def test_neighbor_boundary_high_valid(self):
form = NearNeighborForm({
'seqid': '2015-SEQ-0711',
'number_neighbors': 250
})
self.assertTrue(form.is_valid())
seqid, name, number_neighbors, uploaded_file = form.cleaned_data
self.assertEqual(seqid, '2015-SEQ-0711')
self.assertEqual(number_neighbors, 250)
def test_neighbor_uploaded_file_bad_extension(self):
with open('olc_webportalv2/test_files/config.xml',
'rb') as upload_file:
form = NearNeighborForm({
'seqid':
'',
'uploaded_file':
SimpleUploadedFile(upload_file.name, upload_file.read()),
'number_neighbors':
4
})
self.assertFalse(form.is_valid())
def test_neighbor_uploaded_file_no_seqid(self):
with open('olc_webportalv2/geneseekr/tests/good_fasta.fasta',
'rb') as upload_file:
file_data = {
'uploaded_file':
SimpleUploadedFile(upload_file.name, upload_file.read())
}
form = NearNeighborForm({
'seqid': '',
'number_neighbors': 4
}, file_data)
self.assertTrue(form.is_valid())
def neighbor_request(request):
form = NearNeighborForm()
if request.method == 'POST':
form = NearNeighborForm(request.POST, request.FILES)
if form.is_valid():
seqid, name, number_neighbors, uploaded_file = form.cleaned_data
if name is None:
name = ''
if seqid is None:
seqid = ''
if uploaded_file is None:
uploaded_file_name = ''
else:
uploaded_file_name = uploaded_file.name
nearest_neighbor_task = NearestNeighbors.objects.create(
seqid=seqid,
number_neighbors=number_neighbors,
name=name,
user=request.user,
uploaded_file_name=uploaded_file_name,
status='Processing')
nearest_neighbor_task.save()
if uploaded_file_name != '':
container_name = 'neighbor-{}'.format(nearest_neighbor_task.pk)
blob_client = BlockBlobService(
account_name=settings.AZURE_ACCOUNT_NAME,
account_key=settings.AZURE_ACCOUNT_KEY)
blob_client.create_container(container_name)
blob_client.create_blob_from_bytes(
container_name=container_name,
blob_name=uploaded_file_name,
blob=uploaded_file.read())
run_nearest_neighbors.apply_async(
queue='geneseekr',
args=(nearest_neighbor_task.pk, ),
countdown=10)
return redirect('geneseekr:neighbor_result',
neighbor_request_pk=nearest_neighbor_task.pk)
return render(request, 'geneseekr/neighbor_request.html', {'form': form})
def neighbor_rename(request, neighbor_request_pk):
neighbor_request_object = get_object_or_404(NearestNeighbors,
pk=neighbor_request_pk)
name = {'name': neighbor_request_object.name}
form = NearNeighborForm(initial=name)
if request.method == "POST":
neighbor_request_object.name = request.POST["name"]
neighbor_request_object.save()
return redirect('geneseekr:neighbor_home')
return render(request, 'rename.html', {
'neighbor_request': neighbor_request_object,
'form': form
})
def test_neighbor_boundary_low_invalid(self):
form = NearNeighborForm({'seqid': '2015-SEQ-0711', 'number_neighbors': 0})
self.assertFalse(form.is_valid())
def test_bad_seqid(self):
form = NearNeighborForm({'seqid': '2015-FAKE-0711', 'number_neighbors': 10})
self.assertFalse(form.is_valid())
def test_negative_neighbors(self):
form = NearNeighborForm({'seqid': '2015-SEQ-0711', 'number_neighbors': -10})
self.assertFalse(form.is_valid())