name': "" if condition.name is None else condition.name,
'notes': "" if condition.notes is None else condition.notes
})
return JsonRequest.post(self, request, *args, **kwargs)
def post(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
if Experiment.objects.filter(project=self.project, id=int(request.POST['id'])).exists():
experiment = Experiment.objects.get(project=self.project, id=int(request.POST['id']))
self.data.update({
'name': "" if experiment.name is None else experiment.name,
'notes': "" if experiment.notes is None else experiment.notes
})
return JsonRequest.post(self, request, *args, **kwargs)
def __init__(self):
HasWorkingProject.__init__(self)
self.list_of_models = None
self.model = None
self.modelInstance = None
self.model_id = None
self.model_name = None
self.model_filename = None
self.model_list_of_submodels = []
self.model_list_of_submodels_names = []
self.model_list_of_submodels_types = []
self.model_submodel = None
def post(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
if Treatment.objects.filter(id=int(request.POST['id'])).exists():
treatment = Treatment.objects.get(id=int(request.POST['id']))
self.data.update({
'species': treatment.species,
'time': treatment.time,
'value': treatment.value
})
return JsonRequest.post(self, request, *args, **kwargs)
def post(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
if Treatment.objects.filter(id=int(request.POST['id'])).exists():
treatment = Treatment.objects.get(id=int(request.POST['id']))
self.data.update({
'species': treatment.species,
'time': treatment.time,
'value': treatment.value
})
return JsonRequest.post(self, request, *args, **kwargs)
def get_context_data(self, **kwargs): kwargs = HasWorkingProject.get_context_data(self, **kwargs) kwargs['list_of_simulations'] = self.listOfSimulations kwargs['load_simulation_form'] = self.fileUploadForm return kwargs
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingProject.__init__(self) self.experiment = None self.condition = None self.dataPoints = None self.treatmentPoints = None self.observations = None self.treatments = None self.observationForm = ObservationForm(self) self.treatmentForm = TreatmentForm(self)
def get_context_data(self, **kwargs):
kwargs = HasWorkingProject.get_context_data(self, **kwargs)
kwargs['plots_2d'] = self.listOfPlots2D
kwargs['colors'] = Settings.default_colors
return kwargs
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingProject.__init__(self) self.experiment = None self.condition = None self.dataPoints = None self.treatmentPoints = None self.observations = None self.treatments = None self.observationForm = ObservationForm(self) self.treatmentForm = TreatmentForm(self)
def post(self, request, *args, **kwargs):
self.load(request, *args, **kwargs)
if "action" in request.POST:
if HasWorkingProject.isChooseProject(self, request):
self.loadModels(request)
elif request.POST['action'] == "delete_model":
self.deleteModel(request)
self.load(request, *args, **kwargs)
elif request.POST['action'] == "load_model":
self.loadModel(request)
self.load(request, *args, **kwargs)
elif request.POST['action'] == "duplicate_model":
self.duplicateModel(request)
self.load(request, *args, **kwargs)
elif request.POST['action'] == "new_model":
self.newModel(request)
self.load(request, *args, **kwargs)
elif request.POST['action'] == "load_biomodels":
self.loadBiomodels(request)
self.load(request, *args, **kwargs)
return TemplateView.get(self, request, *args, **kwargs)
def get_context_data(self, **kwargs):
kwargs = HasWorkingProject.get_context_data(self, **kwargs)
kwargs['list_of_simulations'] = self.listOfSimulations
kwargs['load_simulation_form'] = self.fileUploadForm
return kwargs
def post(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
if (Condition.objects.filter(id=int(request.POST['id'])).exists()):
condition = Condition.objects.get(id=int(request.POST['id']))
self.data.update({
'name':
"" if condition.name is None else condition.name,
'notes':
