def loadOptimizations(self, request):
if self.list_of_models is not None and len(self.list_of_models) > 0:
t_model = SbmlModel.objects.get(project=self.project,
id=self.model_id)
optimizations = Optimization.objects.filter(project=self.project,
model=t_model)
self.listOfOptimizations = []
for optimization in optimizations:
t_optim_id = optimization.optimization_id
optim_path = join(
settings.MEDIA_ROOT, str(self.project.folder),
"optimizations/optimization_%s/" % str(t_optim_id))
t_time_of_launch = int(time()) - (int(t_optim_id) / 1000)
t_model_name = ""
if isfile(optim_path + "/model.sbml"):
try:
t_document = SbmlDocument()
t_document.readSbmlFromFile(
str(optim_path + "/model.sbml"))
t_model_name = t_document.model.getName()
except ModelException as e:
t_model_name = "Unknown"
self.listOfOptimizations.append(
(optimization, t_time_of_launch, t_model_name))
def save(self, *args, **kwargs):
if User.objects.filter(id=self.id).exists():
created = False
else:
created = True
super(User, self).save(*args, **kwargs)
if created:
new_project = Project(user=self, name="My first project")
new_project.save()
sbml_model_filename = join(settings.MEDIA_ROOT, "init_model.sbml")
sbml_model = open(sbml_model_filename, 'a')
sbml_model.close()
new_model = SbmlModel(project=new_project,
name="My first model",
sbml_file=File(
open(sbml_model_filename, "rb")))
new_model.save()
os.remove(sbml_model_filename)
doc = SbmlDocument()
doc.model.newModel("My first model")
doc.writeSbmlToFile(
os.path.join(settings.MEDIA_ROOT, str(new_model.sbml_file)))
def loadOptimizations(self, request): if self.list_of_models is not None and len(self.list_of_models) > 0: t_model = SbmlModel.objects.get(project=self.project, id=self.model_id) optimizations = Optimization.objects.filter(project=self.project, model=t_model) self.listOfOptimizations = [] for optimization in optimizations: t_optim_id = optimization.optimization_id optim_path = join(settings.MEDIA_ROOT, str(self.project.folder), "optimizations/optimization_%s/" % str(t_optim_id)) t_time_of_launch = int(time()) - (int(t_optim_id)/1000) t_model_name = "" if isfile(optim_path + "/model.sbml"): try: t_document = SbmlDocument() t_document.readSbmlFromFile(str(optim_path + "/model.sbml")) t_model_name = t_document.model.getName() except ModelException as e: t_model_name = "Unknown" self.listOfOptimizations.append((optimization, t_time_of_launch, t_model_name))
def __loadModelVariables(self):
if self.model_id is not None and SbmlModel.objects.filter(id=self.model_id).exists():
t_model = SbmlModel.objects.get(id=self.model_id)
if self.isProjectOwner(self.__request) or t_model.project.access == "PU":
self.model_filename = os.path.join(settings.MEDIA_ROOT, str(t_model.sbml_file))
t_doc = SbmlDocument()
t_doc.readSbmlFromFile(self.model_filename)
self.model = t_doc.model
self.model_name = self.model.getName()
self.model_list_of_submodels = self.model.listOfSubmodels
self.model_list_of_submodels_names = []
self.model_list_of_submodels_types = []
for submodel in self.model.listOfSubmodels:
if submodel.getModelRef() in self.model.parentDoc.listOfModelDefinitions.sbmlIds():
self.model_list_of_submodels_names.append(self.model.parentDoc.listOfModelDefinitions.getBySbmlId(submodel.getModelRef()).getNameOrSbmlId())
self.model_list_of_submodels_types.append(0)
if submodel.getModelRef() in self.model.parentDoc.listOfExternalModelDefinitions.sbmlIds():
self.model_list_of_submodels_names.append(self.model.parentDoc.listOfExternalModelDefinitions.getBySbmlId(submodel.getModelRef()).getNameOrSbmlId())
self.model_list_of_submodels_types.append(1)
else:
raise PermissionDenied
else:
raise Http404("The model doesn't exist !")
def getListOfObjects(self, request):
if str(request.POST['model_id']) != "":
list_of_project_models = [pm for pm in self.getProjectModels(request) if pm.id != self.model_id]
t_model = list_of_project_models[int(request.POST['model_id'])]
t_filename = join(settings.MEDIA_ROOT, str(t_model.sbml_file))
doc = SbmlDocument()
doc.readSbmlFromFile(t_filename)
if (
'submodel_id' in request.POST
and request.POST['submodel_id'] != ""
and int(request.POST['submodel_id']) > 1
):
submodel = doc.model.listOfSubmodels[int(request.POST['submodel_id'])-1].getModelObject()
self.listOfObjects = []
for t_object in doc.model.listOfSbmlObjects:
if isinstance(t_object, Variable) and not t_object.isStoichiometry():
self.listOfObjects.append(t_object.getNameOrSbmlId() + (" (%s)" % type(t_object).__name__))
return self.listOfObjects
else:
self.listOfObjects = []
for t_object in doc.model.listOfSbmlObjects:
if isinstance(t_object, Variable) and not t_object.isStoichiometry():
self.listOfObjects.append(t_object.getNameOrSbmlId() + (" (%s)" % type(t_object).__name__))
return self.listOfObjects
def getModelSBMLSubmodels(self, request): """ Returning the submodels of a model available within the project """ if self.isUserLoggedIn(request) and self.project is not None and self.model_id is not None: t_filename = os.path.join(settings.MEDIA_ROOT, str(self.model_filename)) doc = SbmlDocument() doc.readSbmlFromFile(t_filename) if doc.useCompPackage: return (doc.listOfModelDefinitions.getListOfModelDefinitions() + doc.listOfExternalModelDefinitions.getListOfModelDefinitions())
def deleteModelHierarchy(model_filename):
doc = SbmlDocument()
doc.readSbmlFromFile(model_filename)
path = dirname(model_filename)
if doc.useCompPackage:
for dependency in doc.getExternalDocumentDependencies():
deleteModelHierarchy(join(path, dependency))
remove(model_filename)
def deleteModelHierarchy(model_filename): doc = SbmlDocument() doc.readSbmlFromFile(model_filename) path = dirname(model_filename) if doc.useCompPackage: for dependency in doc.getExternalDocumentDependencies(): deleteModelHierarchy(join(path, dependency)) remove(model_filename)
def getModelSubmodels(self, request, model_id): """ Returning the submodels of a model available within the project """ if self.isUserLoggedIn(request) and self.project is not None: t_models = [pm for pm in self.getProjectModels(request) if pm.id != self.model_id] t_filename = os.path.join(settings.MEDIA_ROOT, str(t_models[model_id].sbml_file)) doc = SbmlDocument() doc.readSbmlFromFile(t_filename) if doc.useCompPackage: return [doc.model.getSbmlId()] + doc.listOfModelDefinitions.sbmlIds()+doc.listOfExternalModelDefinitions.sbmlIds() else: return [doc.model.getSbmlId()]
def getModelHierarchy(model_filename):
doc = SbmlDocument()
doc.readSbmlFromFile(model_filename)
path = dirname(model_filename)
deps = []
if doc.useCompPackage:
for dependency in doc.getExternalDocumentDependencies():
deps.append(dependency)
deps += getModelHierarchy(join(path, dependency))
return deps
def getModelHierarchy(model_filename): doc = SbmlDocument() doc.readSbmlFromFile(model_filename) path = dirname(model_filename) deps = [] if doc.useCompPackage: for dependency in doc.getExternalDocumentDependencies(): deps.append(dependency) deps += getModelHierarchy(join(path, dependency)) return deps
def newModel(self, request): model_name = str(request.POST['model_name']) model_filename = os.path.join(settings.MEDIA_ROOT, new_model_filename()) open(model_filename, "a") new_model = SbmlModel(project=self.project, name=model_name, sbml_file=File(open(model_filename, "rb"))) os.remove(model_filename) new_model.save() doc = SbmlDocument() doc.model.newModel(model_name) doc.writeSbmlToFile(os.path.join(settings.MEDIA_ROOT, str(new_model.sbml_file)))
def getModelSBMLSubmodels(self, request):
""" Returning the submodels of a model available within the project
"""
if self.isUserLoggedIn(
request
) and self.project is not None and self.model_id is not None:
t_filename = os.path.join(settings.MEDIA_ROOT,
str(self.model_filename))
doc = SbmlDocument()
doc.readSbmlFromFile(t_filename)
if doc.useCompPackage:
return (
doc.listOfModelDefinitions.getListOfModelDefinitions() +
doc.listOfExternalModelDefinitions.
getListOfModelDefinitions())
def duplicateModel(self, request):
model = SbmlModel.objects.get(id=request.POST['id'])
t_file = File(open(os.path.join(settings.MEDIA_ROOT, str(model.sbml_file)), 'rb'))
new_sbml_model = SbmlModel(project=self.project,
name=("%s (copy)" % str(model.name)),
sbml_file=t_file)
new_sbml_model.save()
t_filename = os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file))
doc = SbmlDocument()
doc.readSbmlFromFile(t_filename)
doc.model.setName(str(new_sbml_model.name))
doc.writeSbmlToFile(t_filename)
def newModel(self, request):
model_name = str(request.POST['model_name'])
model_filename = os.path.join(settings.MEDIA_ROOT,
new_model_filename())
open(model_filename, "a")
new_model = SbmlModel(project=self.project,
name=model_name,
sbml_file=File(open(model_filename, "rb")))
os.remove(model_filename)
new_model.save()
doc = SbmlDocument()
doc.model.newModel(model_name)
doc.writeSbmlToFile(
os.path.join(settings.MEDIA_ROOT, str(new_model.sbml_file)))
def getModelSubmodels(self, request, model_id):
""" Returning the submodels of a model available within the project
"""
if self.isUserLoggedIn(request) and self.project is not None:
t_models = [
pm for pm in self.getProjectModels(request)
if pm.id != self.model_id
]
t_filename = os.path.join(settings.MEDIA_ROOT,
str(t_models[model_id].sbml_file))
doc = SbmlDocument()
doc.readSbmlFromFile(t_filename)
if doc.useCompPackage:
return [doc.model.getSbmlId()
] + doc.listOfModelDefinitions.sbmlIds(
) + doc.listOfExternalModelDefinitions.sbmlIds()
else:
return [doc.model.getSbmlId()]
def loadModel(self, request):
self.fileUploadForm = DocumentForm(request.POST, request.FILES)
if self.fileUploadForm.is_valid():
new_sbml_model = SbmlModel(project=self.project,
sbml_file=request.FILES['docfile'])
new_sbml_model.save()
try:
doc = SbmlDocument()
doc.readSbmlFromFile(
os.path.join(settings.MEDIA_ROOT,
str(new_sbml_model.sbml_file)))
dependencies = getDetailedModelDependencies(doc)
if len(dependencies) > 0:
for submodel_filename, submodel_ref in dependencies:
submodel_filename = join(self.project.folder, "models",
submodel_filename)
submodel = SbmlModel.objects.get(
sbml_file=submodel_filename)
new_dependency = ModelsDependency(
project=self.project,
model=new_sbml_model,
submodel=submodel,
submodel_ref=submodel_ref)
new_dependency.save()
new_sbml_model.name = doc.model.getName()
new_sbml_model.save()
except MissingSubmodelException:
new_sbml_model.delete()
self.addError(
"This model is importing some models which were not found in the project folder. Please import them first"
)
