def test_form_renders_seq_text_input_widget(self):
"""
Tests correct rendering of form input text area
:return:
"""
form = QueryForm()
field = form['align_input']
self.assertIn('Paste in your alignment:<br>(FASTA, clustalw, stockholm or phylip)', field.label_tag())
self.assertIn('placeholder="Alignment (FASTA, clustalw, stockholm or phylip)"', form.as_p())
self.assertIn('class="form-control"', form.as_p())
def test_form_validation_returns_correct_seqrecord_alphabet(self):
"""
Tests that seqrecords get correct alphabet according to user input of seq_type
:return:
"""
input_seqs = file_to_string('protein.fasta')
form = QueryForm(data={'align_input': input_seqs, 'seq_type': 'Protein'})
self.assertTrue(form.is_valid())
for f in form.cleaned_data['align_input']:
self.assertEqual(str(f.seq.alphabet), "Gapped(ExtendedIUPACProtein(), '-')", Gapped(ExtendedIUPACProtein()).letters)
input_seqs = file_to_string('DNA.fasta')
form = QueryForm(data={'align_input': input_seqs, 'seq_type': 'DNA'})
self.assertTrue(form.is_valid())
for f in form.cleaned_data['align_input']:
self.assertEqual(str(f.seq.alphabet), "Gapped(ExtendedIUPACDNA(), '-')", Gapped(ExtendedIUPACDNA()).letters)
def validation(self, error_text, input_file='', seq_type='Protein'):
"""
Performs validation test for invalid forms, takes a user alignment input, asserts form.is_valid as false and
checks the error
:param:
:return:
"""
if input_file:
input_seqs = file_to_string(input_file)
else:
input_seqs = ''
form = QueryForm(data={'align_input': input_seqs, 'seq_type': seq_type})
self.assertFalse(form.is_valid())
self.assertEqual(
form.errors['align_input'],
[error_text], format(form.errors['align_input'])
)
def test_form_renders_sequence_type_radio_buttons(self):
"""
Tests correct rendering of form radio buttons
:return:
"""
form = QueryForm()
field = form['seq_type']
self.assertIn('Input sequence type:', field.label_tag())
self.assertIn('<input id="id_seq_type_0" name="seq_type" type="radio" value="Protein"', form.as_p())
self.assertIn('<input checked="checked" id="id_seq_type_1" name="seq_type" type="radio" value="DNA"', form.as_p())
def index(request):
"""
Serves home page
:param request: HTTP request
:return: HttpResponse object
"""
if request.method == 'GET':
form = QueryForm()
return render(request, 'base/index.html', {'form': form})
elif request.method == 'POST':
form = QueryForm(request.POST)
if form.is_valid():
align = form.cleaned_data['align_input']
save_align = Alignment.objects.create_alignment('name', align)
slug = save_align.slug
return redirect('/query-sequences/' + str(slug) + '/')
else:
return render(request, 'base/index.html', {'form': form})
else:
return HttpResponseNotAllowed(['POST', 'GET'])