def geneseekr_query(request):
form = GeneSeekrForm()
if request.method == 'POST':
form = GeneSeekrForm(request.POST, request.FILES)
if form.is_valid():
seqids, query_sequence, name = form.cleaned_data
geneseekr_request = GeneSeekrRequest.objects.create(
user=request.user, seqids=seqids)
# Use query sequence if entered. Otherwise, read in the FASTA file provided.
if query_sequence != '':
geneseekr_request.query_sequence = query_sequence
else:
input_sequence_file = request.FILES['query_file']
# Pointer is at end of file in request, so move back to beginning before doing the read.
input_sequence_file.seek(0)
input_sequence = input_sequence_file.read().decode('utf-8')
geneseekr_request.query_sequence = input_sequence
geneseekr_request.status = 'Processing'
if (name):
geneseekr_request.name = name
geneseekr_request.save()
run_geneseekr.apply_async(queue='geneseekr',
args=(geneseekr_request.pk, ),
countdown=10)
return redirect('geneseekr:geneseekr_processing',
geneseekr_request_pk=geneseekr_request.pk)
return render(request, 'geneseekr/geneseekr_query.html', {
'form': form,
})
def test_invalid_form_no_sequences_in_exclude_genus(self):
form = GeneSeekrForm({
'genus': 'Listeria',
'query_sequence': '>fasta_name\nATCGACTGACTAGTCA',
'everything_but': True,
})
self.assertFalse(form.is_valid())
def geneseekr_query(request):
form = GeneSeekrForm()
if request.method == 'POST':
form = GeneSeekrForm(request.POST, request.FILES)
if form.is_valid():
# seqid_input = form.cleaned_data.get('seqids')
# seqids = seqid_input.split()
seqids, query_sequence = form.cleaned_data
geneseekr_request = GeneSeekrRequest.objects.create(
user=request.user, seqids=seqids)
# Use query sequence if entered. Otherwise, read in the FASTA file provided.
if query_sequence != '':
geneseekr_request.query_sequence = query_sequence
else:
input_sequence_file = request.FILES['query_file']
# Pointer is at end of file in request, so move back to beginning before doing the read.
input_sequence_file.seek(0)
input_sequence = input_sequence_file.read()
geneseekr_request.query_sequence = input_sequence
geneseekr_request.status = 'Processing'
geneseekr_request.save()
run_geneseekr(geneseekr_request_pk=geneseekr_request.pk)
return redirect('geneseekr:geneseekr_processing',
geneseekr_request_pk=geneseekr_request.pk)
return render(request, 'geneseekr/geneseekr_query.html', {'form': form})
def test_invalid_form_bad_fasta_file(self):
with open('olc_webportalv2/geneseekr/tests/bad_fasta.fasta',
'rb') as upload_file:
form = GeneSeekrForm({'seqids': '2015-SEQ-0711 2015-SEQ-0712'}, {
'query_file':
SimpleUploadedFile(upload_file.name, upload_file.read())
})
self.assertFalse(form.is_valid())
def test_invalid_form_fasta_too_long(self):
form = GeneSeekrForm({
'seqids':
'2015-SEQ-0711 2015-SEQ-0712',
'query_sequence':
'>fasta_name\nATCGACTGACTAGTCA' + 'A' * 10000
})
self.assertFalse(form.is_valid())
def test_valid_geneseekr_form_genus_input_fasta_text(self):
form = GeneSeekrForm({
'genus': 'Listeria',
'query_sequence': '>fasta_name\nATCGACTGACTAGTCA'
})
self.assertTrue(form.is_valid())
seqid_list, query_sequence = form.cleaned_data
self.assertEqual(seqid_list, ['2015-SEQ-0711', '2015-SEQ-0712'])
self.assertEqual(query_sequence, '>fasta_name\nATCGACTGACTAGTCA')
def test_valid_form_exclude_genus(self):
form = GeneSeekrForm({
'genus': 'Salmonella',
'query_sequence': '>fasta_name\nATCGACTGACTAGTCA',
'everything_but': True,
})
self.assertTrue(form.is_valid())
seqid_list, query_sequence = form.cleaned_data
self.assertEqual(seqid_list, ['2015-SEQ-0711', '2015-SEQ-0712'])
self.assertEqual(query_sequence, '>fasta_name\nATCGACTGACTAGTCA')
def test_valid_geneseekr_form_genus_input_fasta_file(self):
with open('olc_webportalv2/geneseekr/tests/good_fasta.fasta',
'rb') as upload_file:
form = GeneSeekrForm({'genus': 'Listeria'}, {
'query_file':
SimpleUploadedFile(upload_file.name, upload_file.read())
})
self.assertTrue(form.is_valid())
seqid_list, query_sequence = form.cleaned_data
self.assertEqual(seqid_list, ['2015-SEQ-0711', '2015-SEQ-0712'])
def tree_rename(request, tree_request_pk):
tree_request = get_object_or_404(Tree, pk=tree_request_pk)
name = {'name': tree_request.name}
form = GeneSeekrForm(initial=name)
if request.method == "POST":
tree_request.name = request.POST["name"]
tree_request.save()
return redirect('geneseekr:tree_home')
return render(request, 'rename.html', {
'tree_request': tree_request,
'form': form
})
def geneseekr_rename(request, geneseekr_request_pk):
geneseekr_request = get_object_or_404(GeneSeekrRequest,
pk=geneseekr_request_pk)
name = {'name': geneseekr_request.name}
form = GeneSeekrForm(initial=name)
if request.method == "POST":
geneseekr_request.name = request.POST["name"]
geneseekr_request.save()
return redirect('geneseekr:geneseekr_home')
return render(request, 'rename.html', {
'geneseekr_request': geneseekr_request,
'form': form
})
def test_invalid_form_no_sequences_in_genus(self):
form = GeneSeekrForm({
'genus': 'TotallyFakeGenus',
'query_sequence': '>fasta_name\nATCGACTGACTAGTCA'
})
self.assertFalse(form.is_valid())
def test_invalid_form_missing_seqid(self):
form = GeneSeekrForm({
'seqids': '2222-SEQ-0711 2015-SEQ-0712',
'query_sequence': '>fasta_name\nATCGACTGACTAGTCA'
})
self.assertFalse(form.is_valid())