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 saveSimulation(self, request):
self.form.read(request)
if not self.form.hasErrors():
self.createDocument()
steady_states = self.createSteadyStates()
if self.form.saveModelSnapshot:
sbml_model = join(dirname(self.model_filename),
copyModelHierarchy(self.model_filename))
else:
sbml_model = self.model_filename
variables = []
if self.form.selectedSpeciesIds is not None:
for id_var in self.form.selectedSpeciesIds:
variables.append(self.listOfVariables[id_var])
if self.form.selectedReactionsIds is not None:
for id_var in self.form.selectedReactionsIds:
variables.append(self.listOfVariables[id_var])
model = self.addModel(
sbml_model,
var_input=self.listOfVariables[self.form.speciesId])
self.addSteadyStatesCurve(
steady_states, model,
("Simulation" if self.form.simulationName is None else
self.form.simulationName), variables, self.form.steady_states,
self.listOfVariables[self.form.speciesId])
simulation_filename = join(settings.MEDIA_ROOT,
new_sedml_filename())
open(simulation_filename, "a")
new_simulation = SEDMLSimulation(
project=self.project,
name=("Simulation" if self.form.simulationName is None else
self.form.simulationName),
sedml_file=File(open(simulation_filename, "rb")),
sbml_file=sbml_model)
new_simulation.save()
filename = join(settings.MEDIA_ROOT,
str(new_simulation.sedml_file))
remove(simulation_filename)
self.saveSedml(filename)
def saveSimulation(self, request):
self.form.read(request)
if not self.form.hasErrors():
self.createDocument()
steady_states = self.createSteadyStates()
if self.form.saveModelSnapshot:
sbml_model = join(dirname(self.model_filename), copyModelHierarchy(self.model_filename))
else:
sbml_model = self.model_filename
variables = []
if self.form.selectedSpeciesIds is not None:
for id_var in self.form.selectedSpeciesIds:
variables.append(self.listOfVariables[id_var])
if self.form.selectedReactionsIds is not None:
for id_var in self.form.selectedReactionsIds:
variables.append(self.listOfVariables[id_var])
model = self.addModel(sbml_model, var_input=self.listOfVariables[self.form.speciesId])
self.addSteadyStatesCurve(
steady_states, model,
("Simulation" if self.form.simulationName is None else self.form.simulationName),
variables,
self.form.steady_states,
self.listOfVariables[self.form.speciesId]
)
simulation_filename = join(settings.MEDIA_ROOT, new_sedml_filename())
open(simulation_filename, "a")
new_simulation = SEDMLSimulation(
project=self.project,
name=("Simulation" if self.form.simulationName is None else self.form.simulationName),
sedml_file=File(open(simulation_filename, "rb")),
sbml_file=sbml_model
)
new_simulation.save()
filename = join(settings.MEDIA_ROOT, str(new_simulation.sedml_file))
remove(simulation_filename)
self.saveSedml(filename)
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 saveSimulation(self, request):
self.form.read(request)
if not self.form.hasErrors():
self.createDocument()
timecourse = self.createUniformTimecourse(self.form.timeMin,
self.form.timeMax,
self.form.timeEch)
if self.form.saveModelSnapshot:
sbml_model = join(dirname(self.model_filename),
copyModelHierarchy(self.model_filename))
else:
sbml_model = self.model_filename
if self.form.experimentId is not None:
self.loadExperiments()
t_experiment_id = self.experiments[self.form.experimentId].id
experiment = Experiment.objects.get(id=t_experiment_id)
conditions = Condition.objects.filter(experiment=experiment)
for i, condition in enumerate(conditions):
modifications = []
input_data = Treatment.objects.filter(condition=condition)
for data in input_data:
var = None
if self.getModelInstance().listOfSpecies.containsName(
data.species):
var = self.getModelInstance(
).listOfSpecies.getByName(data.species)
elif self.getModelInstance(
).listOfParameters.containsName(data.species):
var = self.getModelInstance(
).listOfParameters.getByName(data.species)
elif self.getModelInstance(
).listOfCompartments.containsName(data.species):
var = self.getModelInstance(
).listOfCompartments.getByName(data.species)
if var is not None:
modifications.append((var, data.value))
model = self.addModel(self.model_filename, modifications)
variables = []
if self.form.selectedSpeciesIds is not None:
for id_var in self.form.selectedSpeciesIds:
variables.append(self.listOfVariables[id_var])
if self.form.selectedReactionsIds is not None:
for id_var in self.form.selectedReactionsIds:
variables.append(self.listOfVariables[id_var])
self.addTimeseriesCurve(timecourse, model, condition.name,
variables)
else:
model = self.addModel(self.model_filename)
variables = []
