def prokka_request(request):
form = ProkkaForm()
if request.method == 'POST':
form = ProkkaForm(request.POST, request.FILES)
if form.is_valid():
seqids, name, other_files = form.cleaned_data
prokka_request_object = ProkkaRequest.objects.create(
user=request.user, seqids=seqids, status='Processing')
if name is None:
prokka_request_object.name = prokka_request.pk
else:
prokka_request_object.name = name
prokka_request_object.save()
container_name = 'prokka-{}'.format(prokka_request_object.pk)
blob_client = BlockBlobService(
account_name=settings.AZURE_ACCOUNT_NAME,
account_key=settings.AZURE_ACCOUNT_KEY)
blob_client.create_container(container_name)
file_names = list()
for other_file in request.FILES.getlist('other_files'):
file_name = os.path.join(container_name, other_file.name)
file_names.append(file_name)
blob_client.create_blob_from_bytes(
container_name=container_name,
blob_name=other_file.name,
blob=other_file.read())
prokka_request_object.other_input_files = file_names
prokka_request_object.save()
run_prokka.apply_async(queue='cowbat',
args=(prokka_request_object.pk, ),
countdown=10)
return redirect('geneseekr:prokka_result',
prokka_request_pk=prokka_request_object.pk)
return render(request, 'geneseekr/prokka_request.html', {'form': form})
def prokka_rename(request, prokka_request_pk):
prokka_request_object = get_object_or_404(ProkkaRequest,
pk=prokka_request_pk)
name = {'name': prokka_request_object.name}
form = ProkkaForm(initial=name)
if request.method == "POST":
prokka_request_object.name = request.POST["name"]
prokka_request_object.save()
return redirect('geneseekr:prokka_home')
return render(request, 'rename.html', {
'prokka_request': prokka_request_object,
'form': form
})
def test_invalid_form_wrong_seqid_does_not_exist(self):
form = ProkkaForm({
'seqids': '2222-SEQ-0711 2015-SEQ-0712'
}, QueryDict())
self.assertFalse(form.is_valid())
def test_invalid_form_blank(self):
form = ProkkaForm({
'seqids': ''
}, QueryDict())
self.assertFalse(form.is_valid())
def test_valid_form(self):
form = ProkkaForm(QueryDict('seqids=2015-SEQ-0711 2015-SEQ-0712'), QueryDict())
self.assertTrue(form.is_valid())
seqids, name, other_files = form.cleaned_data
self.assertEqual(seqids, ['2015-SEQ-0711', '2015-SEQ-0712'])