def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingProject.__init__(self)
self.listOfSimulations = None
self.fileUploadForm = DocumentForm()
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 __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingProject.__init__(self)
HasUserLoggedIn.__init__(self)
HasErrorMessages.__init__(self)
self.listOfModels = None
self.fileUploadForm = DocumentForm()
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingProject.__init__(self) self.listOfExperiments = None self.experimentId = None self.experimentName = None self.experimentNotes = None self.fileUploadForm = DocumentForm()
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingProject.__init__(self) self.listOfFolders = None self.createFolderShow = None self.createFolderError = None self.sendFolderShow = None self.sendFolderError = None self.fileUploadForm = DocumentForm()
def importExperiment(self, request): if self.isProjectOwner(request): self.fileUploadForm = DocumentForm(request.POST, request.FILES) if self.fileUploadForm.is_valid(): new_experiment = Experiment(project=self.project) new_experiment.save() archive = request.FILES['docfile'] path = default_storage.save(str(archive), ContentFile(archive.read())) importExperimentViaManager(new_experiment, str(join(settings.MEDIA_ROOT, path))) remove(join(settings.MEDIA_ROOT, path))
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 __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingProject.__init__(self) self.listOfSimulations = None self.fileUploadForm = DocumentForm()
def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingProject.__init__(self) HasUserLoggedIn.__init__(self) HasErrorMessages.__init__(self) self.listOfModels = None self.fileUploadForm = DocumentForm()
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 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 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()
class DataView(TemplateView, HasWorkingProject): template_name = 'data/data.html' def __init__(self, **kwargs): TemplateView.__init__(self, **kwargs) HasWorkingProject.__init__(self) self.listOfExperiments = None self.experimentId = None self.experimentName = None self.experimentNotes = None self.fileUploadForm = DocumentForm() def get_context_data(self, **kwargs): kwargs = HasWorkingProject.get_context_data(self, **kwargs) kwargs['experimental_data'] = self.listOfExperiments kwargs['experiment_id'] = self.experimentId kwargs['experiment_name'] = self.experimentName kwargs['experiment_notes'] = self.experimentNotes kwargs['file_upload_form'] = self.fileUploadForm return kwargs def get(self, request, *args, **kwargs): HasWorkingProject.load(self, request, *args, **kwargs) self.loadExperiments(request) return TemplateView.get(self, request, *args, **kwargs) def post(self, request, *args, **kwargs): HasWorkingProject.load(self, request, *args, **kwargs) self.loadExperiments(request) if "action" in request.POST: if HasWorkingProject.isChooseProject(self, request): self.loadExperiments(request) elif request.POST['action'] == "delete": self.deleteExperiment(request) elif request.POST['action'] == "save": self.saveExperiment(request) elif request.POST['action'] == "duplicate": self.duplicateExperiment(request) elif request.POST['action'] == "import": self.importExperiment(request) return TemplateView.get(self, request, *args, **kwargs) def loadExperiments(self, request): self.listOfExperiments = Experiment.objects.filter(project=self.project) def deleteExperiment(self, request): if self.isProjectOwner(request): experiment = Experiment.objects.get(project=self.project, id=request.POST['id']) deleteExperimentViaManager(experiment) def saveExperiment(self, request): if self.isProjectOwner(request): if str(request.POST['experiment_id']) == "": t_experiment = Experiment(project=self.project) else: t_experiment = Experiment.objects.get(project=self.project, id=str(request.POST['experiment_id'])) t_experiment.name = str(request.POST['experiment_name']) t_experiment.notes = str(request.POST['experiment_notes']) t_experiment.save() def duplicateExperiment(self, request): if self.isProjectOwner(request): t_experiment = Experiment.objects.get(project=self.project, id=request.POST['id']) new_experiment = Experiment(project=self.project) new_experiment.save() copyExperimentViaManager(t_experiment, new_experiment) def importExperiment(self, request): if self.isProjectOwner(request): self.fileUploadForm = DocumentForm(request.POST, request.FILES) if self.fileUploadForm.is_valid(): new_experiment = Experiment(project=self.project) new_experiment.save() archive = request.FILES['docfile'] path = default_storage.save(str(archive), ContentFile(archive.read())) importExperimentViaManager(new_experiment, str(join(settings.MEDIA_ROOT, path))) remove(join(settings.MEDIA_ROOT, path))