if self.form.selectedSpeciesIds is not None:
for id_var in self.form.selectedSpeciesIds:
variables.append(self.listOfVariables[id_var])
if self.form.selectedReactionsIds is not None:
for id_var in self.form.selectedReactionsIds:
variables.append(self.listOfVariables[id_var])
x_axis_variable = self.listOfVariables[self.form.speciesId]
self.addPhaseSpaceCurve(
timecourse, model,
("Simulation" if self.form.simulationName is None else
self.form.simulationName), variables, x_axis_variable)
simulation_filename = join(settings.MEDIA_ROOT,
new_sedml_filename())
open(simulation_filename, "a")
new_simulation = SEDMLSimulation(
project=self.project,
name=("Simulation" if self.form.simulationName is None else
self.form.simulationName),
sedml_file=File(open(simulation_filename, "rb")),
sbml_file=sbml_model)
new_simulation.save()
filename = join(settings.MEDIA_ROOT,
str(new_simulation.sedml_file))
remove(simulation_filename)
self.saveSedml(filename)
def saveSimulation(self, request):
self.form.read(request)
if not self.form.hasErrors():
self.createDocument()
timecourse = self.createUniformTimecourse(self.form.timeMin, self.form.timeMax, self.form.timeEch)
if self.form.saveModelSnapshot:
sbml_model = join(dirname(self.model_filename), copyModelHierarchy(self.model_filename))
else:
sbml_model = self.model_filename
if self.form.experimentId is not None:
self.loadExperiments()
t_experiment_id = self.experiments[self.form.experimentId].id
experiment = Experiment.objects.get(id=t_experiment_id)
conditions = Condition.objects.filter(experiment=experiment)
for i, condition in enumerate(conditions):
modifications = []
input_data = Treatment.objects.filter(condition=condition)
for data in input_data:
var = None
if self.getModelInstance().listOfSpecies.containsName(data.species):
var = self.getModelInstance().listOfSpecies.getByName(data.species)
elif self.getModelInstance().listOfParameters.containsName(data.species):
var = self.getModelInstance().listOfParameters.getByName(data.species)
elif self.getModelInstance().listOfCompartments.containsName(data.species):
var = self.getModelInstance().listOfCompartments.getByName(data.species)
if var is not None:
modifications.append((var, data.value))
model = self.addModel(sbml_model, modifications)
variables = []
if self.form.selectedSpeciesIds is not None:
for id_var in self.form.selectedSpeciesIds:
variables.append(self.listOfVariables[id_var])
if self.form.selectedReactionsIds is not None:
for id_var in self.form.selectedReactionsIds:
variables.append(self.listOfVariables[id_var])
self.addTimeseriesCurve(timecourse, model, condition.name, variables)
else:
model = self.addModel(sbml_model)
variables = []
if self.form.selectedSpeciesIds is not None:
for id_var in self.form.selectedSpeciesIds:
variables.append(self.listOfVariables[id_var])
if self.form.selectedReactionsIds is not None:
for id_var in self.form.selectedReactionsIds:
variables.append(self.listOfVariables[id_var])
self.addTimeseriesCurve(
timecourse, model,
("Simulation" if self.form.simulationName is None else self.form.simulationName),
variables
)
simulation_filename = join(settings.MEDIA_ROOT, new_sedml_filename())
open(simulation_filename, "a")
new_simulation = SEDMLSimulation(
project=self.project,
name=("Simulation" if self.form.simulationName is None else self.form.simulationName),
sedml_file=File(open(simulation_filename, "rb")),
sbml_file=sbml_model)
new_simulation.save()
filename = join(settings.MEDIA_ROOT, str(new_simulation.sedml_file))
remove(simulation_filename)
self.saveSedml(filename)
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 copySimulation(simulation, new_project): t_file = File(open(join(settings.MEDIA_ROOT, str(simulation.sedml_file)), 'rb')) new_simulation = SEDMLSimulation(project=new_project, name=simulation.name, sedml_file=t_file) new_simulation.save()
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 saveSimulation(self, request):
self.form.read(request)
if not self.form.hasErrors():
sedml_doc = SedmlDocument()
simulation = sedml_doc.listOfSimulations.createUniformTimeCourse()
simulation.setInitialTime(self.form.timeMin)
simulation.setOutputStartTime(self.form.timeMin)
simulation.setOutputEndTime(self.form.timeMax)
simulation.setNumberOfPoints(
int((self.form.timeMax - self.form.timeMin) /
self.form.timeEch))
simulation.getAlgorithm().setCVODE()
if self.form.experimentId is not None:
self.loadExperiments(request)
t_experiment_id = self.experiments[self.form.experimentId].id
experiment = Experiment.objects.get(id=t_experiment_id)
conditions = Condition.objects.filter(experiment=experiment)