"" if condition.notes is None else condition.notes
})
return JsonRequest.post(self, request, *args, **kwargs)
def post(self, request, *args, **kwargs):
self.load(request, *args, **kwargs)
if "action" in request.POST:
if HasWorkingProject.isChooseProject(self, request):
return redirect('experimental_data')
elif request.POST['data_type'] == 'treatment':
if request.POST['action'] == "delete":
self.deleteTreatment(request)
elif request.POST['action'] == "save":
self.saveTreatment(request)
self.loadTreatments()
elif request.POST['data_type'] == "observation":
if request.POST['action'] == "delete":
self.deleteObservation(request)
elif request.POST['action'] == "save":
self.saveObservation(request)
self.loadObservations()
return TemplateView.get(self, request, *args, **kwargs)
def post(self, request, *args, **kwargs): self.load(request, *args, **kwargs) if "action" in request.POST: if HasWorkingProject.isChooseProject(self, request): self.loadModels(request) elif request.POST['action'] == "delete_model": self.deleteModel(request) self.load(request, *args, **kwargs) elif request.POST['action'] == "load_model": self.loadModel(request) self.load(request, *args, **kwargs) elif request.POST['action'] == "duplicate_model": self.duplicateModel(request) self.load(request, *args, **kwargs) elif request.POST['action'] == "new_model": self.newModel(request) self.load(request, *args, **kwargs) elif request.POST['action'] == "load_biomodels": self.loadBiomodels(request) self.load(request, *args, **kwargs) return TemplateView.get(self, request, *args, **kwargs)
def post(self, request, *args, **kwargs): self.load(request, *args, **kwargs) if "action" in request.POST: if HasWorkingProject.isChooseProject(self, request): self.load(request, *args, **kwargs) elif request.POST['action'] == "new_folder": self.newFolder(request) elif request.POST['action'] == "copy_folder": self.copyFolder(request) elif request.POST['action'] == "delete_folder": self.deleteFolder(request) elif request.POST['action'] == "send_folder": self.sendFolder(request) elif request.POST['action'] == "load_folder": self.loadFolder(request) elif request.POST['action'] == "save_project": self.saveProject(request) return TemplateView.get(self, request, *args, **kwargs)
def __init__(self):
HasWorkingProject.__init__(self)
HasVariablesInSession.__init__(self)
self.list_of_models = None
self.model = None
self.modelInstance = None
self.model_id = None
self.model_name = None
self.model_filename = None
self.model_list_of_submodels = []
self.model_list_of_submodels_names = []
self.model_list_of_submodels_types = []
self.model_submodel = None
self.__request = None
def get_context_data(self, **kwargs): kwargs = HasWorkingProject.get_context_data(self, **kwargs) kwargs = HasErrorMessages.get_context_data(self, **kwargs) kwargs['plots_2d'] = self.listOfPlots2D kwargs['colors'] = Settings.default_colors return kwargs
def __init__(self): HasWorkingProject.__init__(self) HasVariablesInSession.__init__(self) self.list_of_models = None self.model = None self.modelInstance = None self.model_id = None self.model_name = None self.model_filename = None self.model_list_of_submodels = [] self.model_list_of_submodels_names = [] self.model_list_of_submodels_types = [] self.model_submodel = None self.__request = None
def get_context_data(self, **kwargs): kwargs = HasWorkingProject.get_context_data(self, **kwargs) kwargs = HasErrorMessages.get_context_data(self, **kwargs) kwargs['form'] = self.fileUploadForm kwargs['sbml_models'] = self.listOfModels return kwargs
def post(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
if Experiment.objects.filter(project=self.project,
id=int(request.POST['id'])).exists():
experiment = Experiment.objects.get(project=self.project,
id=int(request.POST['id']))
self.data.update({
'name':
"" if experiment.name is None else experiment.name,
'notes':
"" if experiment.notes is None else experiment.notes
})
return JsonRequest.post(self, request, *args, **kwargs)