class ListOfModelsView(TemplateView, HasWorkingProject, HasUserLoggedIn,
HasErrorMessages):
template_name = 'models/models.html'
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingProject.__init__(self)
HasUserLoggedIn.__init__(self)
HasErrorMessages.__init__(self)
self.listOfModels = None
self.fileUploadForm = DocumentForm()
def get_context_data(self, **kwargs):
kwargs = HasWorkingProject.get_context_data(self, **kwargs)
kwargs = HasErrorMessages.get_context_data(self, **kwargs)
kwargs['form'] = self.fileUploadForm
kwargs['sbml_models'] = self.listOfModels
return kwargs
def get(self, request, *args, **kwargs):
if len(args) > 0:
HasWorkingProject.load(self, request, *args, **kwargs)
self.setProject(request, args[0])
return redirect('models')
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):
self.loadModels(request)
elif request.POST['action'] == "delete_model":
self.deleteModel(request)
self.load(request, *args, **kwargs)
elif request.POST['action'] == "load_model":
self.loadModel(request)
self.load(request, *args, **kwargs)
elif request.POST['action'] == "duplicate_model":
self.duplicateModel(request)
self.load(request, *args, **kwargs)
elif request.POST['action'] == "new_model":
self.newModel(request)
self.load(request, *args, **kwargs)
elif request.POST['action'] == "load_biomodels":
self.loadBiomodels(request)
self.load(request, *args, **kwargs)
return TemplateView.get(self, request, *args, **kwargs)
def load(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
self.loadModels(request)
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 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 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 deleteModel(self, request):
model = SbmlModel.objects.get(project=self.project,
id=request.POST['id'])
for model_dependency in ModelsDependency.objects.filter(
project=self.project, submodel=model):
if model_dependency.model != model:
self.addError(
"This model is used as a submodel by %s and cannot be removed."
% model_dependency.model.name)
if not self.hasErrors():
ModelsDependency.objects.filter(project=self.project,
model=model).delete()
os.remove(os.path.join(settings.MEDIA_ROOT, str(model.sbml_file)))
model.delete()
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 loadModels(self, request, *args, **kwargs):
# self.projectId = str(args[0])
# self.project = ModelFolder.objects.get(user=request.user, id=self.projectId)
if self.project is not None:
self.listOfModels = []
for model in SbmlModel.objects.filter(project=self.project):
filename = str(model.sbml_file)
if filename.startswith(settings.MEDIA_ROOT):
filename = filename.replace(settings.MEDIA_ROOT, "")
self.listOfModels.append((model.id, model.name, filename))
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
class ListOfProjectsView(TemplateView, HasWorkingProject):
template_name = 'models/projects.html'
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingProject.__init__(self)
self.listOfFolders = None
self.createFolderShow = None
self.createFolderError = None
self.sendFolderShow = None
self.sendFolderError = None
self.fileUploadForm = DocumentForm()
def get_context_data(self, **kwargs):
kwargs = HasWorkingProject.get_context_data(self, **kwargs)
kwargs['create_folder_error'] = self.createFolderError
kwargs['create_folder_show'] = self.createFolderShow
kwargs['send_folder_error'] = self.sendFolderError
kwargs['send_folder_show'] = self.sendFolderShow
kwargs['load_project_form'] = self.fileUploadForm
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):
self.load(request, *args, **kwargs)
elif request.POST['action'] == "new_folder":
self.newFolder(request)
