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)))
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:
t_model = SbmlModel.objects.get(project=self.project_id,
id=self.model_id)
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.values()
self.model_list_of_submodels_names = []
self.model_list_of_submodels_types = []
for submodel in self.model.listOfSubmodels.values():
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)
def readModel(self, request): self.optimizationModel = SbmlDocument() self.optimizationModel.readSbmlFromFile(os.path.join(self.optimPath, "model.sbml")) if self.optimizationModel.getModelInstance().getNameOrSbmlId() is not None: self.modelName = self.optimizationModel.getModelInstance().getNameOrSbmlId() else: self.modelName = self.optimizationModel.model.getNameOrSbmlId()
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_session_id = optimization.session_id
t_optim_id = optimization.optimization_id
optim_path = join(
settings.MEDIA_ROOT, str(self.project.folder),
"optimizations/optimization_%s/" % str(t_optim_id))
# os.path.abspath(os.path.join(settings.BASE_DIR,"../../../tmp/optimization_%s/" % t_optim_id))
optimization_status = None
if not exists(optim_path):
optimization_status = "Not found"
elif isfile(optim_path + "/logs/score/score"):
optimization_status = "Finished"
elif isfile(optim_path + "/err_optim"):
if getsize(optim_path + "/err_optim") > 0:
optimization_status = "Interrupted"
else:
optimization_status = "Ongoing"
else:
optimization_status = "Ongoing"
t_time_of_launch = self.hms_string(
int(time()) - (int(t_optim_id) / 1000)) + " ago"
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, optimization_status, t_time_of_launch,
t_model_name))
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:
t_file = File(open(sbml_file, 'r'))
sbml_model = SbmlModel(project=self.project,
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 = os.path.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 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 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, "r")))
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 getListOfObjects(self, request):
if str(request.POST['model_id']) != "":
# print "model id = %d" % int(request.POST['model_id'])
# print [pm.name for pm in self.getProjectModels(request)]
# print [pm.id for pm in self.getProjectModels(request)]
# print self.model_name
# print self.model_id
list_of_project_models = [pm for pm in self.getProjectModels(request) if pm.id != self.model_id]
print "list of models : %s" % [pm.name for pm in list_of_project_models]
# print "selected model : %s" % str(list_of_project_models[int(request.POST['model_id'])].name)
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)
self.listOfObjects = []
for t_object in doc.model.listOfSbmlObjects.values():
if isinstance(t_object, Variable) and not t_object.isStoichiometry():
self.listOfObjects.append(t_object.getNameOrSbmlId() + (" (%s)" % type(t_object).__name__))
# print self.listOfObjects
return self.listOfObjects
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))))
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)
class OptimizationResultView(TemplateView, HasWorkingProject):
template_name = 'fit/result.html'
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingProject.__init__(self)
self.optimizationId = None
self.parameters = None
self.inputParameters = None
self.outputParameters = None
self.modelName = None
self.submodelNames = None
self.modifiedSubmodelNames = None
self.optimizationStatus = None
self.showGraph = None
self.optimPath = None
self.experiments = None
self.experimentsData = None
self.scoreTime = []
self.scoreValues = []
self.scoreRawValues = []
self.scoreMinEv = []
self.scoreMaxEv = []
self.optimizationModel = None
def get_context_data(self, **kwargs):
kwargs = HasWorkingProject.get_context_data(self, **kwargs)
kwargs['optimization_id'] = self.optimizationId
kwargs['parameters'] = self.parameters
kwargs['model_name'] = self.modelName
kwargs['submodel_names'] = self.submodelNames
kwargs['modified_submodel_names'] = self.modifiedSubmodelNames
kwargs['show_graph'] = self.showGraph