def post(self, request, *args, **kwargs):
self.load(request, *args, **kwargs)
if "action" in request.POST:
if HasWorkingProject.isChooseProject(self, request):
return redirect('list_of_simulations')
return TemplateView.get(self, request, *args, **kwargs)
def get_context_data(self, **kwargs):
kwargs = HasWorkingProject.get_context_data(self, **kwargs)
kwargs = HasErrorMessages.get_context_data(self, **kwargs)
kwargs['form'] = self.fileUploadForm
kwargs['sbml_models'] = self.listOfModels
return kwargs
def post(self, request, *args, **kwargs):
self.load(request, *args, **kwargs)
if "action" in request.POST:
if HasWorkingProject.isChooseProject(self, request):
return redirect('list_of_simulations')
return TemplateView.get(self, request, *args, **kwargs)
def get_context_data(self, **kwargs):
kwargs = HasWorkingProject.get_context_data(self, **kwargs)
kwargs['experimental_data'] = self.listOfExperiments
kwargs['experiment_id'] = self.experimentId
kwargs['experiment_name'] = self.experimentName
kwargs['experiment_notes'] = self.experimentNotes
return kwargs
def get_context_data(self, **kwargs): kwargs = HasWorkingProject.get_context_data(self, **kwargs) kwargs['experimental_data'] = self.listOfExperiments kwargs['experiment_id'] = self.experimentId kwargs['experiment_name'] = self.experimentName kwargs['experiment_notes'] = self.experimentNotes kwargs['file_upload_form'] = self.fileUploadForm return kwargs
def get_context_data(self, **kwargs):
kwargs = HasWorkingProject.get_context_data(self, **kwargs)
kwargs['create_folder_error'] = self.createFolderError
kwargs['create_folder_show'] = self.createFolderShow
kwargs['send_folder_error'] = self.sendFolderError
kwargs['send_folder_show'] = self.sendFolderShow
return kwargs
def get_context_data(self, **kwargs): kwargs = HasWorkingProject.get_context_data(self, **kwargs) kwargs['create_folder_error'] = self.createFolderError kwargs['create_folder_show'] = self.createFolderShow kwargs['send_folder_error'] = self.sendFolderError kwargs['send_folder_show'] = self.sendFolderShow return kwargs
def get_context_data(self, **kwargs): kwargs = HasWorkingProject.get_context_data(self, **kwargs) kwargs['sbml_models'] = self.list_of_models kwargs['model_id'] = self.model_id kwargs['model_name'] = self.model_name kwargs['model_has_submodels'] = (self.model is not None and self.model.parentDoc.isCompEnabled() and len(self.model.listOfSubmodels) > 0) kwargs['model_submodels'] = ["Model definition"] + [model.getName() for model in self.model.parentDoc.listOfModelDefinitions] kwargs['model_submodel'] = self.model_submodel return kwargs
def post(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
if Observation.objects.filter(id=int(request.POST['id'])).exists():
observation = Observation.objects.get(id=int(request.POST['id']))
self.data.update({
'species': observation.species,
'time': observation.time,
'value': observation.value,
'value': observation.value,
'stddev': observation.stddev,
'steady_state': 1 if observation.steady_state else 0,
'min_steady_state': 0 if observation.min_steady_state is None else observation.min_steady_state,
'max_steady_state': 0 if observation.max_steady_state is None else observation.max_steady_state
})
return JsonRequest.post(self, request, *args, **kwargs)
def post(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
self.load(request, *args, **kwargs)
if "action" in request.POST:
if HasWorkingProject.isChooseProject(self, request):
return redirect('experimental_data')
elif request.POST['action'] == "delete":
self.deleteCondition(request)
elif request.POST['action'] == "save":
self.saveCondition(request)
elif request.POST['action'] == "duplicate":
self.duplicateCondition(request)
return TemplateView.get(self, request, *args, **kwargs)
def get_context_data(self, **kwargs):
kwargs = HasWorkingProject.get_context_data(self, **kwargs)
kwargs['experiment_name'] = self.experiment.name
kwargs['conditions'] = self.listOfConditions