elif request.POST['action'] == "copy_folder":
self.copyFolder(request)
elif request.POST['action'] == "delete_folder":
self.deleteFolder(request)
elif request.POST['action'] == "send_folder":
self.sendFolder(request)
elif request.POST['action'] == "load_folder":
self.loadFolder(request)
elif request.POST['action'] == "save_project":
self.saveProject(request)
return TemplateView.get(self, request, *args, **kwargs)
def load(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
if self.isUserLoggedIn(request):
self.loadFolders(request)
def newFolder(self, request):
name = str(request.POST['project_name'])
access = False
if 'project_access' in request.POST and request.POST['project_access'] == "on":
access = True
if not Project.objects.filter(user=request.user, name=name).exists():
new_folder = Project(user=request.user, name=name)
if access:
new_folder.access = 'PU'
else:
new_folder.access = 'PR'
new_folder.save()
mkdir(join(settings.MEDIA_ROOT, str(new_folder.folder)))
self.loadFolders(request)
else:
self.createFolderShow = True
self.createFolderError = "Project %s already exists !" % name
def copyFolder(self, request):
folder_id = str(request.POST['id'])
if Project.objects.filter(user=request.user, id=folder_id).exists():
folder = Project.objects.get(user=request.user, id=folder_id)
new_folder = Project(user=request.user, name=(str(folder.name) + " (Copy)"))
copyProject(folder, new_folder)
def deleteFolder(self, request):
folder_id = str(request.POST['id'])
if self.project_id == int(folder_id):
self.unsetProject(request)
if Project.objects.filter(user=request.user, id=folder_id).exists():
project = Project.objects.get(user=request.user, id=folder_id)
deleteProject(project)
def sendFolder(self, request):
folder_id = str(request.POST['id'])
t_username = str(request.POST['username'])
try :
t_user = User.objects.get(username=t_username)
if Project.objects.filter(user=request.user, id=folder_id).exists():
folder = Project.objects.get(user=request.user, id=folder_id)
new_folder = Project(user=t_user, name=str(folder.name))
copyProject(folder, new_folder)
except User.DoesNotExist:
self.sendFolderShow = True
self.sendFolderError = "Username %s does not exist" % t_username
def saveProject(self, request):
if 'project_name' in request.POST and 'project_id' in request.POST:
if request.POST['project_id'] != "":
id = request.POST['project_id']
name = request.POST['project_name']
access = False
if 'project_access' in request.POST and request.POST['project_access'] == "on":
access = True
if Project.objects.filter(id=id).exists():
project = Project.objects.get(id=id)
project.name = name
if access:
project.access = 'PU'
else:
project.access = 'PR'
project.save()
else:
self.newFolder(request)
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 loadFolders(self, request):
self.listOfFolders = Project.objects.filter(user=request.user)
class ListOfModelsView(TemplateView, HasWorkingProject, HasUserLoggedIn, HasErrorMessages):
template_name = 'models/models.html'
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingProject.__init__(self)
HasUserLoggedIn.__init__(self)
HasErrorMessages.__init__(self)
self.listOfModels = None
self.fileUploadForm = DocumentForm()
def get_context_data(self, **kwargs):
kwargs = HasWorkingProject.get_context_data(self, **kwargs)
kwargs = HasErrorMessages.get_context_data(self, **kwargs)
kwargs['form'] = self.fileUploadForm
kwargs['sbml_models'] = self.listOfModels
return kwargs
def get(self, request, *args, **kwargs):
if len(args) > 0:
HasWorkingProject.load(self, request, *args, **kwargs)
self.setProject(request, args[0])
return redirect('models')
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):
self.loadModels(request)
elif request.POST['action'] == "delete_model":
self.deleteModel(request)
self.load(request, *args, **kwargs)
elif request.POST['action'] == "load_model":
self.loadModel(request)
self.load(request, *args, **kwargs)
elif request.POST['action'] == "duplicate_model":
self.duplicateModel(request)
self.load(request, *args, **kwargs)
elif request.POST['action'] == "new_model":
self.newModel(request)
self.load(request, *args, **kwargs)
elif request.POST['action'] == "load_biomodels":
self.loadBiomodels(request)
self.load(request, *args, **kwargs)
