def multipartite_view_free_sbol(request):
context = RequestContext(request)
context.update(csrf(request))
if request.method == 'POST':
request_data = request.POST
else:
msg = "To get the sequence you need first to assemble parts"
return HttpResponseBadRequest(msg)
feats = [request_data['vector']]
for k in sorted(request_data.keys()):
if 'part_' in k:
feats.append(request_data[k])
form_class = get_multipartite_free_form(feats)
form = form_class(request_data)
if form.is_valid():
last_feat = Feature.objects.get(uniquename=feats[-1])
last_suffix = last_feat.suffix
if last_suffix == 'CGCT':
protocol_data, part_order = _get_fragments_from_request(request)
assembled_seq = assemble_parts(protocol_data, part_order)
response = HttpResponse(convert_to_sbol(assembled_seq),
content_type='xml/plain')
filename = assembled_seq.name + '.xml'
response['Content-Disposition'] = 'attachment; '
response['Content-Disposition'] += 'filename="{0}"'.format(filename)
return response
return HttpResponseBadRequest('There was an error in the assembly')
def multipartite_view_sbol(request, multi_type=None):
'view of the multipartite tool'
if multi_type is None:
return render_to_response('multipartite_initial.html', {},
context_instance=RequestContext(request))
elif multi_type not in PARTS_TO_ASSEMBLE.keys():
return Http404
context = RequestContext(request)
context.update(csrf(request))
if request.method == 'POST':
request_data = request.POST
elif request.method == 'GET':
request_data = request.GET
else:
request_data = None
form_class = get_multipartite_form(multi_type, request.user)
if request_data:
form = form_class(request_data)
if form.is_valid():
multi_form_data = form.cleaned_data
part_types = [p[0] for p in PARTS_TO_ASSEMBLE[multi_type]]
assembled_seq = assemble_parts(multi_form_data, part_types)
filename = assembled_seq.name + '.xml'
response = HttpResponse(convert_to_sbol(assembled_seq),
content_type='xml/plain')
response['Content-Disposition'] = 'attachment; '
response['Content-Disposition'] += 'filename="{0}"'.format(filename)
return response
return HttpResponseBadRequest()
def test_sbol(self):
# feat = os.path.join(TEST_DATA, 'pEGBAn11.gb')
# print feat.genbank_file
seq = read(os.path.join(TEST_DATA, 'pEGBAn11.gb'), 'gb')
fhand = open('/tmp/sbol.xml', 'w')
fhand.write(convert_to_sbol(seq))
fhand.close()
def function(seq, category, prefix, suffix, enzymes, with_intron):
seq = domesticate(seq, category, prefix, suffix, enzymes,
with_intron)[1]
response = HttpResponse(convert_to_sbol(seq),
content_type='text/xml')
response['Content-Disposition'] = 'attachment; '
response['Content-Disposition'] += 'filename="{0}.xml"'.format(seq.id)
return response
def feature_sbol(request, uniquename):
user = request.user
print(uniquename)
try:
feat = Feature.objects.get(uniquename=uniquename)
except Feature.DoesNotExist:
feat = None
if feat is None:
return Http404
if (feat.is_public or (user.is_staff or user == feat.owner)):
seq = read(feat.genbank_file, 'gb')
response = HttpResponse(convert_to_sbol(seq), content_type='xml/plain')
filename = seq.name + '.xml'
response['Content-Disposition'] = 'attachment; '
response['Content-Disposition'] += 'filename="{0}"'.format(filename)
return response
else:
return HttpResponseForbidden
def bipartite_view_sbol(request):
context = RequestContext(request)
context.update(csrf(request))
if request.method == 'POST':
request_data = request.POST
elif request.method == 'GET':
request_data = request.GET
else:
request_data = None
if request_data:
form = BipartiteForm3(request_data)
if form.is_valid():
seq = assemble_parts(form.cleaned_data, ['part_1', 'part_2'])
response = HttpResponse(convert_to_sbol(seq),
content_type='xml/plain')
filename = seq.name + '.xml'
response['Content-Disposition'] = 'attachment; '
response['Content-Disposition'] += 'filename="{0}"'.format(filename)
return response
return HttpResponseBadRequest()