def export(request, pk):
form = request.GET.get("format", "bioopt")
if form not in ["bioopt", "sbml"]:
return HttpResponseBadRequest("Bad format")
try:
model = DesignModel.objects.get(user=UserProfile.get_profile(
request.user),
pk=pk)
content = model.get_latest_revision().content
except ObjectDoesNotExist:
return HttpResponseBadRequest("Bad Model")
org = Metabolism(StringIO(content))
ss = StringIO()
if form == "sbml":
org.write_sbml(ss)
elif form == "bioopt":
org.write_bioopt(ss)
#org.to_model().dump(fileout=ss, filetype="opt" if form == "bioopt" else "sbml")
response = HttpResponse(ss.getvalue(),
content_type="application/x-bioopt"
if form == "bioopt" else "application/sbml+xml")
ss.close()
response['Content-Disposition'] = "attachment; filename=" + model.filename
return response
def upload(request, pk):
data = {}
if request.method == 'POST':
if pk == "1":
# Uploaded model
form = UploadModelForm(request.POST, request.FILES)
if form.is_valid():
name = form.cleaned_data.get('name')
#save to temporary file
freq = request.FILES['file']
filename = freq.name
ss = StringIO()
for chunk in freq.chunks():
try:
ss.write(chunk.decode("utf-8"))
except UnicodeDecodeError:
form.add_error("file",
"File does not have UTF-8 encoding")
form_html = render_crispy_form(form, context=request)
return {'success': False, 'form_html': form_html}
#try:
ss.seek(0)
model = Metabolism(ss, filename=freq.name)
if len(model.enzymes) == 0 or len(model.mets) == 0:
raise ValueError("Model is empty")
#except Exception as e:
# form.add_error("file", "Not a valid model: " + str(e))
# form_html = render_crispy_form(form, context=request)
# return {'success': False, 'form_html': form_html}
dm = DesignModel.objects.create(user=request.user.profile,
name=name,
filename=filename,
content=ss.getvalue())
#try:
# jm = JsonModel.from_model(model).to_json()
#except ValueError:
# return BadRequest(str(ValueError))
sio = StringIO()
model.write_sbml(fileout=sio)
Revision(model=dm,
content=sio.getvalue(),
reason="Initial version").save()
return {'success': True}
else:
form_html = render_crispy_form(form, context=request)
return {'success': False, 'form_html': form_html}
if pk == "2":
# from template
templates = DesignTemplate.objects.values_list("pk", "name")
form = ModelFromTemplateForm(templates, request.POST,
request.FILES)
if form.is_valid():
name = form.cleaned_data.get('name')
choice = form.cleaned_data.get('choice')
template = DesignTemplate.objects.get(pk=choice)
dm = DesignModel.objects.create(user=UserProfile.get_profile(
request.user),
name=name,
filename=template.filename,
content="")
Revision(model=dm,
content=template.content,
reason="Initial version").save()
return {'success': True}
else:
form_html = render_crispy_form(form, context=request)
return {'success': False, 'form_html': form_html}
return BadRequest()
def save(request, pk):
if not all(x in request.POST for x in ["changes", "objectives"]):
raise BadRequest("Request incomplete")
try:
model = DesignModel.objects.get(user=UserProfile.get_profile(
request.user),
pk=pk)
except ObjectDoesNotExist:
raise BadRequest("Bad Model")
try:
revision = request.POST["revision"]
try:
revision = Revision.objects.get(model=model, pk=revision)
except ObjectDoesNotExist:
raise BadRequest("Bad Revision")
except KeyError:
revision = model.get_latest_revision()
org = Metabolism(StringIO(revision.content))
try:
changes = json.loads(request.POST["changes"])
objectives = json.loads(request.POST["objectives"])
except ValueError:
return BadRequest("Invalid JSON data")
summary = request.POST.get("summary")
try:
apply_commandlist(org, changes)
org = Metabolism(StringIO(revision.content))
changes = compress_command_list(changes)
apply_commandlist(org, changes)
if objectives:
org.objectives = []
for obj in objectives:
if len(obj["name"]) > 0:
obj_reac = org.get_reaction(obj["name"])
if obj_reac is None:
raise BadRequest("Objective not in model: " +
obj["name"])
org.obj = []
org.obj.append(
[obj_reac.id, "1" if obj["maximize"] else "-1"])
except ValueError as e:
raise BadRequest("Model error: " + str(e))
if len(changes) == 0:
raise BadRequest("Model not saved: No changes found")
sio = StringIO()
org.write_sbml(fileout=sio)
Revision(model=model,
content=sio.getvalue(),
changes=dict(changes=changes, objectives=objectives),
reason=summary).save()
return {}