# Is triggered where name is None ??
except ModelException:
name = os.path.splitext(str(new_sbml_model.sbml_file))[0]
new_sbml_model.name = name
new_sbml_model.save()
def __loadModelVariables(self):
if self.model_id is not None and SbmlModel.objects.filter(
id=self.model_id).exists():
t_model = SbmlModel.objects.get(id=self.model_id)
if self.isProjectOwner(
self.__request) or t_model.project.access == "PU":
self.model_filename = os.path.join(settings.MEDIA_ROOT,
str(t_model.sbml_file))
t_doc = SbmlDocument()
t_doc.readSbmlFromFile(self.model_filename)
self.model = t_doc.model
self.model_name = self.model.getName()
self.model_list_of_submodels = self.model.listOfSubmodels
self.model_list_of_submodels_names = []
self.model_list_of_submodels_types = []
for submodel in self.model.listOfSubmodels:
if submodel.getModelRef(
) in self.model.parentDoc.listOfModelDefinitions.sbmlIds():
self.model_list_of_submodels_names.append(
self.model.parentDoc.listOfModelDefinitions.
getBySbmlId(
submodel.getModelRef()).getNameOrSbmlId())
self.model_list_of_submodels_types.append(0)
if submodel.getModelRef(
) in self.model.parentDoc.listOfExternalModelDefinitions.sbmlIds(
):
self.model_list_of_submodels_names.append(
self.model.parentDoc.
listOfExternalModelDefinitions.getBySbmlId(
submodel.getModelRef()).getNameOrSbmlId())
self.model_list_of_submodels_types.append(1)
else:
raise PermissionDenied
else:
raise Http404("The model doesn't exist !")
def renameSbmlIdInModelDependencies(sbml_model, old_sbml_id, new_sbml_id): for model_dependency in ModelsDependency.objects.filter(submodel=sbml_model): doc = SbmlDocument() doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model_dependency.model.sbml_file))) doc.renameSbmlIdInSubstitutions(old_sbml_id, new_sbml_id, model_dependency.submodel_ref) doc.writeSbmlToFile(join(settings.MEDIA_ROOT, str(model_dependency.model.sbml_file)))
def renameSbmlIdInModelDependencies(sbml_model, old_sbml_id, new_sbml_id):
for model_dependency in ModelsDependency.objects.filter(
submodel=sbml_model):
doc = SbmlDocument()
doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model_dependency.model.sbml_file)))
doc.renameSbmlIdInSubstitutions(old_sbml_id, new_sbml_id,
model_dependency.submodel_ref)
doc.writeSbmlToFile(
join(settings.MEDIA_ROOT, str(model_dependency.model.sbml_file)))
def copyModelHierarchy(model_filename):
doc = SbmlDocument()
doc.readSbmlFromFile(model_filename)
path = dirname(model_filename)
master_filename = new_model_filename()
if doc.useCompPackage:
deps = doc.getExternalDocumentDependencies()
new_deps = {}
for dependency in deps:
new_deps.update(
{dependency: copyModelHierarchy(join(path, dependency))})
doc.renameExternalDocumentDependencies(new_deps)
doc.writeSbmlToFile(join(path, master_filename))
return master_filename
def loadModel(self, request): self.fileUploadForm = DocumentForm(request.POST, request.FILES) if self.fileUploadForm.is_valid(): new_sbml_model = SbmlModel(project=self.project, sbml_file=request.FILES['docfile']) new_sbml_model.save() try: doc = SbmlDocument() doc.readSbmlFromFile(os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file))) dependencies = getDetailedModelDependencies(doc) if len(dependencies) > 0: for submodel_filename, submodel_ref in dependencies: submodel_filename = join(self.project.folder, "models", submodel_filename) submodel = SbmlModel.objects.get(sbml_file=submodel_filename) new_dependency = ModelsDependency( project=self.project, model=new_sbml_model, submodel=submodel, submodel_ref=submodel_ref ) new_dependency.save() new_sbml_model.name = doc.model.getName() new_sbml_model.save() except MissingSubmodelException: new_sbml_model.delete() self.addError( "This model is importing some models which were not found in the project folder. Please import them first") # Is triggered where name is None ?? except ModelException: name = os.path.splitext(str(new_sbml_model.sbml_file))[0] new_sbml_model.name = name new_sbml_model.save()
def loadBiomodels(self, request):
model_id = str(request.POST['model_id'])
model_filename = os.path.join(settings.MEDIA_ROOT, new_model_filename())
open(model_filename, "a")
new_model = SbmlModel(project=self.project, sbml_file=File(open(model_filename, "rb")))
os.remove(model_filename)
new_model.save()
doc = SbmlDocument()
try:
doc.readFromBiomodels(model_id)
doc.writeSbmlToFile(os.path.join(settings.MEDIA_ROOT, str(new_model.sbml_file)))
new_model.name = doc.model.getName()
new_model.save()
except:
self.addError("Unable to load model from biomodels")
new_model.delete()
def getListOfObjects(self, request):
if str(request.POST['model_id']) != "":
list_of_project_models = [
pm for pm in self.getProjectModels(request)
if pm.id != self.model_id
]
t_model = list_of_project_models[int(request.POST['model_id'])]
t_filename = join(settings.MEDIA_ROOT, str(t_model.sbml_file))
doc = SbmlDocument()
doc.readSbmlFromFile(t_filename)
if ('submodel_id' in request.POST
and request.POST['submodel_id'] != ""
and int(request.POST['submodel_id']) > 1):
submodel = doc.model.listOfSubmodels[
int(request.POST['submodel_id']) - 1].getModelObject()
self.listOfObjects = []
for t_object in doc.model.listOfSbmlObjects:
if isinstance(t_object,
Variable) and not t_object.isStoichiometry():
self.listOfObjects.append(t_object.getNameOrSbmlId() +
(" (%s)" %
type(t_object).__name__))
return self.listOfObjects
else:
self.listOfObjects = []
for t_object in doc.model.listOfSbmlObjects:
if isinstance(t_object,
Variable) and not t_object.isStoichiometry():
self.listOfObjects.append(t_object.getNameOrSbmlId() +
(" (%s)" %
type(t_object).__name__))
return self.listOfObjects
def save(self, *args, **kwargs):
if User.objects.filter(id=self.id).exists():
created = False
else:
created = True
super(User, self).save(*args, **kwargs)
if created:
new_project = Project(user=self, name="My first project")
new_project.save()
sbml_model_filename = join(settings.MEDIA_ROOT, "init_model.sbml")
sbml_model = open(sbml_model_filename, 'a')
sbml_model.close()
new_model = SbmlModel(project=new_project, name="My first model", sbml_file=File(open(sbml_model_filename, "rb")))
new_model.save()
os.remove(sbml_model_filename)
doc = SbmlDocument()
doc.model.newModel("My first model")
doc.writeSbmlToFile(os.path.join(settings.MEDIA_ROOT, str(new_model.sbml_file)))
def loadSimulation(self, request):
self.fileUploadForm = DocumentForm(request.POST, request.FILES)
if self.fileUploadForm.is_valid():
sedml_archive = SEDMLSimulation(project=self.project, sedml_file=request.FILES['docfile'])
sedml_archive.name = basename(str(request.FILES['docfile'])).split('.')[0]
sedml_archive.save()
# Now everything is in the same folder
sedml_doc = SedmlDocument()
sedml_doc.readSedmlFromFile(join(settings.MEDIA_ROOT, str(sedml_archive.sedml_file)))
sedml_doc.listOfModels.removePaths()
sbml_files = sedml_doc.listOfModels.makeLocalSources()
for sbml_file in sbml_files:
if len(SbmlModel.objects.filter(project=self.project, sbml_file=join(join(str(self.project.folder), "models"), basename(sbml_file)))) == 0:
sbml_model = SbmlModel(project=self.project, sbml_file=File(open(sbml_file, 'rb')))
sbml_model.save()
try:
doc = SbmlDocument()
doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(sbml_model.sbml_file)))
sbml_model.name = doc.model.getName()
sbml_model.save()
except Exception:
name = splitext(str(sbml_model.sbml_file))[0]
sbml_model.name = name
sbml_model.save()
sedml_doc.writeSedmlToFile(join(settings.MEDIA_ROOT, str(sedml_archive.sedml_file)))
self.loadListOfSimulations()
def copyModelHierarchy(model_filename):
doc = SbmlDocument()
doc.readSbmlFromFile(model_filename)
path = dirname(model_filename)
master_filename = new_model_filename()
if doc.useCompPackage:
deps = doc.getExternalDocumentDependencies()
new_deps = {}
for dependency in deps:
new_deps.update({dependency: copyModelHierarchy(join(path, dependency))})
doc.renameExternalDocumentDependencies(new_deps)
doc.writeSbmlToFile(join(path, master_filename))
return master_filename
def duplicateModel(self, request):
model = SbmlModel.objects.get(id=request.POST['id'])
t_file = File(
open(os.path.join(settings.MEDIA_ROOT, str(model.sbml_file)),
'rb'))
new_sbml_model = SbmlModel(project=self.project,
name=("%s (copy)" % str(model.name)),
sbml_file=t_file)
new_sbml_model.save()
t_filename = os.path.join(settings.MEDIA_ROOT,
str(new_sbml_model.sbml_file))
doc = SbmlDocument()
doc.readSbmlFromFile(t_filename)
doc.model.setName(str(new_sbml_model.name))
doc.writeSbmlToFile(t_filename)
def loadBiomodels(self, request):
model_id = str(request.POST['model_id'])
model_filename = os.path.join(settings.MEDIA_ROOT,
new_model_filename())
open(model_filename, "a")
new_model = SbmlModel(project=self.project,
sbml_file=File(open(model_filename, "rb")))
os.remove(model_filename)
new_model.save()
doc = SbmlDocument()
try:
doc.readFromBiomodels(model_id)
doc.writeSbmlToFile(
os.path.join(settings.MEDIA_ROOT, str(new_model.sbml_file)))
new_model.name = doc.model.getName()
new_model.save()
except:
self.addError("Unable to load model from biomodels")
new_model.delete()
def testOptimization(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project, '/models/', status_code=302, target_status_code=200)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
files_folder = join(dirname(__file__), "files")
comp_files_folder = join(files_folder, "comp_model")
model_filename = join(comp_files_folder, "modelcEvRcX.xml")
response_load_submodel_1 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_1.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model_filename = join(comp_files_folder, "modelEHfev9.xml")
response_load_submodel_2 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_2.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 2)
model_filename = join(comp_files_folder, "modelI1vrys.xml")
response_load_submodel_3 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_3.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 3)
model_filename = join(comp_files_folder, "modelz9xdww.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 4)
response_choose_model = c.post('/fit/data/', {
'action': 'choose_model',
'model_id': 3
})
self.assertEqual(response_choose_model.status_code, 200)
experiment_filename = join(files_folder, "ras_data.xml")
response_import_data = c.post('/data/', {
'action': 'import',
'docfile': open(experiment_filename, 'rb')
})
self.assertEqual(response_import_data.status_code, 200)
self.assertEqual(
[experiment.name for experiment in response_import_data.context['experimental_data']],
[u'Ras-GTP quantifications']
)
experiment_id = response_import_data.context['experimental_data'][0].id
