def simulateModel(self, request):
self.form.read(request)
if not self.form.hasErrors():
if self.hasCPUTimeQuota(request):
self.experiment = None
if self.form.experimentId is not None:
t_experiment = Experiment.objects.get(
id=self.experiments[self.form.experimentId].id)
self.experiment = buildExperiment(t_experiment)
try:
t_simulation = TimeseriesSimulation(
list_of_models=[self.getModelInstance()],
experiment=self.experiment,
time_min=self.form.timeMin,
time_max=self.form.timeMax,
time_ech=self.form.timeEch)
t_simulation.run(timeout=self.getCPUTimeQuota(request))
results = t_simulation.getRawData()
self.addCPUTime(request,
t_simulation.getSimulationDuration())
self.read_timeseries(results)
except LibSigNetSimException as e:
self.form.addError(e.message)
else:
self.form.addError(
"You exceeded your allowed computation time. Please contact the administrator"
)
def simulateModel(self, request):
self.form.read(request)
if not self.form.hasErrors():
if self.hasCPUTimeQuota(request):
self.experiment = None
if self.form.experimentId is not None:
t_experiment = Experiment.objects.get(id=self.experiments[self.form.experimentId].id)
self.experiment = buildExperiment(t_experiment)
try:
t_simulation = TimeseriesSimulation(
list_of_models=[self.getModelInstance()],
experiment=self.experiment,
time_min=self.form.timeMin,
time_max=self.form.timeMax,
time_ech=self.form.timeEch)
t_simulation.run(timeout=self.getCPUTimeQuota(request))
results = t_simulation.getRawData()
self.addCPUTime(request, t_simulation.getSimulationDuration())
self.read_timeseries(results)
except LibSigNetSimException as e:
self.form.addError(e.message)
else:
self.form.addError("You exceeded your allowed computation time. Please contact the administrator")
def post(self, request, *args, **kwargs):
self.load(request, *args, **kwargs)
dataset_ind = int(request.POST['dataset_ind'])
experiment_data = Experiment.objects.filter(project=self.project)[dataset_ind]
experiment = buildExperiment(experiment_data)
experiment_variables = experiment.getVariables()
model_variables = {}
model_xpaths = {}
for variable in experiment_variables:
if self.getModelInstance().listOfVariables.containsSbmlId(variable):
var = self.getModelInstance().listOfVariables.getBySbmlId(variable)
model_variables.update({variable: var.getNameOrSbmlId()})
model_xpaths.update({variable: var.getXPath()})
elif self.getModelInstance().listOfVariables.containsName(variable):
var = self.getModelInstance().listOfVariables.getByName(variable)
model_variables.update({variable: var.getNameOrSbmlId()})
model_xpaths.update({variable: var.getXPath()})
else:
model_variables.update({variable: None})
model_xpaths.update({variable: None})
self.data.update({
'dataset_ind': dataset_ind,
'dataset_id': experiment_data.id,
'dataset_name': experiment_data.name,
'model_variables': model_variables,
'model_xpaths': model_xpaths
})
return JsonRequest.post(self, request, *args, **kwargs)
def readSelectedDataset(self, request):
self.selectedDataSetsIds = []
self.selectedExperiments = []
i_dataset_selected = 0
while ("dataset_%d" % i_dataset_selected) in request.POST:
t_id = int(request.POST["dataset_%d" % i_dataset_selected])
self.selectedDataSetsIds.append(t_id)
self.selectedExperiments.append(buildExperiment(Experiment.objects.get(id=t_id)))
i_dataset_selected += 1
def exportProject(project): combine_archive = CombineArchive() for sbml_model in SbmlModel.objects.filter(project=project): combine_archive.addFile(join(settings.MEDIA_ROOT, str(sbml_model.sbml_file))) for sedml_model in SEDMLSimulation.objects.filter(project=project): combine_archive.addFile(join(settings.MEDIA_ROOT, str(sedml_model.sedml_file))) for i, experiment in enumerate(Experiment.objects.filter(project=project)): t_experiment = buildExperiment(experiment) t_experiment.writeNuMLToFile(join(Settings.tempDirectory, "experiment_%d.xml" % i)) combine_archive.addFile(join(Settings.tempDirectory, "experiment_%d.xml" % i)) filename = ''.join(e for e in project.name if e.isalnum()) + ".omex" filename = join(Settings.tempDirectory, filename) combine_archive.writeArchive(filename) return filename
def post(self, request, *args, **kwargs):
self.load(request, *args, **kwargs)
dataset_ind = int(request.POST['dataset_ind'])
experiment_data = Experiment.objects.filter(
project=self.project)[dataset_ind]
experiment = buildExperiment(experiment_data)
experiment_variables = experiment.getVariables()
model_variables = {}
model_xpaths = {}
for variable in experiment_variables:
if self.getModelInstance().listOfVariables.containsSbmlId(
variable):
var = self.getModelInstance().listOfVariables.getBySbmlId(
variable)
model_variables.update({variable: var.getNameOrSbmlId()})
model_xpaths.update({variable: var.getXPath()})
elif self.getModelInstance().listOfVariables.containsName(
variable):
var = self.getModelInstance().listOfVariables.getByName(
variable)
model_variables.update({variable: var.getNameOrSbmlId()})
model_xpaths.update({variable: var.getXPath()})
else:
model_variables.update({variable: None})
model_xpaths.update({variable: None})
self.data.update({
'dataset_ind': dataset_ind,
'dataset_id': experiment_data.id,
'dataset_name': experiment_data.name,
'model_variables': model_variables,
'model_xpaths': model_xpaths
})
return JsonRequest.post(self, request, *args, **kwargs)