self.nbConditions = len(conditions)
self.experimentName = experiment.name
self.experiment = SigNetSimExperiment()
self.conditionNames = []
self.observations = []
for i, condition in enumerate(conditions):
input_data = Treatment.objects.filter(condition=condition)
model = sedml_doc.listOfModels.createModel()
model.setLanguageSbml()
model.setSource(self.model_filename)
for data in input_data:
var = None
if self.getModelInstance().listOfSpecies.containsName(
data.species):
var = self.getModelInstance(
).listOfSpecies.getByName(data.species)
elif self.getModelInstance(
).listOfParameters.containsName(data.species):
var = self.getModelInstance(
).listOfParameters.getByName(data.species)
elif self.getModelInstance(
).listOfCompartments.containsName(data.species):
var = self.getModelInstance(
).listOfCompartments.getByName(data.species)
if var is not None:
change = model.listOfChanges.createChangeAttribute(
)
change.setTarget(var)
change.setNewValue(data.value)
task = sedml_doc.listOfTasks.createTask()
task.setModel(model)
task.setSimulation(simulation)
data_time = sedml_doc.listOfDataGenerators.createDataGenerator(
)
data_time.setName("Time")
var_time = data_time.listOfVariables.createVariable(
"time_%d" % i)
var_time.setTask(task)
var_time.setModel(model)
var_time.setSymbolTime()
data_time.getMath().setInternalMathFormula(
var_time.getSympySymbol())
plot2D = sedml_doc.listOfOutputs.createPlot2D()
plot2D.setName(str(condition.name))
i_var = 0
if self.form.selectedSpeciesIds is not None:
for id_var in self.form.selectedSpeciesIds:
i_var += 1
data = sedml_doc.listOfDataGenerators.createDataGenerator(
"data_%d_%d" % (i, i_var))
data.setName(
self.listOfVariables[id_var].getNameOrSbmlId())
var = data.listOfVariables.createVariable(
"var_%d_%d" % (i, i_var))
var.setTask(task)
var.setModel(model)
var.setTarget(self.listOfVariables[id_var])
data.getMath().setInternalMathFormula(
var.getSympySymbol())
curve = plot2D.listOfCurves.createCurve(
"curve_%d_%d" % (i, i_var))
curve.setXData(data_time)
curve.setYData(data)
if self.form.selectedReactionsIds is not None:
for id_var in self.form.selectedReactionsIds:
i_var += 1
data = sedml_doc.listOfDataGenerators.createDataGenerator(
"data_%d_%d" % (i, i_var))
data.setName(
self.listOfVariables[id_var].getNameOrSbmlId())
var = data.listOfVariables.createVariable(
"var_%d_%d" % (i, i_var))
var.setTask(task)
var.setModel(model)
var.setTarget(self.listOfVariables[id_var])
data.getMath().setInternalMathFormula(
var.getSympySymbol())
curve = plot2D.listOfCurves.createCurve(
"curve_%d_%d" % (i, i_var))
curve.setXData(data_time)
curve.setYData(data)
else:
model = sedml_doc.listOfModels.createModel()
model.setLanguageSbml()
model.setSource(self.model_filename)
task = sedml_doc.listOfTasks.createTask()
task.setModel(model)
task.setSimulation(simulation)
data_time = sedml_doc.listOfDataGenerators.createDataGenerator(
)
data_time.setName("Time")
var_time = data_time.listOfVariables.createVariable("time")
var_time.setTask(task)
var_time.setModel(model)
var_time.setSymbolTime()
data_time.getMath().setInternalMathFormula(
var_time.getSympySymbol())
plot2D = sedml_doc.listOfOutputs.createPlot2D()
plot2D.setName("Simulation")
i_var = 0
if self.form.selectedSpeciesIds is not None:
for id_var in self.form.selectedSpeciesIds:
i_var += 1
data = sedml_doc.listOfDataGenerators.createDataGenerator(
"data_%d" % i_var)
data.setName(
self.listOfVariables[id_var].getNameOrSbmlId())
var = data.listOfVariables.createVariable("var_%d" %
i_var)
var.setTask(task)
var.setModel(model)
var.setTarget(self.listOfVariables[id_var])
data.getMath().setInternalMathFormula(
var.getSympySymbol())
curve = plot2D.listOfCurves.createCurve("curve_%d" %
i_var)
curve.setXData(data_time)
curve.setYData(data)
if self.form.selectedReactionsIds is not None:
for id_var in self.form.selectedReactionsIds:
i_var += 1
data = sedml_doc.listOfDataGenerators.createDataGenerator(
"data_%d" % i_var)
data.setName(
self.listOfVariables[id_var].getNameOrSbmlId())
var = data.listOfVariables.createVariable("var_%d" %
i_var)
var.setTask(task)
var.setModel(model)
var.setTarget(self.listOfVariables[id_var])
data.getMath().setInternalMathFormula(
var.getSympySymbol())
curve = plot2D.listOfCurves.createCurve("curve_%d" %
i_var)
curve.setXData(data_time)
curve.setYData(data)
open("simulation.xml", "a")
new_simulation = SEDMLSimulation(project=self.project,
name="Simulation",
sedml_file=File(
open("simulation.xml", "r")))
new_simulation.save()
filename = join(settings.MEDIA_ROOT,
str(new_simulation.sedml_file))
sedml_doc.writeSedmlToFile(filename)