response_get_fit_data = c.get('/fit/data/')
self.assertEqual(response_get_fit_data.status_code, 200)
self.assertEqual(
[dataset for dataset in response_get_fit_data.context['experimental_data_sets']],
[u'Ras-GTP quantifications']
)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(len(response_list_optimizations.context['optimizations']), 0)
response_add_dataset = c.post('/json/add_dataset/', {
'dataset_ind': 0
})
self.assertEqual(response_add_dataset.status_code, 200)
mapping = loads(response_add_dataset.content.decode('utf-8'))['model_xpaths']
sbml_filename = str(SbmlModel.objects.filter(project=project)[3].sbml_file)
doc = SbmlDocument()
doc.readSbmlFromFile(join(settings.MEDIA_ROOT, sbml_filename))
self.assertEqual(sorted(list(mapping.keys())), ['FGF2', 'Total Ras-GTP'])
self.assertEqual(doc.getModelInstance().listOfSpecies.index(doc.getByXPath(mapping['FGF2'], instance=True)), 4)
self.assertEqual(doc.getModelInstance().listOfSpecies.index(doc.getByXPath(mapping['Total Ras-GTP'], instance=True)), 13)
response_create_optimization = c.post('/fit/data/', {
'action': 'create',
'dataset_0': experiment_id, #response_get_fit_data.context['experimental_data_sets'][0].id,
'list_dataset_0_data_species_0_value': "FGF2",
'list_dataset_0_species_0_value': 4,
'list_dataset_0_data_species_1_value': "Total Ras-GTP",
'list_dataset_0_species_1_value': 13,
'parameter_0_id': 1,
'parameter_0_name': "SOS activation by FGF2",
'parameter_0_value': 1.0,
'parameter_0_min': 1e-4,
'parameter_0_max': 1e+4,
'parameter_0_precision': 7,
'parameter_1_active': "on",
'parameter_1_id': 1,
'parameter_1_name': "SOS inactivation by Mapk catalytic constant",
'parameter_1_value': 1.0,
'parameter_1_min': 1e-6,
'parameter_1_max': 1e+6,
'parameter_1_precision': 7,
'nb_cores': 2,
'lambda': 0.02,
'score_precision': 0.001,
'param_precision': 7,
'initial_temperature': 1,
'initial_moves': 200,
'freeze_count': 1,
'negative_penalty': 0
})
self.assertEqual(response_create_optimization.status_code, 200)
self.assertEqual(response_create_optimization.context['form'].getErrors(), [])
sleep(10)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(len(response_list_optimizations.context['optimizations']), 1)
self.assertEqual(response_list_optimizations.context['optimizations'][0][0].status, "Running")
sleep(10)
optimization_id = response_list_optimizations.context['optimizations'][0][0].optimization_id
response_get_optimization = c.get('/fit/%s/' % optimization_id)
self.assertEqual(response_get_optimization.status_code, 200)
max_time = 360
sleep(360)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(response_list_optimizations.context['optimizations'][0][0].status, "Finished")
response_get_optimization = c.get('/fit/%s/' % optimization_id)
self.assertEqual(response_get_optimization.status_code, 200)
scores = response_get_optimization.context['score_values']
self.assertTrue(scores[len(scores)-1] < 1.01)
def testReactions(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project,
'/models/',
status_code=302,
target_status_code=200)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_4')
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'],
"Project")
response_choose_model = c.post('/edit/reactions/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'],
"SOS-Ras-MAPK with n17")
self.assertEqual([
t_reaction.getReactionDescription() for t_reaction in
response_choose_model.context['list_of_reactions']
], [
t_reaction.getReactionDescription()
for t_reaction in sbml_model.listOfReactions
])
response_get_reaction = c.post('/json/get_reaction/',
{'sbml_id': 'reaction_4'})
self.assertEqual(response_get_reaction.status_code, 200)
json_response = loads(response_get_reaction.content.decode('utf-8'))
self.assertEqual(json_response[u'id'],
sbml_model.listOfReactions.index(reaction))
self.assertEqual(json_response[u'sbml_id'], reaction.getSbmlId())
self.assertEqual(json_response[u'name'], reaction.getName())
self.assertEqual(json_response[u'kinetic_law'],
reaction.kineticLaw.getPrettyPrintMathFormula())
self.assertEqual(json_response[u'reaction_type'],
reaction.getReactionType())
self.assertEqual(json_response[u'reaction_type_name'],
KineticLaw.reactionTypes[reaction.getReactionType()])
self.assertEqual(json_response[u'reversible'], reaction.reversible)
self.assertEqual(json_response[u'list_of_reactants'], [[
sbml_model.listOfSpecies.index(reactant.getSpecies()),
reactant.stoichiometry.getPrettyPrintMathFormula()
] for reactant in reaction.listOfReactants])
self.assertEqual(json_response[u'list_of_modifiers'], [[
sbml_model.listOfSpecies.index(modifier.getSpecies()),
modifier.stoichiometry.getPrettyPrintMathFormula()
] for modifier in reaction.listOfModifiers])
self.assertEqual(json_response[u'list_of_products'], [[
sbml_model.listOfSpecies.index(product.getSpecies()),
product.stoichiometry.getPrettyPrintMathFormula()
] for product in reaction.listOfProducts])
response_delete_reaction = c.post('/edit/reactions/', {
'action': 'delete',
'reaction_id': 2
})
self.assertEqual(response_delete_reaction.status_code, 200)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
self.assertEqual(len(sbml_model.listOfReactions), 21)
self.assertEqual(sbml_model.listOfReactions.getBySbmlId('reaction_4'),
None)
response_create_creation = c.post(
'/edit/reactions/', {
'action': 'save',
'reaction_id': "",
'reaction_sbml_id': "reaction_4",
'reaction_name': "Ras activation by SOS-Ras-GDP",
'reaction_reactant_0': 1,
'reaction_reactant_0_stoichiometry': "1",
'reaction_modifier_0': 3,
'reaction_modifier_0_stoichiometry': "1",
'reaction_product_0': 2,
'reaction_product_0_stoichiometry': "1",
'reaction_type': 1,
'reaction_parameter_0': 2,
'reaction_parameter_1': 3,
'reaction_sboterm': ""
})
self.assertEqual(response_create_creation.status_code, 200)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_4')
self.assertEqual(len(sbml_model.listOfReactions), 22)
self.assertEqual(reaction.getName(), "Ras activation by SOS-Ras-GDP")
response_modify_creation = c.post(
'/edit/reactions/', {
'action': 'save',
'reaction_id': sbml_model.listOfReactions.index(reaction),
'reaction_sbml_id': "reaction_4",
'reaction_name': "Ras activation by SOS-Ras-GDP, modified",
'reaction_reactant_0': 1,
'reaction_reactant_0_stoichiometry': "1",
'reaction_modifier_0': 3,
'reaction_modifier_0_stoichiometry': "1",
'reaction_product_0': 2,
'reaction_product_0_stoichiometry': "1",
'reaction_type': 1,
'reaction_parameter_0': 2,
'reaction_parameter_1': 3,
'reaction_sboterm': ""
})
self.assertEqual(response_modify_creation.status_code, 200)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_4')
self.assertEqual(len(sbml_model.listOfReactions), 22)
self.assertEqual(reaction.getName(),
"Ras activation by SOS-Ras-GDP, modified")
def testOptimization(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project, '/models/', status_code=302, target_status_code=200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelx8Ow70.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
response_create_experiment = c.post('/data/', {
'action': 'save',
'experiment_id': "",
'experiment_name': "Enzymatic reaction",
'experiment_notes': "Something"
})
self.assertEqual(response_create_experiment.status_code, 200)
self.assertEqual(
[experiment.name for experiment in response_create_experiment.context['experimental_data']],
[u'Enzymatic reaction']
)
experiment_id = response_create_experiment.context['experimental_data'][0].id
# Testing conditions
response_choose_experiment = c.get('/data/%d/' % experiment_id)
self.assertEqual(response_choose_experiment.status_code, 200)
self.assertEqual(response_choose_experiment.context['experiment_name'], u'Enzymatic reaction')
self.assertEqual(
[condition.name for condition in response_choose_experiment.context['conditions']],
[]
)
response_new_condition = c.post('/data/%d/' % experiment_id, {
'action': 'save',
'condition_id': "",
'condition_name': "Test condition",
'condition_notes': "Some notes"
})
self.assertEqual(response_new_condition.status_code, 200)
self.assertEqual(
[condition.name for condition in response_new_condition.context['conditions']],
[u'Test condition']
)
condition_id = response_new_condition.context['conditions'][0].id
response_choose_experiment = c.get('/data/%d/%d/' % (experiment_id, condition_id))
self.assertEqual(response_choose_experiment.status_code, 200)
self.assertEqual(len(response_choose_experiment.context['experiment_initial_data']), 0)
response_add_treatment = c.post('/data/%d/%d/' % (experiment_id, condition_id), {
'data_type': 'treatment',
'action': 'save',
'id': "",
'name': 'Substrate',
'time': 0,
'value': 15
})
self.assertEqual(response_add_treatment.status_code, 200)
self.assertEqual(len(response_add_treatment.context['experiment_initial_data']), 1)
self.assertEqual(len(response_add_treatment.context['experiment_data']), 0)
response_add_observation = c.post('/data/%d/%d/' % (experiment_id, condition_id), {
'data_type': 'observation',
'action': 'save',
'id': "",
'name': 'Product',
'time': 0,
'value': 0,
'stddev': 0,
'steady_state': 'off',
'min_steady_state': "0",
'max_steady_state': "0"
})
self.assertEqual(response_add_observation.status_code, 200)
self.assertEqual(len(response_add_observation.context['experiment_data']), 1)
response_add_observation = c.post('/data/%d/%d/' % (experiment_id, condition_id), {
'data_type': 'observation',
'action': 'save',
'id': "",
'name': 'Product',
'time': 10,
'value': 10,
'stddev': 0,
'steady_state': 'off',
'min_steady_state': "0",
'max_steady_state': "0"
})
self.assertEqual(response_add_observation.status_code, 200)
self.assertEqual(len(response_add_observation.context['experiment_data']), 2)
response_add_observation = c.post('/data/%d/%d/' % (experiment_id, condition_id), {
'data_type': 'observation',
'action': 'save',
'id': "",
'name': 'Product',
'time': 20,
'value': 15,
'stddev': 0,
'steady_state': 'off',
'min_steady_state': "0",
'max_steady_state': "0"
})
self.assertEqual(response_add_observation.status_code, 200)
self.assertEqual(len(response_add_observation.context['experiment_data']), 3)
response_add_observation = c.post('/data/%d/%d/' % (experiment_id, condition_id), {
'data_type': 'observation',
'action': 'save',
'id': "",
'name': 'Product',
'time': 50,
'value': 15,
'stddev': 0,
'steady_state': 'off',
'min_steady_state': "0",
'max_steady_state': "0"
})
self.assertEqual(response_add_observation.status_code, 200)
self.assertEqual(len(response_add_observation.context['experiment_data']), 4)
response_get_fit_data = c.get('/fit/data/')
self.assertEqual(response_get_fit_data.status_code, 200)
self.assertEqual(