kwargs['optimization_status'] = self.optimizationStatus
kwargs['score_time'] = self.scoreTime
kwargs['score_values'] = self.scoreValues
kwargs['score_rawvalues'] = self.scoreRawValues
kwargs['score_minev'] = self.scoreMinEv
kwargs['score_maxev'] = self.scoreMaxEv
kwargs['colors'] = Settings.default_colors
kwargs['experiments'] = self.experimentsData
return kwargs
def get(self, request, *args, **kwargs):
self.load(request, *args, **kwargs)
return TemplateView.get(self, request, *args, **kwargs)
def post(self, request, *args, **kwargs):
self.load(request, *args, **kwargs)
if "action" in request.POST:
if HasWorkingProject.isChooseProject(self, request):
return redirect('list_of_optimizations')
if request.POST['action'] == "save_model":
self.saveFittedModel(request)
elif request.POST['action'] == "stop_optim":
self.stopOptimization()
elif request.POST['action'] == "restart_optim":
self.restartOptimization()
return TemplateView.get(self, request, *args, **kwargs)
def load(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
if self.isProjectLoaded():
self.loadOptimization(request, *args)
def stopOptimization(self):
stopOptimization(self.optimPath)
self.optimizationStatus = Optimization.objects.get(optimization_id=self.optimizationId).status
def restartOptimization(self):
t = Thread(
group=None,
target=restartOptimization,
args=(self.optimPath,)
)
t.setDaemon(True)
t.start()
sleep(2)
self.optimizationStatus = Optimization.objects.get(optimization_id=self.optimizationId).status
def saveFittedModel(self, request):
t_document = SbmlDocument()
t_document.readSbmlFromFile(str(self.optimPath + "/model.sbml"))
model = t_document.model
if request.POST.get('model_name') is not None:
self.modelName = str(request.POST['model_name'])
elif model.getName() is not None:
self.modelName = model.getName()
else:
self.modelName = self.model_name
if not SbmlModel.objects.filter(name=self.modelName):
document = SbmlDocument()
document.readSbmlFromFile(os.path.join(settings.MEDIA_ROOT, os.path.join(self.optimPath, "model.sbml")))
if not document.useCompPackage:
file = File(open(os.path.join(settings.MEDIA_ROOT, os.path.join(self.optimPath, "model.sbml"))))
new_sbml_model = SbmlModel(project=self.project, name=self.modelName, sbml_file=file)
new_sbml_model.save()
new_document = SbmlDocument()
new_document.readSbmlFromFile(os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file)))
new_document.model.setName(self.modelName)
for i_param, (xpath, value) in enumerate(self.outputParameters):
param = new_document.getByXPath(xpath)
param.setValue(value)
new_document.writeSbmlToFile(os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file)))
else:
modifieds = []
for i_param, (xpath, value) in enumerate(self.outputParameters):
param = document.getModelInstance().getDefinitionVariableByXPath(xpath)
modifieds.append(param[0].getModel().parentDoc)
modifieds = list(set(modifieds))
submodel_names = []
i_submodel = 0
while request.POST.get("submodel_%d_name" % i_submodel) is not None:
submodel_names.append(request.POST["submodel_%d_name" % i_submodel])
i_submodel += 1
modified_files = {}
for i_modified, modified in enumerate(modifieds):
file = File(open(os.path.join(settings.MEDIA_ROOT, os.path.join(self.optimPath, modified.documentFilename)), 'rb'))
new_sbml_model = SbmlModel(project=self.project, name=submodel_names[i_modified], sbml_file=file)
new_sbml_model.save()
new_document = SbmlDocument()
new_document.readSbmlFromFile(os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file)))
new_document.model.setName(str(submodel_names[i_modified]))
new_document.writeSbmlToFile(os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file)))
modified_files.update({modified.documentFilename: os.path.basename(str(new_sbml_model.sbml_file))})
print(modified_files)
print(subdoc.documentFilename for subdoc in document.documentDependencies)
renaming = {}
for subdoc in document.documentDependencies:
if subdoc.documentFilename in modified_files:
renaming.update({subdoc.documentFilename: modified_files[subdoc.documentFilename]})
else:
renaming.update({subdoc.documentFilename: subdoc.documentFilename})
print(renaming)
file = File(open(os.path.join(settings.MEDIA_ROOT, os.path.join(self.optimPath, "model.sbml")), 'rb'))
