def load(self, request, *args, **kwargs):
HasWorkingModel.load(self, request, *args, **kwargs)
self.listOfCompartments = self.getModel().listOfCompartments
self.listOfReactions = self.getModel().listOfReactions
if self.isModelLoaded():
if self.isCompModelDefinition():
self.listOfSpecies = [
species for species in self.getModel().listOfSpecies
]
elif self.isCompInternalSubmodel():
self.listOfSpecies = [
species for species in self.getModel().listOfSpecies
]
elif self.isFlattenModel():
# Would be nice to also draw the boundaries of the submodels here
self.listOfSpecies = [
species for species in self.getModel().listOfSpecies
if species.isInReactions(including_modifiers=True)
]
else:
self.listOfSpecies = [
species for species in self.getModel().listOfSpecies
if species.isInReactions(including_modifiers=True)
]
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingModel.__init__(self)
self.listOfSpecies = None
self.listOfReactions = None
def load(self, request, *args, **kwargs): HasErrorMessages.clearErrors(self) HasWorkingModel.load(self, request, *args, **kwargs) if self.isModelLoaded(): self.listOfCompartments = self.getModel().listOfCompartments self.listOfUnits = self.getModel().listOfUnitDefinitions
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingModel.__init__(self)
self.listOfUnitDefinitions = None
self.form = ModelUnitsForm(self)
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingModel.__init__(self) self.listOfUnitDefinitions = None self.form = ModelUnitsForm(self)
def load(self, request, *args, **kwargs):
HasErrorMessages.clearErrors(self)
HasWorkingModel.load(self, request, *args, **kwargs)
if self.isModelLoaded():
self.listOfCompartments = self.getModel().listOfCompartments
self.listOfUnits = self.getModel().listOfUnitDefinitions
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingModel.__init__(self) self.optimization = None self.form = DataOptimizationForm(self)
def load(self, request, *args, **kwargs):
HasWorkingModel.load(self, request, *args, **kwargs)
t_model = SbmlModel.objects.get(project=self.project_id,
id=self.model_id)
self.listOfComputations = Continuation.objects.filter(
project=self.project, model=t_model)
def load(self, request, *args, **kwargs): HasErrorMessages.clearErrors(self) HasWorkingModel.load(self, request, *args, **kwargs) if self.isModelLoaded(): self.loadRules() self.loadGlobalVariables()
def load(self, request, *args, **kwargs): HasErrorMessages.clearErrors(self) HasWorkingModel.load(self, request, *args, **kwargs) if self.isModelLoaded(): self.loadSpecies() self.loadCompartments() self.loadUnits()
def load(self, request, *args, **kwargs):
HasErrorMessages.clearErrors(self)
HasWorkingModel.load(self, request, *args, **kwargs)
if self.isModelLoaded():
self.loadRules()
self.loadGlobalVariables()
def load(self, request, *args, **kwargs):
HasWorkingModel.load(self, request, *args, **kwargs)
if self.isModelLoaded():
self.loadVariables()
self.loadReactions()
self.loadExperiments()
def load(self, request, *args, **kwargs):
HasWorkingModel.load(self, request, *args, **kwargs)
if self.isModelLoaded():
self.loadSpecies()
self.loadDataSets(request)
self.loadParameters(request)
def load(self, request, *args, **kwargs):
HasErrorMessages.clearErrors(self)
HasWorkingModel.load(self, request, *args, **kwargs)
if self.isModelLoaded():
self.loadSpecies()
self.loadCompartments()
self.loadUnits()
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingModel.__init__(self) self.listOfSpecies = None self.listOfReactions = None self.listOfCompartments = None
def load(self, request, *args, **kwargs): HasWorkingModel.load(self, request, *args, **kwargs) if self.isModelLoaded(): self.loadVariables() self.loadReactions() self.loadExperiments()
def load(self, request, *args, **kwargs): HasWorkingModel.load(self, request, *args, **kwargs) self.listOfObjects = [] for object in self.getModel().listOfSbmlObjects: if isinstance(object, Variable) and not object.isStoichiometry(): self.listOfObjects.append(object) self.listOfSubmodels = self.getModel().listOfSubmodels