[dataset for dataset in response_get_fit_data.context['experimental_data_sets']],
[u'Enzymatic reaction']
)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(len(response_list_optimizations.context['optimizations']), 0)
response_add_dataset = c.post('/json/add_dataset/', {
'dataset_ind': 0
})
self.assertEqual(response_add_dataset.status_code, 200)
mapping = loads(response_add_dataset.content.decode('utf-8'))['model_xpaths']
sbml_filename = str(SbmlModel.objects.filter(project=project)[0].sbml_file)
doc = SbmlDocument()
doc.readSbmlFromFile(join(settings.MEDIA_ROOT, sbml_filename))
self.assertEqual(sorted(list(mapping.keys())), ['Product', 'Substrate'])
self.assertEqual(doc.model.listOfSpecies.index(doc.getByXPath(mapping['Substrate'])), 0)
self.assertEqual(doc.model.listOfSpecies.index(doc.getByXPath(mapping['Product'])), 3)
response_create_optimization = c.post('/fit/data/', {
'action': 'create',
'dataset_0': experiment_id,
'list_dataset_0_data_species_0_value': "Product",
'list_dataset_0_species_0_value': 3,
'list_dataset_0_data_species_1_value': "Substrate",
'list_dataset_0_species_1_value': 0,
'parameter_0_active': "on",
'parameter_0_id': 0,
'parameter_0_name': "Binding rate",
'parameter_0_value': 1.0,
'parameter_0_min': 1e-4,
'parameter_0_max': 1e+4,
'parameter_0_precision': 7,
'parameter_1_active': "on",
'parameter_1_id': 0,
'parameter_1_name': "Unbinding rate",
'parameter_1_value': 1.0,
'parameter_1_min': 1e-4,
'parameter_1_max': 1e+4,
'parameter_1_precision': 7,
'parameter_2_active': "on",
'parameter_2_id': 0,
'parameter_2_name': "Catalytic rate",
'parameter_2_value': 1.0,
'parameter_2_min': 1e-4,
'parameter_2_max': 1e+4,
'parameter_2_precision': 7,
'nb_cores': 2,
'lambda': 0.001,
'score_precision': 0.001,
'param_precision': 7,
'initial_temperature': 1,
'initial_moves': 2000,
'freeze_count': 100,
'negative_penalty': 0
})
self.assertEqual(response_create_optimization.status_code, 200)
self.assertEqual(response_create_optimization.context['form'].getErrors(), [])
sleep(5)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(len(response_list_optimizations.context['optimizations']), 1)
self.assertEqual(response_list_optimizations.context['optimizations'][0][0].status, "Running")
sleep(10)
response_get_optimization = c.get('/fit/%s/' % response_list_optimizations.context['optimizations'][0][0].optimization_id)
self.assertEqual(response_get_optimization.status_code, 200)
sleep(240)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(response_list_optimizations.context['optimizations'][0][0].status, "Finished")
response_get_optimization = c.get(
'/fit/%s/' % response_list_optimizations.context['optimizations'][0][0].optimization_id)
self.assertEqual(response_get_optimization.status_code, 200)
scores = response_get_optimization.context['score_values']
self.assertTrue(scores[len(scores)-1] < 0.24)
def testCompartment(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project,
'/models/',
status_code=302,
target_status_code=200)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
compartment = sbml_model.listOfCompartments.getBySbmlId('cell')
response_get_compartment = c.post('/json/get_compartment/', {
'sbml_id': 'cell',
})
self.assertEqual(response_get_compartment.status_code, 200)
json_response = loads(response_get_compartment.content.decode('utf-8'))
self.assertEqual(json_response[u'id'],
sbml_model.listOfCompartments.index(compartment))
self.assertEqual(json_response[u'sbml_id'], compartment.getSbmlId())
self.assertEqual(json_response[u'name'], compartment.getName())
self.assertEqual(json_response[u'value'], compartment.getValue())
self.assertEqual(json_response[u'constant'],
1 if compartment.constant else 0)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'],
"Project")
response_choose_model = c.post('/edit/compartments/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'],
"SOS-Ras-MAPK with n17")
response_save_compartment = c.post(
'/edit/compartments/', {
'action': 'save',
'compartment_id':
sbml_model.listOfCompartments.index(compartment),
'compartment_name': "New name",
'compartment_sbml_id': "new_name",
'compartment_size': 75,
'compartment_unit': 2,
'compartment_constant': "on",
'compartment_sboterm': "",
})
self.assertEqual(response_save_compartment.status_code, 200)
self.assertEqual(response_save_compartment.context['getErrors'], [])
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
compartment = sbml_model.listOfCompartments.getBySbmlId('new_name')
self.assertTrue(compartment is not None)
self.assertEqual(compartment.getName(), "New name")
self.assertEqual(compartment.getValue(), 75)
self.assertEqual(compartment.constant, True)
self.assertEqual(compartment.getUnits(),
sbml_model.listOfUnitDefinitions[2])
response_delete_compartment = c.post(
'/edit/compartments/', {
'action': 'delete',
'compartment_id':
sbml_model.listOfCompartments.index(compartment)
})
self.assertEqual(response_delete_compartment.status_code, 200)
self.assertEqual(response_delete_compartment.context['getErrors'],
['Compartment contains 25 species'])
response_save_new_compartment = c.post(
'/edit/compartments/', {
'action': 'save',
'compartment_id': "",
'compartment_name': "New compartment",
'compartment_sbml_id': "new_compartment",
'compartment_size': 75,
'compartment_unit': "",
'compartment_constant': "on",
'compartment_sboterm': "",
})
self.assertEqual(response_save_new_compartment.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
compartment = sbml_model.listOfCompartments.getBySbmlId(
'new_compartment')
self.assertTrue(compartment != None)
self.assertEqual(compartment.getName(), "New compartment")
self.assertEqual(compartment.getValue(), 75)
self.assertEqual(compartment.getUnits(), None)
self.assertEqual(compartment.constant, True)
response_delete_compartment = c.post(
'/edit/compartments/', {
'action': 'delete',
'compartment_id':
sbml_model.listOfCompartments.index(compartment)
})
self.assertEqual(response_delete_compartment.status_code, 200)
self.assertEqual(response_delete_compartment.context['getErrors'], [])
def testCreateModel(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project, '/models/', status_code=302, target_status_code=200)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
files_folder = join(dirname(__file__), "files")
comp_files_folder = join(files_folder, "comp_model")
model_filename = join(comp_files_folder, "modelcEvRcX.xml")
response_load_submodel_1 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_1.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model_filename = join(comp_files_folder, "modelEHfev9.xml")
response_load_submodel_2 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_2.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 2)
model_filename = join(comp_files_folder, "modelI1vrys.xml")
response_load_submodel_3 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_3.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 3)
model_filename = join(comp_files_folder, "modelz9xdww.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 4)
response_choose_model = c.post('/edit/species/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(
[sbml_model.name for sbml_model in response_choose_model.context['sbml_models']],
[u'SOS', u'Ras', u'MAPK', u'SOS-Ras-MAPK']
)
self.assertEqual(
[submodel for submodel in response_choose_model.context['model_submodels']],
['Model definition']
)
self.assertEqual(
[species.getNameOrSbmlId() for species in response_choose_model.context['list_of_species']],
['SOS', 'SOS_inactive', 'FGF2', 'ERK-PP']
)
response_choose_model = c.post('/edit/species/', {
'action': 'choose_model',
'model_id': 1
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(
[sbml_model.name for sbml_model in response_choose_model.context['sbml_models']],
[u'SOS', u'Ras', u'MAPK', u'SOS-Ras-MAPK']
)
self.assertEqual(
[submodel for submodel in response_choose_model.context['model_submodels']],
['Model definition']
)
self.assertEqual(
[species.getNameOrSbmlId() for species in response_choose_model.context['list_of_species']],
[
'SOS', 'Ras-GDP', 'Ras-GTP', 'SOS-Ras-GDP', 'SOS-Ras-GTP',
'GAP', 'GEF', 'Ras-N17', 'SOS-Ras-N17', 'GEF-RasN17', 'Total Ras-GTP'
]
)
response_choose_model = c.post('/edit/species/', {
'action': 'choose_model',
'model_id': 2
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(
[sbml_model.name for sbml_model in response_choose_model.context['sbml_models']],
[u'SOS', u'Ras', u'MAPK', u'SOS-Ras-MAPK']
)
self.assertEqual(
[submodel for submodel in response_choose_model.context['model_submodels']],
['Model definition']
)
self.assertEqual(
[species.getNameOrSbmlId() for species in response_choose_model.context['list_of_species']],
[
'Ras-GTP', 'Raf', 'Raf-P', 'Mek', 'Mek-P', 'Mek-PP',
'Mapk', 'Mapk-P', 'Mapk-PP', 'Total MEK activated', 'Total MAPK activated'
]
)
response_choose_model = c.post('/edit/species/', {
'action': 'choose_model',
'model_id': 3
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(
[sbml_model.name for sbml_model in response_choose_model.context['sbml_models']],
[u'SOS', u'Ras', u'MAPK', u'SOS-Ras-MAPK']
)
self.assertEqual(
[submodel for submodel in response_choose_model.context['model_submodels']],
['Model definition', 'Test submodel']
)
self.assertEqual(
[species.getNameOrSbmlId() for species in response_choose_model.context['list_of_species']],
['SOS', 'Ras-GTP', 'ERK-PP']
)
response_choose_submodel = c.post('/edit/species/', {
'action': 'choose_submodel',
'submodel_id': 0
})
self.assertEqual(response_choose_submodel.status_code, 200)
self.assertEqual(
[species.getNameOrSbmlId() for species in response_choose_submodel.context['list_of_species']],
['SOS', 'Ras-GTP', 'ERK-PP']
)
response_choose_submodel = c.post('/edit/species/', {
'action': 'choose_submodel',
'submodel_id': 2
})
self.assertEqual(response_choose_submodel.status_code, 200)
self.assertEqual(
[species.getNameOrSbmlId() for species in response_choose_submodel.context['list_of_species']],
['SOS', 'Ras-GTP', 'ERK-PP', 'SOS_inactive', 'FGF2', 'Ras-GDP', 'SOS-Ras-GDP', 'SOS-Ras-GTP', 'GAP', 'GEF',
'Ras-N17', 'SOS-Ras-N17', 'GEF-RasN17', 'Total Ras-GTP', 'Raf', 'Raf-P', 'Mek', 'Mek-P', 'Mek-PP', 'Mapk',
'Mapk-P', 'Total MEK activated', 'Total MAPK activated']
)
response_choose_submodel = c.post('/edit/species/', {
'action': 'choose_submodel',
'submodel_id': 2
})
self.assertEqual(response_choose_submodel.status_code, 200)
self.assertEqual(
[species.getNameOrSbmlId() for species in response_choose_submodel.context['list_of_species']],
['SOS', 'Ras-GTP', 'ERK-PP', 'SOS_inactive', 'FGF2', 'Ras-GDP', 'SOS-Ras-GDP', 'SOS-Ras-GTP', 'GAP', 'GEF',