return TemplateView.get(self, request, *args, **kwargs)
def load(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
self.loadModels(request)
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 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 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 deleteModel(self, request):
model = SbmlModel.objects.get(project=self.project, id=request.POST['id'])
for model_dependency in ModelsDependency.objects.filter(project=self.project, submodel=model):
if model_dependency.model != model:
self.addError("This model is used as a submodel by %s and cannot be removed." % model_dependency.model.name)
if not self.hasErrors():
ModelsDependency.objects.filter(project=self.project, model=model).delete()
os.remove(os.path.join(settings.MEDIA_ROOT, str(model.sbml_file)))
model.delete()
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 loadModels(self, request, *args, **kwargs):
# self.projectId = str(args[0])
# self.project = ModelFolder.objects.get(user=request.user, id=self.projectId)
if self.project is not None:
self.listOfModels = []
for model in SbmlModel.objects.filter(project=self.project):
filename = str(model.sbml_file)
if filename.startswith(settings.MEDIA_ROOT):
filename = filename.replace(settings.MEDIA_ROOT, "")
self.listOfModels.append((model.id, model.name, filename))
class ListOfSimulationsView(TemplateView, HasWorkingProject):
template_name = 'simulate/list_of_simulations.html'
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingProject.__init__(self)
self.listOfSimulations = None
self.fileUploadForm = DocumentForm()
def get_context_data(self, **kwargs):
kwargs = HasWorkingProject.get_context_data(self, **kwargs)
kwargs['list_of_simulations'] = self.listOfSimulations
kwargs['load_simulation_form'] = self.fileUploadForm
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):
self.load(request, *args, **kwargs)
elif request.POST['action'] == "delete_simulation":
self.deleteSimulation(request)
elif request.POST['action'] == "load_simulation":
self.loadSimulation(request)
return TemplateView.get(self, request, *args, **kwargs)
def load(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
self.loadListOfSimulations()
def loadListOfSimulations(self):
self.listOfSimulations = []
for simulation in SEDMLSimulation.objects.filter(project=self.project):
self.listOfSimulations.append(
(simulation.name, str(simulation.sedml_file)))
def deleteSimulation(self, request):
if 'id' in request.POST and request.POST['id'] != "":
t_simulation = SEDMLSimulation.objects.filter(
project=self.project)[int(request.POST['id'])]
remove(join(settings.MEDIA_ROOT, str(t_simulation.sedml_file)))
t_simulation.delete()
self.loadListOfSimulations()
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()
class ListOfSimulationsView(TemplateView, HasWorkingProject):
template_name = 'simulate/list_of_simulations.html'
def __init__(self, **kwargs):
TemplateView.__init__(self, **kwargs)
HasWorkingProject.__init__(self)
self.listOfSimulations = None
self.fileUploadForm = DocumentForm()
def get_context_data(self, **kwargs):
kwargs = HasWorkingProject.get_context_data(self, **kwargs)
kwargs['list_of_simulations'] = self.listOfSimulations
kwargs['load_simulation_form'] = self.fileUploadForm
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):
self.load(request, *args, **kwargs)
elif request.POST['action'] == "delete_simulation":
self.deleteSimulation(request)
elif request.POST['action'] == "load_simulation":
self.loadSimulation(request)
return TemplateView.get(self, request, *args, **kwargs)
def load(self, request, *args, **kwargs):
HasWorkingProject.load(self, request, *args, **kwargs)
self.loadListOfSimulations()
def loadListOfSimulations(self):
self.listOfSimulations = []
for simulation in SEDMLSimulation.objects.filter(project=self.project):
self.listOfSimulations.append((simulation.id, simulation.name, str(simulation.sedml_file)))
def deleteSimulation(self, request):
if 'id' in request.POST and request.POST['id'] != "":
t_simulation = SEDMLSimulation.objects.get(project=self.project, id=int(request.POST['id']))
deleteSimulation(t_simulation)
self.loadListOfSimulations()
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()