def load(self, request, *args, **kwargs): HasErrorMessages.clearErrors(self) HasWorkingModel.load(self, request, *args, **kwargs) if self.isModelLoaded(): self.loadParameters() self.loadReactions() self.loadUnits()
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasErrorMessages.__init__(self) HasWorkingModel.__init__(self) self.modelHistory = None self.modelPublication = None self.form = ModelAnnotationsForm(self)
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasErrorMessages.__init__(self)
HasWorkingModel.__init__(self)
self.listOfVariables = None
self.listOfEvents = None
self.form = ModelEventsForm(self)
def load(self, request, *args, **kwargs):
HasErrorMessages.clearErrors(self)
HasWorkingModel.load(self, request, *args, **kwargs)
if self.isModelLoaded():
self.loadParameters()
self.loadReactions()
self.loadUnits()
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasErrorMessages.__init__(self) HasWorkingModel.__init__(self) self.listOfVariables = None self.listOfEvents = None self.form = ModelEventsForm(self)
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasErrorMessages.__init__(self)
HasWorkingModel.__init__(self)
self.modelHistory = None
self.modelPublication = None
self.form = ModelAnnotationsForm(self)
def load(self, request, *args, **kwargs):
HasWorkingModel.load(self, request, *args, **kwargs)
for variable in self.getModel().listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies() or variable.isCompartment()
or variable.isStoichiometry()):
self.listOfVariables.append(variable)
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingModel.__init__(self)
HasErrorMessages.__init__(self)
self.listOfCompartments = None
self.listOfUnits = None
self.form = ModelCompartmentsForm(self)
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingModel.__init__(self) HasErrorMessages.__init__(self) self.listOfCompartments = None self.listOfUnits = None self.form = ModelCompartmentsForm(self)
def load(self, request, *args, **kwargs): HasWorkingModel.load(self, request, *args, **kwargs) for variable in self.getModel().listOfVariables: if ((variable.isParameter() and variable.isGlobal()) or variable.isSpecies() or variable.isCompartment() or variable.isStoichiometry()): self.listOfVariables.append(variable)
def post(self, request, *args, **kwargs):
HasWorkingModel.load(self, request, *args, **kwargs)
if "action" in request.POST:
if self.isChooseModel(request):
# Already done !
pass
return TemplateView.get(self, request, *args, **kwargs)
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingModel.__init__(self) # init_printing() self.modelInstance = None self.latex_odes = [] self.latex_conslaws = [] self.latex_cfes = [] self.latex_daes = []
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingModel.__init__(self) HasErrorMessages.__init__(self) self.listOfConstants = None self.listOfVariables = None self.listComputations = None self.computation = None
def post(self, request, *args, **kwargs): HasWorkingModel.load(self, request, *args, **kwargs) if "action" in request.POST: if self.isChooseModel(request): # Already done ! pass return TemplateView.get(self, request, *args, **kwargs)
def load(self, request, *args, **kwargs): HasErrorMessages.clearErrors(self) HasWorkingModel.load(self, request, *args, **kwargs) if self.isModelLoaded(): self.loadSubmodels() self.loadProjectModels(request) self.loadConversionFactors() self.loadObjects() self.loadSubstitutions()
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasErrorMessages.__init__(self) HasWorkingModel.__init__(self) self.listOfParameters = None self.listOfReactions = None self.listOfUnits = None self.form = ModelParametersForm(self)
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingModel.__init__(self) HasErrorMessages.__init__(self) self.listOfConstants = None self.listComputations = None self.computation = None self.form = AnalyseBifurcationsForm(self)