'Ras-N17', 'SOS-Ras-N17', 'GEF-RasN17', 'Total Ras-GTP', 'Raf', 'Raf-P', 'Mek', 'Mek-P', 'Mek-PP', 'Mapk',
'Mapk-P', 'Total MEK activated', 'Total MAPK activated']
)
response_choose_submodel = c.post('/edit/submodels/', {
'action': 'choose_submodel',
'submodel_id': 0
})
self.assertEqual(response_choose_submodel.status_code, 200)
self.assertEqual(response_choose_submodel.context['model_submodels'], ['Model definition', 'Test submodel'])
response_add_submodel = c.post('/edit/submodels/', {
'action': 'save',
'submodel_id': "",
'submodel_name': "Internal model",
'submodel_sbml_id': "internal",
'submodel_type': 0,
'extent_conversion_factor': "",
'time_conversion_factor': ""
})
self.assertEqual(response_add_submodel.status_code, 200)
model = SbmlModel.objects.filter(project=project)[3]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.model
self.assertEqual(sbml_doc.listOfModelDefinitions[1].getName(), "Internal model")
self.assertEqual(sbml_model.listOfSubmodels[4].getSbmlId(), "internal")
self.assertEqual(response_add_submodel.context['model_submodels'], ['Model definition', 'Test submodel', 'Internal model'])
response_add_submodel = c.post('/edit/submodels/', {
'action': 'save',
'submodel_id': 4,
'submodel_name': "Internal model, modified",
'submodel_sbml_id': "internal_modified",
'submodel_type': 0,
'extent_conversion_factor': "",
'time_conversion_factor': ""
})
self.assertEqual(response_add_submodel.status_code, 200)
model = SbmlModel.objects.filter(project=project)[3]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.model
self.assertEqual(sbml_doc.listOfModelDefinitions[1].getName(), "Internal model, modified")
self.assertEqual(sbml_model.listOfSubmodels[4].getSbmlId(), "internal_modified")
self.assertEqual(response_add_submodel.context['model_submodels'], ['Model definition', 'Test submodel', 'Internal model, modified'])
def testRule(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project, '/models/', status_code=302, target_status_code=200)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfRules = sbml_model.listOfRules + sbml_model.listOfInitialAssignments
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies()
or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
rule = listOfRules[0]
response_get_compartment = c.post('/json/get_rule/', {
'rule_ind': '0',
})
self.assertEqual(response_get_compartment.status_code, 200)
json_response = loads(response_get_compartment.content.decode('utf-8'))
self.assertEqual(json_response[u'rule_id'], listOfRules.index(rule))
self.assertEqual(json_response[u'rule_type'], 1)
self.assertEqual(json_response[u'variable'], listOfVariables.index(sbml_model.listOfVariables.getBySbmlId('total_ras_gtp')))
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'], "Project")
response_choose_model = c.post('/edit/rules/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'], "SOS-Ras-MAPK with n17")
response_save_rule = c.post('/edit/rules/', {
'action': 'save',
'rule_id': listOfRules.index(rule),
'rule_type': 1,
'variable_id': listOfVariables.index(sbml_model.listOfVariables.getBySbmlId('total_mapk_activated')),
'rule_expression': "75*ras_gtp",
})
self.assertEqual(response_save_rule.status_code, 200)
self.assertEqual(response_save_rule.context['form'].getErrors(), [])
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfRules = sbml_model.listOfRules + sbml_model.listOfInitialAssignments
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies()
or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
rule = listOfRules[0]
self.assertEqual(rule.getType(), 1)
self.assertEqual(rule.getVariable(), sbml_model.listOfVariables.getBySbmlId('total_mapk_activated'))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("75*ras_gtp", rawFormula=True)
self.assertEqual(simplify(rule.getDefinition().getDeveloppedInternalMathFormula()-formula.getDeveloppedInternalMathFormula()), 0)
response_delete_rule = c.post('/edit/rules/', {
'action': 'delete',
'rule_id': 0
})
self.assertEqual(response_delete_rule.status_code, 200)
self.assertEqual(response_delete_rule.context['form'].getErrors(), [])
def testEvents(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project,
'/models/',
status_code=302,
target_status_code=200)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies() or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'],
"Project")
response_choose_model = c.post('/edit/events/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'],
"SOS-Ras-MAPK with n17")
response_save_event = c.post(
'/edit/events/', {
'action':
'save',
'event_id':
'',
'event_sbmlid':
'test_event',
'event_name':
"Test event",
'event_trigger':
"time==0",
'event_priority':
"",
'event_delay':
"",
'event_assignment_0_id':
listOfVariables.index(
sbml_model.listOfVariables.getBySbmlId('ras_gtp')),
'event_assignment_0_expression':
'ras_gtp*2'
})
self.assertEqual(response_save_event.status_code, 200)
self.assertEqual(response_save_event.context['form'].getErrors(), [])
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies() or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
response_get_event = c.post('/json/get_event/', {
'event_ind': '0',
})
self.assertEqual(response_get_event.status_code, 200)
json_response = loads(response_get_event.content.decode('utf-8'))
self.assertEqual(json_response[u'event_ind'], 0)
self.assertEqual(json_response[u'event_name'], "Test event")
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("time==0", rawFormula=True)
formula_response = MathFormula(sbml_model)
formula_response.setPrettyPrintMathFormula(
json_response[u'event_trigger'], rawFormula=True)
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() -
formula_response.getDeveloppedInternalMathFormula()), 0)
self.assertEqual(json_response[u'event_delay'], "")
self.assertEqual(
json_response[u'list_of_assignments'][0][0],
listOfVariables.index(
sbml_model.listOfVariables.getBySbmlId('ras_gtp')))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("ras_gtp*2", rawFormula=True)
formula_response = MathFormula(sbml_model)
formula_response.setPrettyPrintMathFormula(
json_response[u'list_of_assignments'][0][2], rawFormula=True)
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() -
formula_response.getDeveloppedInternalMathFormula()), 0)
self.assertTrue(u'event_assignment_variable_1' not in json_response)
# Modifying an event
response_save_event = c.post(
'/edit/events/', {
'action':
'save',
'event_id':
'0',
'event_sbmlid':
'test_event',
'event_name':
"Test event",
'event_trigger':
"time==100",
'event_priority':
"",
'event_delay':
"",
'event_assignment_0_id':
listOfVariables.index(
sbml_model.listOfVariables.getBySbmlId('ras_gtp')),
'event_assignment_0_expression':
'ras_gtp*2',
'event_assignment_1_id':
listOfVariables.index(
sbml_model.listOfVariables.getBySbmlId('ras_gdp')),
'event_assignment_1_expression':
'ras_gdp/2',
})
self.assertEqual(response_save_event.status_code, 200)
self.assertEqual(response_save_event.context['form'].getErrors(), [])
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
event = sbml_model.listOfEvents[0]
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies() or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
self.assertEqual(event.getNameOrSbmlId(), "Test event")
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("time==100", rawFormula=True)
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() -
event.trigger.getDeveloppedInternalMathFormula()), 0)
self.assertEqual(event.priority, None)
self.assertEqual(event.delay, None)
self.assertEqual(event.listOfEventAssignments[0].getVariable(),
sbml_model.listOfVariables.getBySbmlId('ras_gtp'))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("ras_gtp*2")
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() -
event.listOfEventAssignments[0].getDefinition(
).getDeveloppedInternalMathFormula()), 0)
self.assertEqual(event.listOfEventAssignments[1].getVariable(),
sbml_model.listOfVariables.getBySbmlId('ras_gdp'))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("ras_gdp/2")
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() -
event.listOfEventAssignments[1].getDefinition(
).getDeveloppedInternalMathFormula()), 0)
response_delete_event = c.post('/edit/events/', {
'action': 'delete',
'event_id': 0
})
self.assertEqual(response_delete_event.status_code, 200)
self.assertEqual(response_delete_event.context['form'].getErrors(), [])
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
self.assertEqual(len(sbml_model.listOfEvents), 0)
def testReactions(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project, '/models/', status_code=302, target_status_code=200)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_4')
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'], "Project")
response_choose_model = c.post('/edit/reactions/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'], "SOS-Ras-MAPK with n17")
self.assertEqual(
[t_reaction.getReactionDescription() for t_reaction in response_choose_model.context['list_of_reactions']],
[t_reaction.getReactionDescription() for t_reaction in sbml_model.listOfReactions]
)
response_get_reaction = c.post('/json/get_reaction/', {
'sbml_id': 'reaction_4'
})
self.assertEqual(response_get_reaction.status_code, 200)
json_response = loads(response_get_reaction.content.decode('utf-8'))
self.assertEqual(json_response[u'id'], sbml_model.listOfReactions.index(reaction))
self.assertEqual(json_response[u'sbml_id'], reaction.getSbmlId())
self.assertEqual(json_response[u'name'], reaction.getName())
self.assertEqual(json_response[u'kinetic_law'], reaction.kineticLaw.getPrettyPrintMathFormula())
self.assertEqual(json_response[u'reaction_type'], reaction.getReactionType())
self.assertEqual(json_response[u'reaction_type_name'], KineticLaw.reactionTypes[reaction.getReactionType()])
self.assertEqual(json_response[u'reversible'], reaction.reversible)
self.assertEqual(json_response[u'list_of_reactants'], [
[
sbml_model.listOfSpecies.index(reactant.getSpecies()),
reactant.stoichiometry.getPrettyPrintMathFormula()
]
for reactant in reaction.listOfReactants
])
self.assertEqual(json_response[u'list_of_modifiers'], [
[
sbml_model.listOfSpecies.index(modifier.getSpecies()),
modifier.stoichiometry.getPrettyPrintMathFormula()
]
for modifier in reaction.listOfModifiers
])
self.assertEqual(json_response[u'list_of_products'], [
[
sbml_model.listOfSpecies.index(product.getSpecies()),
product.stoichiometry.getPrettyPrintMathFormula()
]
for product in reaction.listOfProducts
])
response_delete_reaction = c.post('/edit/reactions/', {
'action': 'delete',
'reaction_id': 2
})
self.assertEqual(response_delete_reaction.status_code, 200)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