new_sbml_model = SbmlModel(project=self.project, name=self.modelName, sbml_file=file)
new_sbml_model.save()
new_document = SbmlDocument()
new_document.readSbmlFromFile(os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file)))
new_document.renameExternalDocumentDependencies(renaming)
new_document.model.setName(self.modelName)
new_document.writeSbmlToFile(os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file)))
def loadOptimization(self, request, *args):
self.optimizationId = str(args[0])
self.optimPath = os.path.join(self.getProjectFolder(),
"optimizations/optimization_%s/" % self.optimizationId)
self.optimizationStatus = Optimization.objects.get(optimization_id=self.optimizationId).status
self.showGraph = None
self.parameters = []
self.loadOptimizationResults(request)
self.loadOptimizationScore(request)
self.readModel(request)
self.loadParameters(request)
self.loadSubmodels(request)
request.session['optim_dir'] = self.optimPath
request.session['logdir'] = os.path.join(self.optimPath, "logs")
def loadOptimizationResults(self, request):
nb_experiments = 0
nb_conditions = 0
self.max_conditions = 0
self.max_vars = 0
vars_structure = []
data_structure = []
while (os.path.isfile(os.path.join(self.optimPath, "logs/exp_%d_cond_%d_var_%d" % (
nb_experiments, 0, 0)))):
nb_conditions = 0
t_cond_vars_structure = []
t_cond_data_structure = []
while (os.path.isfile(os.path.join(self.optimPath, "logs/exp_%d_cond_%d_var_0" % (nb_experiments, nb_conditions)))):
nb_vars = 0
t_var_data_structure = []
while(os.path.isfile(os.path.join(self.optimPath, "logs/exp_%d_cond_%d_var_%d" % (nb_experiments, nb_conditions, nb_vars)))):
t_var_data_structure.append((self.readModelSimulation(nb_experiments,nb_conditions, nb_vars), self.readObservation(nb_experiments, nb_conditions, nb_vars)))
nb_vars += 1
#print t_var_data_structure
t_cond_vars_structure.append(nb_vars)
t_cond_data_structure.append(t_var_data_structure)
nb_conditions += 1
self.max_vars = max(self.max_vars, nb_vars)
self.max_conditions = max(self.max_conditions, nb_conditions)
vars_structure.append(t_cond_vars_structure)
data_structure.append(t_cond_data_structure)
nb_experiments += 1
#print data_structure
self.experiments = vars_structure
self.experimentsData = data_structure
def readObservation(self, experiment, condition, var):
f_optim = open(
os.path.join(self.optimPath, "logs/exp_%d_cond_%d_var_%d" %
(experiment, condition, var)), "r")
res = []
for line in f_optim:
data = re.split("\t", line.strip())
res.append((float(data[0]), float(data[1]), float(data[2])))
f_optim.close()
return res
def readModelSimulation(self, experiment, condition, var, proc=0):
if os.path.isfile(os.path.join(self.optimPath,
"logs/res/model_exp_%d_cond_%d_var_%d_proc_%d" %
(experiment, condition, var, proc))):
f_optim = open(
os.path.join(self.optimPath,
"logs/res/model_exp_%d_cond_%d_var_%d_proc_%d" %
(experiment, condition, var, proc)), "r")
elif os.path.isfile(os.path.join(self.optimPath,
"logs/best_res/model_exp_%d_cond_%d_var_%d_proc_%d" %
(experiment, condition, var, proc))):
f_optim = open(
os.path.join(self.optimPath,
"logs/best_res/model_exp_%d_cond_%d_var_%d_proc_%d" %
(experiment, condition, var, proc)), "r")
else:
return
res = []
for line in f_optim:
data = re.split("\t", line.strip())
res.append((float(data[0]), float(data[1])))
f_optim.close()
return res
def loadOptimizationScore(self, request):
if os.path.isfile(os.path.join(self.optimPath, "plsa.log")):
# Reading file
f_optim = open(os.path.join(self.optimPath, "plsa.log"), "r")
for line in f_optim:
data = re.split("\t", line.strip())
self.scoreTime.append(float(data[0]))
self.scoreValues.append(float(data[5]))
self.scoreRawValues.append(float(data[3]))
self.scoreMinEv.append(max(0.0, float(data[5])-float(data[6])))
self.scoreMaxEv.append(float(data[5])+float(data[6]))
def loadParameters(self, request):
self.inputParameters = []
self.outputParameters = []
if os.path.isfile(os.path.join(self.optimPath, "logs/params/input")):
f_input = open(os.path.join(self.optimPath, "logs/params/input"))
for line in f_input:
res = re.split(" ", line.strip())
xpath = res[0]
value = res[2]
self.inputParameters.append((xpath, value))