kwargs['condition_id'] = self.conditionId
kwargs['condition_name'] = self.conditionName
kwargs['condition_notes'] = self.conditionNotes
return kwargs
def post(self, request, *args, **kwargs): HasWorkingProject.load(self, request, *args, **kwargs) self.loadExperiments(request) if "action" in request.POST: if HasWorkingProject.isChooseProject(self, request): self.loadExperiments(request) elif request.POST['action'] == "delete": self.deleteExperiment(request) elif request.POST['action'] == "save": self.saveExperiment(request) elif request.POST['action'] == "duplicate": self.duplicateExperiment(request) elif request.POST['action'] == "import": self.importExperiment(request) return TemplateView.get(self, request, *args, **kwargs)
def post(self, request, *args, **kwargs): self.load(request, *args, **kwargs) if "action" in request.POST: if HasWorkingProject.isChooseProject(self, request): self.load(request, *args, **kwargs) elif request.POST['action'] == "delete_simulation": self.deleteSimulation(request) elif request.POST['action'] == "load_simulation": self.loadSimulation(request) return TemplateView.get(self, request, *args, **kwargs)
def get(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
if len(args) > 0:
if Experiment.objects.filter(id=int(args[0])).exists():
experiment = Experiment.objects.get(id=int(args[0]))
if experiment.project.access == 'PU' or experiment.project.user == request.user:
filename = exportExperiment(experiment)
response = HttpResponse(open(filename, 'rb'), content_type='text/xml')
response['Content-Disposition'] = 'attachment; filename=' + basename(filename)
remove(filename)
return response
else:
raise PermissionDenied
else:
raise Http404("Data doesn't exists")
redirect('experimental_data')
def post(self, request, *args, **kwargs):
self.load(request, *args, **kwargs)
if "action" in request.POST:
if HasWorkingProject.isChooseProject(self, request):
return redirect('list_of_optimizations')
if request.POST['action'] == "save_model":
self.saveFittedModel(request)
elif request.POST['action'] == "stop_optim":
self.stopOptimization()
elif request.POST['action'] == "restart_optim":
self.restartOptimization()
return TemplateView.get(self, request, *args, **kwargs)
def isChooseModel(self, request): if HasWorkingProject.isChooseProject(self, request): self.list_of_models = None self.__clearModelVariables() self.__clearPickledModel(request) return True elif request.POST['action'] == "choose_model": self.__setModel(request) return True elif request.POST['action'] == "choose_submodel": self.__setSubmodel(request) return True else: return False
def get_context_data(self, **kwargs): kwargs = HasWorkingProject.get_context_data(self, **kwargs) kwargs['experiment_name'] = self.experiment.name kwargs['condition_name'] = self.condition.name kwargs['experiment_id'] = self.experiment.id kwargs['experiment_data'] = self.dataPoints kwargs['experiment_initial_data'] = self.treatmentPoints kwargs['observations'] = self.observations kwargs['treatments'] = self.treatments kwargs['observation_form'] = self.observationForm kwargs['treatment_form'] = self.treatmentForm kwargs['colors'] = ['#009ece', '#ff9e00', '#9ccf31', '#f7d708', '#ce0000', '#e400ff'] return kwargs
def get_context_data(self, **kwargs): kwargs = HasWorkingProject.get_context_data(self, **kwargs) kwargs['optimization_id'] = self.optimizationId kwargs['parameters'] = self.parameters kwargs['model_name'] = self.modelName kwargs['submodel_names'] = self.submodelNames kwargs['modified_submodel_names'] = self.modifiedSubmodelNames kwargs['show_graph'] = self.showGraph kwargs['optimization_status'] = self.optimizationStatus kwargs['score_time'] = self.scoreTime kwargs['score_values'] = self.scoreValues kwargs['score_rawvalues'] = self.scoreRawValues kwargs['score_minev'] = self.scoreMinEv kwargs['score_maxev'] = self.scoreMaxEv kwargs['colors'] = Settings.default_colors kwargs['experiments'] = self.experimentsData return kwargs