self.assertEqual(len(sbml_model.listOfReactions), 21)
self.assertEqual(sbml_model.listOfReactions.getBySbmlId('reaction_4'), None)
response_create_creation = c.post('/edit/reactions/', {
'action': 'save',
'reaction_id': "",
'reaction_sbml_id': "reaction_4",
'reaction_name': "Ras activation by SOS-Ras-GDP",
'reaction_reactant_0': 1,
'reaction_reactant_0_stoichiometry': "1",
'reaction_modifier_0': 3,
'reaction_modifier_0_stoichiometry': "1",
'reaction_product_0': 2,
'reaction_product_0_stoichiometry': "1",
'reaction_type': 1,
'reaction_parameter_0': 2,
'reaction_parameter_1': 3,
'reaction_sboterm': ""
})
self.assertEqual(response_create_creation.status_code, 200)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_4')
self.assertEqual(len(sbml_model.listOfReactions), 22)
self.assertEqual(reaction.getName(), "Ras activation by SOS-Ras-GDP")
response_modify_creation = c.post('/edit/reactions/', {
'action': 'save',
'reaction_id': sbml_model.listOfReactions.index(reaction),
'reaction_sbml_id': "reaction_4",
'reaction_name': "Ras activation by SOS-Ras-GDP, modified",
'reaction_reactant_0': 1,
'reaction_reactant_0_stoichiometry': "1",
'reaction_modifier_0': 3,
'reaction_modifier_0_stoichiometry': "1",
'reaction_product_0': 2,
'reaction_product_0_stoichiometry': "1",
'reaction_type': 1,
'reaction_parameter_0': 2,
'reaction_parameter_1': 3,
'reaction_sboterm': ""
})
self.assertEqual(response_modify_creation.status_code, 200)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_4')
self.assertEqual(len(sbml_model.listOfReactions), 22)
self.assertEqual(reaction.getName(), "Ras activation by SOS-Ras-GDP, modified")
def testEvents(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project, '/models/', status_code=302, target_status_code=200)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies()
or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'], "Project")
response_choose_model = c.post('/edit/events/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'], "SOS-Ras-MAPK with n17")
response_save_event = c.post('/edit/events/', {
'action': 'save',
'event_id': '',
'event_sbmlid': 'test_event',
'event_name': "Test event",
'event_trigger': "time==0",
'event_priority': "",
'event_delay': "",
'event_assignment_0_id': listOfVariables.index(sbml_model.listOfVariables.getBySbmlId('ras_gtp')),
'event_assignment_0_expression': 'ras_gtp*2'
})
self.assertEqual(response_save_event.status_code, 200)
self.assertEqual(response_save_event.context['form'].getErrors(), [])
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies()
or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
response_get_event = c.post('/json/get_event/', {
'event_ind': '0',
})
self.assertEqual(response_get_event.status_code, 200)
json_response = loads(response_get_event.content.decode('utf-8'))
self.assertEqual(json_response[u'event_ind'], 0)
self.assertEqual(json_response[u'event_name'], "Test event")
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("time==0", rawFormula=True)
formula_response = MathFormula(sbml_model)
formula_response.setPrettyPrintMathFormula(json_response[u'event_trigger'], rawFormula=True)
self.assertEqual(simplify(formula.getDeveloppedInternalMathFormula()-formula_response.getDeveloppedInternalMathFormula()), 0)
self.assertEqual(json_response[u'event_delay'], "")
self.assertEqual(json_response[u'list_of_assignments'][0][0], listOfVariables.index(sbml_model.listOfVariables.getBySbmlId('ras_gtp')))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("ras_gtp*2", rawFormula=True)
formula_response = MathFormula(sbml_model)
formula_response.setPrettyPrintMathFormula(json_response[u'list_of_assignments'][0][2], rawFormula=True)
self.assertEqual(simplify(formula.getDeveloppedInternalMathFormula()-formula_response.getDeveloppedInternalMathFormula()), 0)
self.assertTrue(u'event_assignment_variable_1' not in json_response)
# Modifying an event
response_save_event = c.post('/edit/events/', {
'action': 'save',
'event_id': '0',
'event_sbmlid': 'test_event',
'event_name': "Test event",
'event_trigger': "time==100",
'event_priority': "",
'event_delay': "",
'event_assignment_0_id': listOfVariables.index(sbml_model.listOfVariables.getBySbmlId('ras_gtp')),
'event_assignment_0_expression': 'ras_gtp*2',
'event_assignment_1_id': listOfVariables.index(sbml_model.listOfVariables.getBySbmlId('ras_gdp')),
'event_assignment_1_expression': 'ras_gdp/2',
})
self.assertEqual(response_save_event.status_code, 200)
self.assertEqual(response_save_event.context['form'].getErrors(), [])
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
event = sbml_model.listOfEvents[0]
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies()
or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
self.assertEqual(event.getNameOrSbmlId(), "Test event")
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("time==100", rawFormula=True)
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() - event.trigger.getDeveloppedInternalMathFormula()),
0)
self.assertEqual(event.priority, None)
self.assertEqual(event.delay, None)
self.assertEqual(event.listOfEventAssignments[0].getVariable(), sbml_model.listOfVariables.getBySbmlId('ras_gtp'))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("ras_gtp*2")
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() - event.listOfEventAssignments[0].getDefinition().getDeveloppedInternalMathFormula()),
0)
self.assertEqual(event.listOfEventAssignments[1].getVariable(), sbml_model.listOfVariables.getBySbmlId('ras_gdp'))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("ras_gdp/2")
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() - event.listOfEventAssignments[1].getDefinition().getDeveloppedInternalMathFormula()),
0)
response_delete_event = c.post('/edit/events/', {
'action': 'delete',
'event_id': 0
})
self.assertEqual(response_delete_event.status_code, 200)
self.assertEqual(response_delete_event.context['form'].getErrors(), [])
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
self.assertEqual(len(sbml_model.listOfEvents), 0)
def testSpecies(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project,
'/models/',
status_code=302,
target_status_code=200)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('ras_gtp')
response_get_species = c.post('/json/get_species/',
{'sbml_id': 'ras_gtp'})
self.assertEqual(response_get_species.status_code, 200)
json_response = loads(response_get_species.content.decode('utf-8'))
self.assertEqual(json_response[u'id'],
sbml_model.listOfSpecies.index(species))
self.assertEqual(json_response[u'sbml_id'], species.getSbmlId())
self.assertEqual(json_response[u'name'], species.getName())
self.assertEqual(json_response[u'compartment_name'],
species.getCompartment().getName())
self.assertEqual(
json_response[u'compartment_id'],
sbml_model.listOfCompartments.index(species.getCompartment()))
self.assertEqual(json_response[u'value'], species.getValue())
self.assertEqual(json_response[u'isConcentration'],
1 if not species.hasOnlySubstanceUnits else 0)
self.assertEqual(json_response[u'constant'],
1 if species.constant else 0)
self.assertEqual(json_response[u'boundaryCondition'],
1 if species.boundaryCondition else 0)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'],
"Project")
response_choose_model = c.post('/edit/species/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'],
"SOS-Ras-MAPK with n17")
response_save_species = c.post(
'/edit/species/', {
'action': 'save',
'species_id': 2,
'species_name': "New name",
'species_sbml_id': "new_name",
'species_value': 75,
'species_value_type': 0,
'species_compartment': 0,
'species_unit': 2,
'species_constant': "on",
'species_boundary': "on",
'species_sboterm': "",
})
self.assertEqual(response_save_species.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('new_name')
self.assertTrue(species is not None)
self.assertEqual(species.getName(), "New name")
self.assertEqual(species.getValue(), 75)
self.assertEqual(species.hasOnlySubstanceUnits, True)
self.assertEqual(species.constant, True)
self.assertEqual(species.boundaryCondition, True)
response_delete_species = c.post(
'/edit/species/', {
'action': 'delete',
'species_id': sbml_model.listOfSpecies.index(species)
})
self.assertEqual(response_delete_species.status_code, 200)
self.assertEqual(response_delete_species.context['getErrors'],
['Species is used in reactions'])
response_save_new_species = c.post(
'/edit/species/', {
'action': 'save',
'species_id': "",
'species_name': "New species",
'species_sbml_id': "new_species",
'species_value': 2500,
'species_value_type': 0,
'species_compartment': 0,
'species_unit': 2,
'species_constant': "off",
'species_boundary': "off",
'species_sboterm': "",
})
self.assertEqual(response_save_new_species.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('new_species')
self.assertTrue(species != None)
self.assertEqual(species.getName(), "New species")
self.assertEqual(species.getValue(), 2500)
self.assertEqual(species.isConcentration(), False)
self.assertEqual(species.getCompartment().getName(), "cell")
self.assertEqual(species.constant, False)
self.assertEqual(species.boundaryCondition, False)
response_delete_species = c.post(
'/edit/species/', {
'action': 'delete',
'species_id': sbml_model.listOfSpecies.index(species)
})
self.assertEqual(response_delete_species.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('new_species')
self.assertEqual(species, None)
def testCompartment(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project, '/models/', status_code=302, target_status_code=200)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
compartment = sbml_model.listOfCompartments.getBySbmlId('cell')
response_get_compartment = c.post('/json/get_compartment/', {
'sbml_id': 'cell',
})
self.assertEqual(response_get_compartment.status_code, 200)
json_response = loads(response_get_compartment.content.decode('utf-8'))
self.assertEqual(json_response[u'id'], sbml_model.listOfCompartments.index(compartment))
self.assertEqual(json_response[u'sbml_id'], compartment.getSbmlId())
self.assertEqual(json_response[u'name'], compartment.getName())
self.assertEqual(json_response[u'value'], compartment.getValue())
self.assertEqual(json_response[u'constant'], 1 if compartment.constant else 0)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'], "Project")
response_choose_model = c.post('/edit/compartments/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'], "SOS-Ras-MAPK with n17")
response_save_compartment = c.post('/edit/compartments/', {
'action': 'save',
'compartment_id': sbml_model.listOfCompartments.index(compartment),