if os.path.isfile(os.path.join(self.optimPath, "logs/params/output")):
f_input = open(os.path.join(self.optimPath, "logs/params/output"))
for line in f_input:
res = re.split(" ", line.strip())
xpath = res[0]
value = res[2]
self.outputParameters.append((xpath, value))
elif os.path.isfile(os.path.join(self.optimPath, "logs/best_res/parameters_0")):
f_input = open(os.path.join(self.optimPath, "logs/best_res/parameters_0"))
for line in f_input:
res = re.split(" ", line.strip())
xpath = res[0]
value = res[2]
self.outputParameters.append((xpath, value))
if len(self.inputParameters) > 0 and len(self.outputParameters) == len(self.inputParameters):
self.parameters = []
for i, (xpath, value) in enumerate(self.inputParameters):
parameter = self.optimizationModel.getByXPath(xpath, instance=self.optimizationModel.useCompPackage)
self.parameters.append((parameter.getNameOrSbmlId(), value, self.outputParameters[i][1]))
def loadSubmodels(self, request):
if self.optimizationModel.useCompPackage:
self.optimizationModel.loadExternalDocumentDependencies()
self.modifiedSubmodelNames = {}
for subdoc in self.optimizationModel.documentDependencies:
self.modifiedSubmodelNames[subdoc.model.getNameOrSbmlId()] = False
for i_param, (xpath, value) in enumerate(self.outputParameters):
param = self.optimizationModel.getModelInstance().getDefinitionVariableByXPath(xpath)
self.modifiedSubmodelNames[param[0].getModel().getName()] = True
self.submodelNames = []
for subdoc in self.optimizationModel.documentDependencies:
if self.modifiedSubmodelNames[subdoc.model.getNameOrSbmlId()]:
if subdoc.model.getNameOrSbmlId() is None:
self.submodelNames.append("")
else:
self.submodelNames.append(subdoc.model.getNameOrSbmlId())
def readModel(self, request):
self.optimizationModel = SbmlDocument()
self.optimizationModel.readSbmlFromFile(os.path.join(self.optimPath, "model.sbml"))
if self.optimizationModel.getModelInstance().getNameOrSbmlId() is not None:
self.modelName = self.optimizationModel.getModelInstance().getNameOrSbmlId()
else:
self.modelName = self.optimizationModel.model.getNameOrSbmlId()
def saveFittedModel(self, request):
t_document = SbmlDocument()
t_document.readSbmlFromFile(str(self.optimPath + "/model.sbml"))
model = t_document.model
if request.POST.get('model_name') is not None:
self.modelName = str(request.POST['model_name'])
elif model.getName() is not None:
self.modelName = model.getName()
else:
self.modelName = self.model_name
if not SbmlModel.objects.filter(name=self.modelName):
document = SbmlDocument()
document.readSbmlFromFile(os.path.join(settings.MEDIA_ROOT, os.path.join(self.optimPath, "model.sbml")))
if not document.useCompPackage:
file = File(open(os.path.join(settings.MEDIA_ROOT, os.path.join(self.optimPath, "model.sbml"))))
new_sbml_model = SbmlModel(project=self.project, name=self.modelName, sbml_file=file)
new_sbml_model.save()
new_document = SbmlDocument()
new_document.readSbmlFromFile(os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file)))
new_document.model.setName(self.modelName)
for i_param, (xpath, value) in enumerate(self.outputParameters):
param = new_document.getByXPath(xpath)
param.setValue(value)
new_document.writeSbmlToFile(os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file)))
else:
modifieds = []
for i_param, (xpath, value) in enumerate(self.outputParameters):
param = document.getModelInstance().getDefinitionVariableByXPath(xpath)
modifieds.append(param[0].getModel().parentDoc)
modifieds = list(set(modifieds))
submodel_names = []
i_submodel = 0
while request.POST.get("submodel_%d_name" % i_submodel) is not None:
submodel_names.append(request.POST["submodel_%d_name" % i_submodel])
i_submodel += 1
modified_files = {}
for i_modified, modified in enumerate(modifieds):
file = File(open(os.path.join(settings.MEDIA_ROOT, os.path.join(self.optimPath, modified.documentFilename)), 'rb'))
new_sbml_model = SbmlModel(project=self.project, name=submodel_names[i_modified], sbml_file=file)
new_sbml_model.save()
new_document = SbmlDocument()
new_document.readSbmlFromFile(os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file)))
new_document.model.setName(str(submodel_names[i_modified]))
