def cowbat_processing(request, sequencing_run_pk):
sequencing_run = get_object_or_404(SequencingRun, pk=sequencing_run_pk)
if sequencing_run.status == 'Unprocessed':
SequencingRun.objects.filter(pk=sequencing_run.pk).update(
status='Processing')
run_cowbat_batch.apply_async(queue='cowbat',
args=(sequencing_run.pk, ))
# Find percent complete (approximately). Not sure that having calls to azure batch API in views is a good thing.
# Will have to see if performance is terrible because of it.
if sequencing_run.status == 'Processing':
progress = find_percent_complete(sequencing_run)
else:
progress = 1
form = EmailForm()
if request.method == 'POST':
form = EmailForm(request.POST)
if form.is_valid():
Email = form.cleaned_data.get('email')
if Email not in sequencing_run.emails_array:
sequencing_run.emails_array.append(Email)
sequencing_run.save()
form = EmailForm()
messages.success(request, _('Email saved'))
return render(request, 'cowbat/cowbat_processing.html', {
'sequencing_run': sequencing_run,
'form': form,
'progress': str(progress)
})
def neighbor_result(request, neighbor_request_pk):
neighbor_request_object = get_object_or_404(NearestNeighbors,
pk=neighbor_request_pk)
result_dict = dict()
if neighbor_request_object.status == 'Complete':
neighbor_details = NearNeighborDetail.objects.filter(
near_neighbor_request=neighbor_request_object)
for neighbor_detail in neighbor_details:
result_dict[neighbor_detail.seqid] = neighbor_detail.distance
id_dict = id_sync(result_dict.keys())
form = EmailForm()
if request.method == 'POST':
form = EmailForm(request.POST)
if form.is_valid():
email = form.cleaned_data.get('email')
if email not in neighbor_request_object.emails_array:
neighbor_request_object.emails_array.append(email)
neighbor_request_object.save()
form = EmailForm()
messages.success(request, _('Email saved'))
return render(
request, 'geneseekr/neighbor_result.html', {
'neighbor_request': neighbor_request_object,
'results': result_dict,
'idDict': id_dict,
'form': form
})
def amr_result(request, amr_request_pk):
amr_request_object = get_object_or_404(AMRSummary, pk=amr_request_pk)
form = EmailForm()
if request.method == 'POST':
form = EmailForm(request.POST)
if form.is_valid():
email = form.cleaned_data.get('email')
if email not in amr_request.emails_array:
amr_request_object.emails_array.append(email)
amr_request_object.save()
form = EmailForm()
messages.success(request, _('Email saved'))
return render(request, 'geneseekr/amr_result.html', {
'amr_request': amr_request_object,
'form': form,
})
def geneseekr_processing(request, geneseekr_request_pk):
geneseekr_request = get_object_or_404(GeneSeekrRequest,
pk=geneseekr_request_pk)
form = EmailForm()
if request.method == 'POST':
form = EmailForm(request.POST)
if form.is_valid():
email = form.cleaned_data.get('email')
if email not in geneseekr_request.emails_array:
geneseekr_request.emails_array.append(email)
geneseekr_request.save()
form = EmailForm()
messages.success(request, _('Email saved'))
return render(request, 'geneseekr/geneseekr_processing.html', {
'geneseekr_request': geneseekr_request,
'form': form
})
def prokka_result(request, prokka_request_pk):
prokka_request_object = get_object_or_404(ProkkaRequest,
pk=prokka_request_pk)
form = EmailForm()
if request.method == 'POST':
form = EmailForm(request.POST)
if form.is_valid():
email = form.cleaned_data.get('email')
if email not in prokka_request.emails_array:
prokka_request_object.emails_array.append(email)
prokka_request_object.save()
form = EmailForm()
messages.success(request, _('Email saved'))
return render(request, 'geneseekr/prokka_result.html', {
'prokka_request': prokka_request_object,
'form': form,
})
def tree_result(request, tree_request_pk):
tree_request = get_object_or_404(Tree, pk=tree_request_pk)
id_dict = id_sync(tree_request.seqids)
form = EmailForm()
if request.method == 'POST':
form = EmailForm(request.POST)
if form.is_valid():
email = form.cleaned_data.get('email')
if email not in tree_request.emails_array:
tree_request.emails_array.append(email)
tree_request.save()
form = EmailForm()
messages.success(request, _('Email saved'))
return render(request, 'geneseekr/tree_result.html', {
'tree_request': tree_request,
'form': form,
'idDict': id_dict,
})
def test_email_form_bad(self):
form = EmailForm({
'email': 'not_an_email_at_all'
})
self.assertFalse(form.is_valid())
def test_email_form_good(self):
form = EmailForm({
'email': '*****@*****.**'
})
self.assertTrue(form.is_valid())