'compartment_name': "New name",
'compartment_sbml_id': "new_name",
'compartment_size': 75,
'compartment_unit': 2,
'compartment_constant': "on",
'compartment_sboterm': "",
})
self.assertEqual(response_save_compartment.status_code, 200)
self.assertEqual(response_save_compartment.context['getErrors'], [])
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
compartment = sbml_model.listOfCompartments.getBySbmlId('new_name')
self.assertTrue(compartment is not None)
self.assertEqual(compartment.getName(), "New name")
self.assertEqual(compartment.getValue(), 75)
self.assertEqual(compartment.constant, True)
self.assertEqual(compartment.getUnits(), sbml_model.listOfUnitDefinitions[2])
response_delete_compartment = c.post('/edit/compartments/', {
'action': 'delete',
'compartment_id': sbml_model.listOfCompartments.index(compartment)
})
self.assertEqual(response_delete_compartment.status_code, 200)
self.assertEqual(response_delete_compartment.context['getErrors'], ['Compartment contains 25 species'])
response_save_new_compartment = c.post('/edit/compartments/', {
'action': 'save',
'compartment_id': "",
'compartment_name': "New compartment",
'compartment_sbml_id': "new_compartment",
'compartment_size': 75,
'compartment_unit': "",
'compartment_constant': "on",
'compartment_sboterm': "",
})
self.assertEqual(response_save_new_compartment.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
compartment = sbml_model.listOfCompartments.getBySbmlId('new_compartment')
self.assertTrue(compartment != None)
self.assertEqual(compartment.getName(), "New compartment")
self.assertEqual(compartment.getValue(), 75)
self.assertEqual(compartment.getUnits(), None)
self.assertEqual(compartment.constant, True)
response_delete_compartment = c.post('/edit/compartments/', {
'action': 'delete',
'compartment_id': sbml_model.listOfCompartments.index(compartment)
})
self.assertEqual(response_delete_compartment.status_code, 200)
self.assertEqual(response_delete_compartment.context['getErrors'], [])
def testUnits(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project,
'/models/',
status_code=302,
target_status_code=200)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'],
"Project")
response_choose_model = c.post('/edit/units/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'],
"SOS-Ras-MAPK with n17")
self.assertEqual(response_choose_model.context['unit_definitions'], [
'Litre', 'Nanomoles', 'Nanomoles per litre', 'Seconds',
'per Seconds', 'per Nanomoles ', 'Dimensionless',
'per Nanomoles per Seconds', 'Nanomoles per seconds',
'Nanomoles per litre per seconds',
'per Nanomoles per liter per Seconds'
])
response_save_unit = c.post(
'/edit/units/', {
'action': 'save',
'unit_definition_id': '',
'unit_definition_name': "Nanomolars",
'unit_definition_identifier': "nanomolars",
'subunit_id_0': list(Unit.unit_id.values()).index("mole"),
'subunit_exponent_0': 1,
'subunit_scale_0': -9,
'subunit_multiplier_0': 1,
'subunit_id_1': list(Unit.unit_id.values()).index("litre"),
'subunit_exponent_1': -1,
'subunit_scale_1': 1,
'subunit_multiplier_1': 1,
})
self.assertEqual(response_save_unit.status_code, 200)
self.assertEqual(response_save_unit.context['form'].getErrors(), [])
self.assertEqual(response_save_unit.context['unit_definitions'], [
'Litre', 'Nanomoles', 'Nanomoles per litre', 'Seconds',
'per Seconds', 'per Nanomoles ', 'Dimensionless',
'per Nanomoles per Seconds', 'Nanomoles per seconds',
'Nanomoles per litre per seconds',
'per Nanomoles per liter per Seconds', 'Nanomolars'
])
response_get_unit_definition = c.post(
'/json/get_unit_definition/', {
'id':
response_save_unit.context['unit_definitions'].index(
'Nanomolars'),
})
self.assertEqual(response_get_unit_definition.status_code, 200)
json_response = loads(
response_get_unit_definition.content.decode('utf-8'))
self.assertEqual(json_response[u'unit_id'], "nanomolars")
self.assertEqual(json_response[u'name'], "Nanomolars")
self.assertEqual(json_response[u'desc'], "nmole.litre^-1")
self.assertEqual(json_response[u'list_of_units'][0],
[u'nmole', 20, u'mole', 1, -9, 1.0])
self.assertEqual(json_response[u'list_of_units'][1],
[u'litre^-1', 16, u'litre', -1, 1, 1.0])
response_delete_unit_definition = c.post(
'/edit/units/', {
'action':
'delete',
'id':
response_save_unit.context['unit_definitions'].index(
'Nanomolars')
})
self.assertEqual(response_delete_unit_definition.status_code, 200)
self.assertEqual(
response_delete_unit_definition.context['unit_definitions'], [
'Litre', 'Nanomoles', 'Nanomoles per litre', 'Seconds',
'per Seconds', 'per Nanomoles ', 'Dimensionless',
'per Nanomoles per Seconds', 'Nanomoles per seconds',
'Nanomoles per litre per seconds',
'per Nanomoles per liter per Seconds'
])
def testOptimization(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project,
'/models/',
status_code=302,
target_status_code=200)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
files_folder = join(dirname(__file__), "files")
comp_files_folder = join(files_folder, "comp_model")
model_filename = join(comp_files_folder, "modelcEvRcX.xml")
response_load_submodel_1 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_1.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model_filename = join(comp_files_folder, "modelEHfev9.xml")
response_load_submodel_2 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_2.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 2)
model_filename = join(comp_files_folder, "modelI1vrys.xml")
response_load_submodel_3 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_3.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 3)
model_filename = join(comp_files_folder, "modelz9xdww.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 4)
response_choose_model = c.post('/fit/data/', {
'action': 'choose_model',
'model_id': 3
})
self.assertEqual(response_choose_model.status_code, 200)
experiment_filename = join(files_folder, "ras_data.xml")
response_import_data = c.post(
'/data/', {
'action': 'import',
'docfile': open(experiment_filename, 'rb')
})
self.assertEqual(response_import_data.status_code, 200)
self.assertEqual([
experiment.name
for experiment in response_import_data.context['experimental_data']
], [u'Ras-GTP quantifications'])
experiment_id = response_import_data.context['experimental_data'][0].id
response_get_fit_data = c.get('/fit/data/')
self.assertEqual(response_get_fit_data.status_code, 200)
self.assertEqual([
dataset for dataset in
response_get_fit_data.context['experimental_data_sets']
], [u'Ras-GTP quantifications'])
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(
len(response_list_optimizations.context['optimizations']), 0)
response_add_dataset = c.post('/json/add_dataset/', {'dataset_ind': 0})
self.assertEqual(response_add_dataset.status_code, 200)
mapping = loads(
response_add_dataset.content.decode('utf-8'))['model_xpaths']
sbml_filename = str(
SbmlModel.objects.filter(project=project)[3].sbml_file)
doc = SbmlDocument()
doc.readSbmlFromFile(join(settings.MEDIA_ROOT, sbml_filename))
self.assertEqual(sorted(list(mapping.keys())),
['FGF2', 'Total Ras-GTP'])
self.assertEqual(
doc.getModelInstance().listOfSpecies.index(
doc.getByXPath(mapping['FGF2'], instance=True)), 4)
self.assertEqual(
doc.getModelInstance().listOfSpecies.index(
doc.getByXPath(mapping['Total Ras-GTP'], instance=True)), 13)
response_create_optimization = c.post(
'/fit/data/',
{
'action': 'create',
'dataset_0':
experiment_id, #response_get_fit_data.context['experimental_data_sets'][0].id,
'list_dataset_0_data_species_0_value': "FGF2",
'list_dataset_0_species_0_value': 4,
'list_dataset_0_data_species_1_value': "Total Ras-GTP",
'list_dataset_0_species_1_value': 13,
'parameter_0_id': 1,
'parameter_0_name': "SOS activation by FGF2",
'parameter_0_value': 1.0,
'parameter_0_min': 1e-4,
'parameter_0_max': 1e+4,
'parameter_0_precision': 7,
'parameter_1_active': "on",
'parameter_1_id': 1,
'parameter_1_name':
"SOS inactivation by Mapk catalytic constant",
'parameter_1_value': 1.0,
'parameter_1_min': 1e-6,
'parameter_1_max': 1e+6,
'parameter_1_precision': 7,
'nb_cores': 2,
'lambda': 0.02,
'score_precision': 0.001,
'param_precision': 7,
'initial_temperature': 1,
'initial_moves': 200,
'freeze_count': 1,
'negative_penalty': 0
})
self.assertEqual(response_create_optimization.status_code, 200)
self.assertEqual(
response_create_optimization.context['form'].getErrors(), [])
sleep(10)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(
len(response_list_optimizations.context['optimizations']), 1)
self.assertEqual(
response_list_optimizations.context['optimizations'][0][0].status,
"Running")
sleep(10)
optimization_id = response_list_optimizations.context['optimizations'][
0][0].optimization_id
response_get_optimization = c.get('/fit/%s/' % optimization_id)
self.assertEqual(response_get_optimization.status_code, 200)
max_time = 360
sleep(360)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(
response_list_optimizations.context['optimizations'][0][0].status,
"Finished")
response_get_optimization = c.get('/fit/%s/' % optimization_id)
self.assertEqual(response_get_optimization.status_code, 200)
scores = response_get_optimization.context['score_values']
self.assertTrue(scores[len(scores) - 1] < 1.01)
def importProject(new_folder, filename):
new_combine_archive = CombineArchive()
new_folder.name = basename(filename).split('.')[0]
new_folder.save()
try:
new_combine_archive.readArchive(filename)
deps = []
for sbml_file in new_combine_archive.getAllSbmls():
t_file = File(open(sbml_file, 'rb'))
sbml_model = SbmlModel(project=new_folder, sbml_file=t_file)
sbml_model.save()
try:
doc = SbmlDocument()
doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(sbml_model.sbml_file)))
dependencies = getDetailedModelDependencies(doc)
if len(dependencies) > 0:
deps.append((sbml_model, dependencies))
sbml_model.name = doc.model.getName()
sbml_model.save()
except ModelException:
name = splitext(str(sbml_model.sbml_file))[0]
sbml_model.name = name
sbml_model.save()
for model, submodels in deps:
for submodel_filename, submodel_ref in submodels:
submodel_filename = join(new_folder.folder, "models", submodel_filename)
submodel = SbmlModel.objects.get(sbml_file=submodel_filename)
new_dependency = ModelsDependency(project=new_folder, model=model, submodel=submodel, submodel_ref=submodel_ref)
new_dependency.save()
for sedml_filename in new_combine_archive.getAllSedmls():
sedml_archive = SEDMLSimulation(project=new_folder, sedml_file=File(open(sedml_filename, 'rb')))
sedml_archive.name = basename(sedml_filename).split('.')[0]
sedml_archive.save()
# Now everything is in the same folder
sedml_doc = SedmlDocument()