new_document.writeSbmlToFile(os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file)))
modified_files.update({modified.documentFilename: os.path.basename(str(new_sbml_model.sbml_file))})
print(modified_files)
print(subdoc.documentFilename for subdoc in document.documentDependencies)
renaming = {}
for subdoc in document.documentDependencies:
if subdoc.documentFilename in modified_files:
renaming.update({subdoc.documentFilename: modified_files[subdoc.documentFilename]})
else:
renaming.update({subdoc.documentFilename: subdoc.documentFilename})
print(renaming)
file = File(open(os.path.join(settings.MEDIA_ROOT, os.path.join(self.optimPath, "model.sbml")), 'rb'))
new_sbml_model = SbmlModel(project=self.project, name=self.modelName, sbml_file=file)
new_sbml_model.save()
new_document = SbmlDocument()
new_document.readSbmlFromFile(os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file)))
new_document.renameExternalDocumentDependencies(renaming)
new_document.model.setName(self.modelName)
new_document.writeSbmlToFile(os.path.join(settings.MEDIA_ROOT, str(new_sbml_model.sbml_file)))
def loadFolder(self, request):
self.fileUploadForm = DocumentForm(request.POST, request.FILES)
if self.fileUploadForm.is_valid():
new_folder = Project(user=request.user)
new_folder.save()
mkdir(join(settings.MEDIA_ROOT, str(new_folder.folder)))
new_archive = CombineArchiveModel(project=new_folder, archive_file=request.FILES['docfile'])
new_archive.save()
new_combine_archive = CombineArchive()
filename = join(settings.MEDIA_ROOT, str(new_archive.archive_file))
t_name = basename(str(new_archive.archive_file))
new_folder.name = t_name.split('.')[0]
new_folder.save()
try:
new_combine_archive.readArchive(filename)
for sbml_file in new_combine_archive.getAllSbmls():
t_file = File(open(sbml_file, 'r'))
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()
for sedml_filename in new_combine_archive.getAllSedmls():
sedml_archive = SEDMLSimulation(project=new_folder, sedml_file=File(open(sedml_filename, 'r')))
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, 'r'))
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)))
except CombineException as e:
print e.message
def testSpecies(self):
settings.MEDIA_ROOT = "/tmp/"
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, 'r')
})
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)
self.assertEqual(json_response[u'id'], sbml_model.listOfSpecies.values().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.values().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.values().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.values().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 testCompaartment(self):
settings.MEDIA_ROOT = "/tmp/"
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, 'r')
})
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)
self.assertEqual(
json_response[u'id'],
sbml_model.listOfCompartments.values().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/parameters/', {
'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.values().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.values().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.values().index(compartment)
})
self.assertEqual(response_delete_compartment.status_code, 200)
self.assertEqual(response_delete_compartment.context['getErrors'], [])
def testReactions(self):
settings.MEDIA_ROOT = "/tmp/"
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, 'r')
})
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_2')
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.values()
])
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)
self.assertEqual(json_response[u'id'],
sbml_model.listOfReactions.values().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.values()])
self.assertEqual(json_response[u'list_of_modifiers'], [[
sbml_model.listOfSpecies.index(modifier.getSpecies()),
modifier.stoichiometry.getPrettyPrintMathFormula()
] for modifier in reaction.listOfModifiers.values()])
self.assertEqual(json_response[u'list_of_products'], [[
sbml_model.listOfSpecies.index(product.getSpecies()),
product.stoichiometry.getPrettyPrintMathFormula()
] for product in reaction.listOfProducts.values()])