def load(self, request, *args, **kwargs):
HasErrorMessages.clearErrors(self)
HasWorkingModel.load(self, request, *args, **kwargs)
if self.isModelLoaded():
self.loadSubmodels()
self.loadProjectModels(request)
self.loadConversionFactors()
self.loadObjects()
self.loadSubstitutions()
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasErrorMessages.__init__(self)
HasWorkingModel.__init__(self)
self.listOfParameters = None
self.listOfReactions = None
self.listOfUnits = None
self.form = ModelParametersForm(self)
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasErrorMessages.__init__(self) HasWorkingModel.__init__(self) self.listOfUnits = None self.listOfParameters = None self.sbmlLevels = None self.modelHistory = None self.modelPublication = None self.form = ModelMiscForm(self)
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingModel.__init__(self)
self.listOfUnitDefinitions = None
self.unitDefinition = None
self.listOfUnits = []
self.addingNewUnit = None
self.editingUnitDefinition = None
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasErrorMessages.__init__(self)
HasWorkingModel.__init__(self)
self.listOfUnits = None
self.listOfParameters = None
self.sbmlLevels = None
self.modelHistory = None
self.modelPublication = None
self.form = ModelMiscForm(self)
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingModel.__init__(self)
self.listOfDataSets = None
self.selectedDataSets = None
self.selectedDataSetsIds = None
self.listOfSpecies = None
self.speciesMapping = None
self.selectedParameters = None
def load(self, request, *args, **kwargs):
HasErrorMessages.clearErrors(self)
HasWorkingModel.load(self, request, *args, **kwargs)
if len(args) > 0:
self.setModel(request, int(args[0]))
if self.isModelLoaded():
self.listOfUnits = self.getModel().listOfUnitDefinitions
self.listOfParameters = self.getModel().listOfParameters
self.sbmlLevels = self.getModel().getSbmlLevels()
self.form.load()
def load(self, request, *args, **kwargs): HasErrorMessages.clearErrors(self) HasWorkingModel.load(self, request, *args, **kwargs) if len(args) > 0: self.setModel(request, int(args[0])) if self.isModelLoaded(): self.form.load() self.modelHistory = self.getModel().modelHistory if len(self.getModel().getAnnotation().getIsDescribedBy()) > 0: self.modelPublication = self.getModel().getAnnotation().getIsDescribedBy()[0]
def load(self, request, *args, **kwargs): HasErrorMessages.clearErrors(self) HasWorkingModel.load(self, request, *args, **kwargs) if len(args) > 0: self.setModel(request, int(args[0])) if self.isModelLoaded(): self.listOfUnits = self.getModel().listOfUnitDefinitions self.listOfParameters = self.getModel().listOfParameters self.sbmlLevels = self.getModel().getSbmlLevels() self.form.load()
def load(self, request, *args, **kwargs):
HasErrorMessages.clearErrors(self)
HasWorkingModel.load(self, request, *args, **kwargs)
if len(args) > 0:
self.setModel(request, int(args[0]))
if self.isModelLoaded():
self.form.load()
self.modelHistory = self.getModel().modelHistory
if len(self.getModel().getAnnotation().getIsDescribedBy()) > 0:
self.modelPublication = self.getModel().getAnnotation(
).getIsDescribedBy()[0]
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasErrorMessages.__init__(self)
HasWorkingModel.__init__(self)
self.listOfReactions = None
self.listOfSpecies = None
self.listOfParameters = None
self.listOfKineticLaws = None
self.reactionTypes = KineticLaw.reactionTypes
self.parametersList = KineticLaw.parametersList
self.allowReversibleList = KineticLaw.allowReversibleList
self.form = ModelReactionsForm(self)
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasErrorMessages.__init__(self) HasWorkingModel.__init__(self) self.listOfReactions = None self.listOfSpecies = None self.listOfParameters = None self.listOfKineticLaws = None self.reactionTypes = KineticLaw.reactionTypes self.parametersList = KineticLaw.parametersList self.allowReversibleList = KineticLaw.allowReversibleList self.form = ModelReactionsForm(self)