sedml_doc.readSedmlFromFile(join(settings.MEDIA_ROOT, str(sedml_archive.sedml_file)))
sedml_doc.listOfModels.removePaths()
sbml_files = sedml_doc.listOfModels.makeLocalSources()
for sbml_file in sbml_files:
if len(SbmlModel.objects.filter(project=new_folder, sbml_file=join(join(str(new_folder.folder), "models"), basename(sbml_file)))) == 0:
t_file = File(open(sbml_file, 'rb'))
sbml_model = SbmlModel(project=new_folder, sbml_file=t_file)
sbml_model.save()
try:
doc = SbmlDocument()
doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(sbml_model.sbml_file)))
sbml_model.name = doc.model.getName()
sbml_model.save()
except ModelException:
name = splitext(str(sbml_model.sbml_file))[0]
sbml_model.name = name
sbml_model.save()
sedml_doc.writeSedmlToFile(join(settings.MEDIA_ROOT, str(sedml_archive.sedml_file)))
for numl_file in new_combine_archive.getAllNumls():
new_experiment = Experiment(project=new_folder)
new_experiment.save()
importExperiment(new_experiment, numl_file)
except CombineException as e:
print(e.message)
def testSpecies(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project, '/models/', status_code=302, target_status_code=200)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('ras_gtp')
response_get_species = c.post('/json/get_species/', {
'sbml_id': 'ras_gtp'
})
self.assertEqual(response_get_species.status_code, 200)
json_response = loads(response_get_species.content.decode('utf-8'))
self.assertEqual(json_response[u'id'], sbml_model.listOfSpecies.index(species))
self.assertEqual(json_response[u'sbml_id'], species.getSbmlId())
self.assertEqual(json_response[u'name'], species.getName())
self.assertEqual(json_response[u'compartment_name'], species.getCompartment().getName())
self.assertEqual(json_response[u'compartment_id'], sbml_model.listOfCompartments.index(species.getCompartment()))
self.assertEqual(json_response[u'value'], species.getValue())
self.assertEqual(json_response[u'isConcentration'], 1 if not species.hasOnlySubstanceUnits else 0)
self.assertEqual(json_response[u'constant'], 1 if species.constant else 0)
self.assertEqual(json_response[u'boundaryCondition'], 1 if species.boundaryCondition else 0)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'], "Project")
response_choose_model = c.post('/edit/species/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'], "SOS-Ras-MAPK with n17")
response_save_species = c.post('/edit/species/', {
'action': 'save',
'species_id': 2,
'species_name': "New name",
'species_sbml_id': "new_name",
'species_value': 75,
'species_value_type': 0,
'species_compartment': 0,
'species_unit': 2,
'species_constant': "on",
'species_boundary': "on",
'species_sboterm': "",
})
self.assertEqual(response_save_species.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('new_name')
self.assertTrue(species is not None)
self.assertEqual(species.getName(), "New name")
self.assertEqual(species.getValue(), 75)
self.assertEqual(species.hasOnlySubstanceUnits, True)
self.assertEqual(species.constant, True)
self.assertEqual(species.boundaryCondition, True)
response_delete_species = c.post('/edit/species/', {
'action': 'delete',
'species_id': sbml_model.listOfSpecies.index(species)
})
self.assertEqual(response_delete_species.status_code, 200)
self.assertEqual(response_delete_species.context['getErrors'], ['Species is used in reactions'])
response_save_new_species = c.post('/edit/species/', {
'action': 'save',
'species_id': "",
'species_name': "New species",
'species_sbml_id': "new_species",
'species_value': 2500,
'species_value_type': 0,
'species_compartment': 0,
'species_unit': 2,
'species_constant': "off",
'species_boundary': "off",
'species_sboterm': "",
})
self.assertEqual(response_save_new_species.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('new_species')
self.assertTrue(species != None)
self.assertEqual(species.getName(), "New species")
self.assertEqual(species.getValue(), 2500)
self.assertEqual(species.isConcentration(), False)
self.assertEqual(species.getCompartment().getName(), "cell")
self.assertEqual(species.constant, False)
self.assertEqual(species.boundaryCondition, False)
response_delete_species = c.post('/edit/species/', {
'action': 'delete',
'species_id': sbml_model.listOfSpecies.index(species)
})
self.assertEqual(response_delete_species.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('new_species')
self.assertEqual(species, None)
def testRule(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project,
'/models/',
status_code=302,
target_status_code=200)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfRules = sbml_model.listOfRules + sbml_model.listOfInitialAssignments
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies() or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
rule = listOfRules[0]
response_get_compartment = c.post('/json/get_rule/', {
'rule_ind': '0',
})
self.assertEqual(response_get_compartment.status_code, 200)
json_response = loads(response_get_compartment.content.decode('utf-8'))
self.assertEqual(json_response[u'rule_id'], listOfRules.index(rule))
self.assertEqual(json_response[u'rule_type'], 1)
self.assertEqual(
json_response[u'variable'],
listOfVariables.index(
sbml_model.listOfVariables.getBySbmlId('total_ras_gtp')))
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'],
"Project")
response_choose_model = c.post('/edit/rules/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'],
"SOS-Ras-MAPK with n17")
response_save_rule = c.post(
'/edit/rules/', {
'action':
'save',
'rule_id':
listOfRules.index(rule),
'rule_type':
1,
'variable_id':
listOfVariables.index(
sbml_model.listOfVariables.getBySbmlId(
'total_mapk_activated')),
'rule_expression':
"75*ras_gtp",
})
self.assertEqual(response_save_rule.status_code, 200)
self.assertEqual(response_save_rule.context['form'].getErrors(), [])
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfRules = sbml_model.listOfRules + sbml_model.listOfInitialAssignments
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies() or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
rule = listOfRules[0]
self.assertEqual(rule.getType(), 1)
self.assertEqual(
rule.getVariable(),
sbml_model.listOfVariables.getBySbmlId('total_mapk_activated'))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("75*ras_gtp", rawFormula=True)
self.assertEqual(
simplify(rule.getDefinition().getDeveloppedInternalMathFormula() -
formula.getDeveloppedInternalMathFormula()), 0)
response_delete_rule = c.post('/edit/rules/', {
'action': 'delete',
'rule_id': 0
})
self.assertEqual(response_delete_rule.status_code, 200)
self.assertEqual(response_delete_rule.context['form'].getErrors(), [])
def testLocalParameter(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project, '/models/', status_code=302, target_status_code=200)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
parameter = sbml_model.listOfParameters.getBySbmlId('sos_ras_gdp_comp')
response_get_reaction = c.post('/json/get_reaction/', {
'sbml_id': 'reaction_2',
})
self.assertEqual(response_get_reaction.status_code, 200)
json_response = loads(response_get_reaction.content.decode('utf-8'))
self.assertEqual(json_response[u'kinetic_law'], '-1 * sos_ras_gdp * sos_ras_gdp_decomp + ras_gdp * sos * sos_ras_gdp_comp')
response_get_parameter = c.post('/json/get_parameter/', {
'sbml_id': 'sos_ras_gdp_comp',
'reaction': ''
})
self.assertEqual(response_get_parameter.status_code, 200)
json_response = loads(response_get_parameter.content.decode('utf-8'))
self.assertEqual(json_response[u'id'], sbml_model.listOfParameters.index(parameter))
self.assertEqual(json_response[u'reaction_id'], "")
response_to_local_parameter = c.post('/edit/parameters/', {
'action': 'save',
'parameter_id': json_response[u'id'],
'parameter_name': json_response[u'name'],
'parameter_sbml_id': json_response[u'sbml_id'],
'parameter_value': json_response[u'value'],
'parameter_unit': json_response[u'unit_id'],
'parameter_constant': "on" if json_response[u'constant'] == 1 else "",
'parameter_scope': 1,
'parameter_sboterm': "",
})
self.assertEqual(response_to_local_parameter.status_code, 200)
self.assertEqual(response_to_local_parameter.context['getErrors'], [])
self.assertEqual(response_to_local_parameter.context['form'].getErrors(), [])
response_get_reaction = c.post('/json/get_reaction/', {
'sbml_id': 'reaction_2',
})
self.assertEqual(response_get_reaction.status_code, 200)
json_response = loads(response_get_reaction.content.decode('utf-8'))
self.assertEqual(
json_response[u'kinetic_law'],
'-1 * sos_ras_gdp * sos_ras_gdp_decomp + sos_ras_gdp_comp * ras_gdp * sos'
)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_2')
self.assertEqual(
str(reaction.kineticLaw.getDefinition().getInternalMathFormula()),
"_local_0_sos_ras_gdp_comp*ras_gdp*sos - sos_ras_gdp*sos_ras_gdp_decomp"
)
self.assertEqual(sbml_model.listOfParameters.getBySbmlId("sos_ras_gdp_comp"), None)
response_get_parameter = c.post('/json/get_parameter/', {
'sbml_id': 'sos_ras_gdp_comp',
'reaction': '1'
})
self.assertEqual(response_get_parameter.status_code, 200)
json_response = loads(response_get_parameter.content.decode('utf-8'))
response_list_parameters = c.get('/edit/parameters/')
self.assertEqual(response_list_parameters.status_code, 200)
list_of_parameters = [param.getSbmlId() for param in response_list_parameters.context['list_of_parameters']]
response_to_global_parameter = c.post('/edit/parameters/', {
'action': 'save',
'parameter_id': list_of_parameters.index("sos_ras_gdp_comp"),
'parameter_name': json_response[u'name'],
'parameter_sbml_id': json_response[u'sbml_id'],
'parameter_value': json_response[u'value'],
'parameter_unit': json_response[u'unit_id'],
'parameter_constant': "on" if json_response[u'constant'] == 1 else "",
'parameter_scope': 0,
'parameter_sboterm': "",
})
self.assertEqual(response_to_global_parameter.status_code, 200)
self.assertEqual(response_to_global_parameter.context['getErrors'], [])
self.assertEqual(response_to_global_parameter.context['form'].getErrors(), [])
response_get_reaction = c.post('/json/get_reaction/', {
'sbml_id': 'reaction_2',
})
self.assertEqual(response_get_reaction.status_code, 200)
json_response = loads(response_get_reaction.content.decode('utf-8'))
# print json_response
self.assertEqual(
json_response[u'kinetic_law'],
'-1 * sos_ras_gdp * sos_ras_gdp_decomp + ras_gdp * sos * sos_ras_gdp_comp'
)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_2')
self.assertEqual(
str(reaction.kineticLaw.getDefinition().getInternalMathFormula()),
"ras_gdp*sos*sos_ras_gdp_comp - sos_ras_gdp*sos_ras_gdp_decomp"
)
self.assertEqual(sbml_model.listOfParameters.getBySbmlId("sos_ras_gdp_comp").getSbmlId(), "sos_ras_gdp_comp")