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasErrorMessages.__init__(self) HasWorkingModel.__init__(self) self.listOfVariables = None self.listOfRules = None self.ruleTypes = ["Algebraic rule", "Assignment rule", "Rate rule", "Initial assignment"] self.form = ModelRulesForm(self)
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasErrorMessages.__init__(self)
HasWorkingModel.__init__(self)
self.listOfVariables = None
self.listOfRules = None
self.ruleTypes = [
"Algebraic rule", "Assignment rule", "Rate rule",
"Initial assignment"
]
self.form = ModelRulesForm(self)
def load(self, request, *args, **kwargs):
HasErrorMessages.clearErrors(self)
HasWorkingModel.load(self, request, *args, **kwargs)
if self.isModelLoaded():
self.listOfEvents = self.getModel().listOfEvents
self.getModel().listOfVariables.classifyVariables()
self.listOfVariables = []
for variable in self.getModel().listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies() or variable.isCompartment()
or variable.isStoichiometry()):
self.listOfVariables.append(variable)
def get_context_data(self, **kwargs): kwargs = HasWorkingModel.get_context_data(self, **kwargs) kwargs['list_of_species'] = self.listOfSpecies kwargs['list_of_reactions'] = self.listOfReactions kwargs['list_of_compartments'] = self.listOfCompartments return kwargs
def load(self, request, *args, **kwargs): HasErrorMessages.clearErrors(self) HasWorkingModel.load(self, request, *args, **kwargs) if self.isModelLoaded(): self.listOfEvents = self.getModel().listOfEvents self.getModel().listOfVariables.classifyVariables() self.listOfVariables = [] for variable in self.getModel().listOfVariables: if ((variable.isParameter() and variable.isGlobal()) or variable.isSpecies() or variable.isCompartment() or variable.isStoichiometry()): self.listOfVariables.append(variable)
def get_context_data(self, **kwargs): kwargs = HasWorkingModel.get_context_data(self, **kwargs) kwargs['unit_definitions'] = self.listOfUnitDefinitions kwargs['unit_list'] = Unit.unit_id.values() kwargs['form'] = self.form return kwargs
def get_context_data(self, **kwargs): kwargs = HasErrorMessages.get_context_data(self, **kwargs) kwargs = HasWorkingModel.get_context_data(self, **kwargs) kwargs['list_of_events'] = self.listOfEvents kwargs['list_of_variables'] = [var.getNameOrSbmlId() for var in self.listOfVariables] kwargs['form'] = self.form return kwargs
def get_context_data(self, **kwargs): kwargs = HasWorkingModel.get_context_data(self, **kwargs) kwargs = HasErrorMessages.get_context_data(self, **kwargs) kwargs['list_of_compartments'] = self.listOfCompartments kwargs['list_of_units'] = [unit.getName() for unit in self.listOfUnits] kwargs['form'] = self.form return kwargs
def post(self, request, *args, **kwargs): self.load(request, *args, **kwargs) if "action" in request.POST: if HasWorkingModel.isChooseModel(self, request): self.load(request, *args, **kwargs) return TemplateView.get(self, request, *args, **kwargs)
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasErrorMessages.__init__(self) HasWorkingModel.__init__(self) self.listOfSubmodels = [] self.listOfSubmodelTypes = [] self.listOfSubstitutions = None self.listOfProjectModels = None self.listOfSubmodelsRefs = None self.listOfObjects = None self.listOfObjectsMetaIds = None self.listOfConversionFactors = None self.form = ModelSubmodelsForm(self) self.formSubstitutions = ModelSubmodelSubstitutionForm(self)
def get_context_data(self, **kwargs): kwargs = HasWorkingModel.get_context_data(self, **kwargs) kwargs = HasErrorMessages.get_context_data(self, **kwargs) kwargs['list_of_constants'] = [const.getNameOrSbmlId() for const in self.listOfConstants] kwargs['list_of_computations'] = self.listOfComputations kwargs['colors'] = Settings.default_colors kwargs['form'] = self.form return kwargs
